Marker:Article Title: Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts.
Article Snippet: Carl Roth 4621.1 D(+)-Glucose p. a., ACS, anhydrous Carl Roth X997.2 Dextrin for microbiology (from potato starch) Carl Roth 3488.1 di-Potassium hydrogen phosphate trihydrate Carl Roth 6878.1 di-Potassium hydrogen phosphate, R 99%, p.a., anhydrous Carl Roth P749.1 DNase I Sigma-Aldrich 10104159001 E-64 Sigma-Aldrich E3132-1MG EDTA disodium salt dihydrate, min. 99%, p.a., ACS Carl Roth 8043.2 Glycine Serva 23391.02 HEPES PUFFERAN , min. 99.5%, p.-1 kg Carl Roth 9105.3 Iron (III) sulfate hydrate, 80%, pure Carl Roth 0492.1 Isopropanol Carl Roth CP41.1 Leupeptin Sigma-Aldrich L2884-1MG Magnesium chloride hexahydrate, min. 99%, p.a., ACS Carl Roth 2189.1 Magnesium sulfate heptahydrate, R 99%, p.a., ACS Carl Roth P027.1 Methanol Carl Roth 4627.6 Milk powder Carl Roth T145.3 Pefabloc Sigma-Aldrich 11585916001 Pepstatin A Sigma-Aldrich 77170-5MG Peptone ex casein Carl Roth 8986.1 Phosphate buffered saline tablets (PBS) Sigma-Aldrich P4417 Potassium chloride min. 99.5%, 1 kg Carl Roth 6781.1 (Continued on next page) e1 Cell Reports 34, 108727, February 9, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Potassium dihydrogen phosphate, R 99%, p.a., ACS Carl Roth 3904.2 Precision plus protein all blue standards (marker) BIO-RAD 161-0373 Sodium chloride 99,5%, p.a., ACS, ISO Carl Roth 3957.2 Sodium dodecyl sulfate (SDS) Carl Roth 0183.2 Sodium nitrate, R 99%, p.a., ACS, ISO Carl Roth A136.1 TEMED Carl Roth 2367.3 Tris Carl Roth AE15.2 Tris Hydrochloride Carl Roth 9090.2 Tween 20 Carl Roth 9127.1 Tryptone Sigma-Aldrich T7293 Yeast Extract, micro-granulated Carl Roth 2904.3 Critical commercial assays A-KG Dehydrogenase activity assay kit Sigma-Aldrich MAK189-1KT PDH Activity assay kit Sigma-Aldrich MAK183-1KT Deposited data Cryo-EM structure of human E2p core Jiang et al., 2018 PDB: 6CT0 Proteomics data Kastritis et al., 2017 PXD006660 Crosslinking data Kastritis et al., 2017 PXD006626 Crystallographic structure of human E1p Seifert et al., 2007 PDB: 2OZL Cryo-EM structure of human E2o core 10.2210/pdb6H05/pdb PDB: 6H05 Crystallographic structure of cattle E2b core Kato et al., 2006) PDB: 2II3 Crystallographic structure of E3 Szabo et al., 2019 PDB: 6I4R Crystallographic structure of A. vinelandii cubic E2p core Mattevi et al., 1993 PDB: 1EAA Model of C. thermophilum PDHc E2p core from cryo-EM This study PDB: 7BGJ Cryo-EM structure of native PDHc E2p core (icosahedrally-averaged and asymmetric) and native, asymmetric PDHc This study EMDB: EMD-12181 Negative stain reconstructions of PDHc core, Fraction 6, and asymmetric reconstructions from Fractions 5-10 This study EMDB: EMD-12234 Negative stain reconstructions of hybrid BCKDc/OGDHc core, Fraction 6, and asymmetric reconstructions from Fractions 5-11 This study EMDB: EMD-12233 Model of C. thermophilum PDHc E2p core from negative stain This study https://data.sbgrid.org/817 Model of C. thermophilum E1p PDHc This study https://data.sbgrid.org/817 Model of C. thermophilum E2o OGDHc from negative stain This study https://data.sbgrid.org/817 Model of C. thermophilum E2b BCKDHc from negative stain This study https://data.sbgrid.org/817 Model ofC. thermophilum E3BP trimer from cryo-EM This study https://data.sbgrid.org/817) ‘‘SBGRID: 817’’ Model of C. thermophilum E3 This study https://data.sbgrid.org/817 (Continued on next page) Cell Reports 34, 108727, February 9, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw cryo- and negative stain micrographs of a native extract from C. thermophilum used to reconstruct oxo acid dehydrogenase complexes This study EMPIAR: 10625 Experimental models: organisms/strains Chaetomium thermophilum var. thermophilum (Freeze-dried) DSMZ DSM 1495 Software and algorithms 3DFSC Tan et al., 2017 https://3dfsc.salk.edu/ Eman 2.0 Tang et al., 2007 https://blake.bcm.edu/emanwiki/EMAN2 Fiji Schindelin et al., 2012 https://imagej.net/Fiji Gctf Zhang, 2016 https://www.mrc-lmb.cam.ac.uk/kzhang/ Gen5 BioTek Instruments https://www.biotek.com/products/ software-robotics-software/ gen5-microplatereader-and-imager-software/ Haddock van Zundert et al., 2016 https://alcazar.science.uu.nl/services/ HADDOCK2.2/ Image Lab Software 6.1 BIO-RAD https://www.bio-rad.com/en-us/product/ image-lab-software?ID=KRE6P5E8Z Modeler Eswar et al., 2006 https://salilab.org/modeller/ MotionCor2 Zheng et al., 2017 https://emcore.ucsf.edu/ucsf-software Needle Needleman and Wunsch, 1970 https://www.ebi.ac.uk/Tools/psa/ emboss_needle/ Phenix Afonine et al., 2018 https://www.phenix-online.org Pymol Schrödinger, inc https://pymol.org/2/ Relion 3.0 Zivanov et al., 2018 https://github.com/3dem/relion Scipion 2.0 de la Rosa-Trevı́n et al., 2016 https://scipion-em.github.io/docs/ Segger Pintilie and Chiu, 2012 https://www.cgl.ucsf.edu/chimera/ Sphire-cryolo Wagner and Raunser, 2020 http://sphire.mpg.de/ UCSF Chimera Pettersen et al., 2004 https://www.cgl.ucsf.edu/chimera/ UCSF ChimeraX Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ UNICORN 7 Workstation for ÄKTA pure, pilot, process, Ready To Process WAVE 25 GE Healthcare Europe GmbH https://www.cytivalifesciences.com/en/us/ shop/chromatography/software/ unicorn-7-p-05649 Xmipp Sorzano et al., 2004 https://github.com/I2PC/xmipp
Article Title: Cryo-EM and artificial intelligence visualize endogenous protein community members.
Article Snippet: Carl Roth Cat#6908.4 Acrylamide/Bis solution, 37.5:1 Serva Cat#10688.01 Agar-Agar, bacteriological highly pure Carl Roth Cat#2266.3 Ammonium acetate, R97%, p.a., ACS Carl Roth Cat#7869.2 Ammonium persulfate Serva Cat#13376.02 Aprotinin from bovine lung Merck Cat#A1153-1MG Bestatin, 10MG Merck Cat#10874515001 Clarity Western ECL substrate BIO-RAD Cat#170-5060 D-Sucrose, R99,5%, p.a. .. Carl Roth Cat#4621.1 D(+)-Glucose p. a., ACS, anhydrous Carl Roth Cat#X997.2 Dextrin for microbiology (from potato starch) Carl Roth Cat#3488.1 di-Potassium hydrogen phosphate trihydrate Carl Roth Cat#6878.1 di-Potassium hydrogen phosphate, R99%, p.a., anhydrous Carl Roth Cat#P749.1 DNAse I Merck Cat#10104159001 E-64 Merck Cat#E3132-1MG EDTA disodium salt dihydrate, min. 99%, p.a., ACS Carl Roth Cat#8043.2 Glycine Serva Cat#23391.02 HEPES PUFFERAN , min. 99.5%, p.-1 kg Carl Roth Cat#9105.3 Iron (III) sulphate hydrate, 80%, pure Carl Roth Cat#0492.1 Isopropanol Carl Roth Cat#CP41.1 Leupeptin Merck Cat#L2884-1MG Magnesium chloride hexahydrate, min. 99%, p.a., ACS Carl Roth Cat#2189.1 Magnesium sulphate heptahydrate, R99%, p.a., ACS Carl Roth Cat#P027.1 Methanol Carl Roth Cat#4627.6 Milk powder Carl Roth Cat#T145.3 Pefabloc Merck Cat#11585916001 Pepstatin A Merck Cat#77170-5MG Peptone ex casein Carl Roth Cat#8986.1 Phosphate buffered saline tablets (PBS) Merck Cat#P4417 Potassium chloride min. 99.5%, -1 kg Carl Roth Cat#6781.1 Potassium dihydrogen phosphate, R99%, p.a., ACS Carl Roth Cat#3904.2 Precision plus protein all blue standards (marker) BIO-RAD Cat161-0373 Sodium chloride 99,5%, p.a., ACS, ISO Carl Roth Cat#3957.2 Sodium dodecyl sulfate (SDS) Carl Roth Cat#0183.2 Sodium nitrate, R99%, p.a., ACS, ISO Carl Roth Cat#A136.1 TEMED Carl Roth Cat#2367.3 Tris Carl Roth Cat#AE15.2 (Continued on next page) e1 Structure 30, 575–589.e1–e6, April 7, 2022 .. Closed dimer (C2) of human ATM (Ataxia telangiectasia mutated) (Baretic et al., 2017) EMDB: EMD-3668 Cryo-EM structure of CSN-N8-CRL4ADDB2 at 8.3 A resolution (Cavadini et al., 2016) EMDB: EMD-3316 Experimental models: Organisms/strains Chaetomium thermophilum var. thermophilum (Freeze Dried) DSMZ DSM 1495 Software and algorithms Image Lab Software 6.1 BIO-RAD https://www.bio-rad.com/de-de/product/ image-lab-software UNICORN 7 Workstation for ÄKTA pure, pilot, process, Ready to Process WAVE 25 GE Healthcare Europe GmbH https://www.gelifesciences.com/en/us/ shop/chromatography/software/unicorn7-p-05649 UCSF ChimeraX (Pettersen et al., 2021) https://www.rbvi.ucsf.edu/chimerax/ Omokage Search (Suzuki et al., 2015) https://pdbj.org/emnavi/omo-search.php RELION (Zivanov et al., 2018) https://github.com/3dem/relion PHENIX (Liebschner et al., 2019) https://www.phenix-online.org Pymol Schrödinger, inc https://pymol.org/ cryoSPARC Structura Biotechnology Inc. https://cryosparc.com/ Topaz (Bepler et al., 2020) https://emgweb.nysbc.org/topaz.html MODELLER (Webb and Sali, 2016) https://salilab.org/modeller/ COOT (Emsley and Cowtan, 2004) https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ AlphaFold2 (Jumper et al., 2021) https://github.com/deepmind/alphafold ColabFold (Mirdita et al., 2021) https://colab.research.google.com/ github/sokrypton/ColabFold/blob/main/ AlphaFold2.ipynb FindMySequence (Chojnowski et al., 2022) https://gitlab.com/gchojnowski/findmy sequence ARP/wARP (Chojnowski et al., 2021) https://www.embl-hamburg.de/ARP/ BoxPlotR (Spitzer et al., 2014) http://shiny.chemgrid.org/boxplotr/ Data Analysis ToolPak/MS Excel Microsoft Corporation https://office.microsoft.com/excel
Activity Assay:Article Title: Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts.
Article Snippet: Carl Roth 4621.1 D(+)-Glucose p. a., ACS, anhydrous Carl Roth X997.2 Dextrin for microbiology (from potato starch) Carl Roth 3488.1 di-Potassium hydrogen phosphate trihydrate Carl Roth 6878.1 di-Potassium hydrogen phosphate, R 99%, p.a., anhydrous Carl Roth P749.1 DNase I Sigma-Aldrich 10104159001 E-64 Sigma-Aldrich E3132-1MG EDTA disodium salt dihydrate, min. 99%, p.a., ACS Carl Roth 8043.2 Glycine Serva 23391.02 HEPES PUFFERAN , min. 99.5%, p.-1 kg Carl Roth 9105.3 Iron (III) sulfate hydrate, 80%, pure Carl Roth 0492.1 Isopropanol Carl Roth CP41.1 Leupeptin Sigma-Aldrich L2884-1MG Magnesium chloride hexahydrate, min. 99%, p.a., ACS Carl Roth 2189.1 Magnesium sulfate heptahydrate, R 99%, p.a., ACS Carl Roth P027.1 Methanol Carl Roth 4627.6 Milk powder Carl Roth T145.3 Pefabloc Sigma-Aldrich 11585916001 Pepstatin A Sigma-Aldrich 77170-5MG Peptone ex casein Carl Roth 8986.1 Phosphate buffered saline tablets (PBS) Sigma-Aldrich P4417 Potassium chloride min. 99.5%, 1 kg Carl Roth 6781.1 (Continued on next page) e1 Cell Reports 34, 108727, February 9, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Potassium dihydrogen phosphate, R 99%, p.a., ACS Carl Roth 3904.2 Precision plus protein all blue standards (marker) BIO-RAD 161-0373 Sodium chloride 99,5%, p.a., ACS, ISO Carl Roth 3957.2 Sodium dodecyl sulfate (SDS) Carl Roth 0183.2 Sodium nitrate, R 99%, p.a., ACS, ISO Carl Roth A136.1 TEMED Carl Roth 2367.3 Tris Carl Roth AE15.2 Tris Hydrochloride Carl Roth 9090.2 Tween 20 Carl Roth 9127.1 Tryptone Sigma-Aldrich T7293 Yeast Extract, micro-granulated Carl Roth 2904.3 Critical commercial assays A-KG Dehydrogenase activity assay kit Sigma-Aldrich MAK189-1KT PDH Activity assay kit Sigma-Aldrich MAK183-1KT Deposited data Cryo-EM structure of human E2p core Jiang et al., 2018 PDB: 6CT0 Proteomics data Kastritis et al., 2017 PXD006660 Crosslinking data Kastritis et al., 2017 PXD006626 Crystallographic structure of human E1p Seifert et al., 2007 PDB: 2OZL Cryo-EM structure of human E2o core 10.2210/pdb6H05/pdb PDB: 6H05 Crystallographic structure of cattle E2b core Kato et al., 2006) PDB: 2II3 Crystallographic structure of E3 Szabo et al., 2019 PDB: 6I4R Crystallographic structure of A. vinelandii cubic E2p core Mattevi et al., 1993 PDB: 1EAA Model of C. thermophilum PDHc E2p core from cryo-EM This study PDB: 7BGJ Cryo-EM structure of native PDHc E2p core (icosahedrally-averaged and asymmetric) and native, asymmetric PDHc This study EMDB: EMD-12181 Negative stain reconstructions of PDHc core, Fraction 6, and asymmetric reconstructions from Fractions 5-10 This study EMDB: EMD-12234 Negative stain reconstructions of hybrid BCKDc/OGDHc core, Fraction 6, and asymmetric reconstructions from Fractions 5-11 This study EMDB: EMD-12233 Model of C. thermophilum PDHc E2p core from negative stain This study https://data.sbgrid.org/817 Model of C. thermophilum E1p PDHc This study https://data.sbgrid.org/817 Model of C. thermophilum E2o OGDHc from negative stain This study https://data.sbgrid.org/817 Model of C. thermophilum E2b BCKDHc from negative stain This study https://data.sbgrid.org/817 Model ofC. thermophilum E3BP trimer from cryo-EM This study https://data.sbgrid.org/817) ‘‘SBGRID: 817’’ Model of C. thermophilum E3 This study https://data.sbgrid.org/817 (Continued on next page) Cell Reports 34, 108727, February 9, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw cryo- and negative stain micrographs of a native extract from C. thermophilum used to reconstruct oxo acid dehydrogenase complexes This study EMPIAR: 10625 Experimental models: organisms/strains Chaetomium thermophilum var. thermophilum (Freeze-dried) DSMZ DSM 1495 Software and algorithms 3DFSC Tan et al., 2017 https://3dfsc.salk.edu/ Eman 2.0 Tang et al., 2007 https://blake.bcm.edu/emanwiki/EMAN2 Fiji Schindelin et al., 2012 https://imagej.net/Fiji Gctf Zhang, 2016 https://www.mrc-lmb.cam.ac.uk/kzhang/ Gen5 BioTek Instruments https://www.biotek.com/products/ software-robotics-software/ gen5-microplatereader-and-imager-software/ Haddock van Zundert et al., 2016 https://alcazar.science.uu.nl/services/ HADDOCK2.2/ Image Lab Software 6.1 BIO-RAD https://www.bio-rad.com/en-us/product/ image-lab-software?ID=KRE6P5E8Z Modeler Eswar et al., 2006 https://salilab.org/modeller/ MotionCor2 Zheng et al., 2017 https://emcore.ucsf.edu/ucsf-software Needle Needleman and Wunsch, 1970 https://www.ebi.ac.uk/Tools/psa/ emboss_needle/ Phenix Afonine et al., 2018 https://www.phenix-online.org Pymol Schrödinger, inc https://pymol.org/2/ Relion 3.0 Zivanov et al., 2018 https://github.com/3dem/relion Scipion 2.0 de la Rosa-Trevı́n et al., 2016 https://scipion-em.github.io/docs/ Segger Pintilie and Chiu, 2012 https://www.cgl.ucsf.edu/chimera/ Sphire-cryolo Wagner and Raunser, 2020 http://sphire.mpg.de/ UCSF Chimera Pettersen et al., 2004 https://www.cgl.ucsf.edu/chimera/ UCSF ChimeraX Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ UNICORN 7 Workstation for ÄKTA pure, pilot, process, Ready To Process WAVE 25 GE Healthcare Europe GmbH https://www.cytivalifesciences.com/en/us/ shop/chromatography/software/ unicorn-7-p-05649 Xmipp Sorzano et al., 2004 https://github.com/I2PC/xmipp
Cryo-EM Sample Prep:Article Title: Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts.
Article Snippet: Carl Roth 4621.1 D(+)-Glucose p. a., ACS, anhydrous Carl Roth X997.2 Dextrin for microbiology (from potato starch) Carl Roth 3488.1 di-Potassium hydrogen phosphate trihydrate Carl Roth 6878.1 di-Potassium hydrogen phosphate, R 99%, p.a., anhydrous Carl Roth P749.1 DNase I Sigma-Aldrich 10104159001 E-64 Sigma-Aldrich E3132-1MG EDTA disodium salt dihydrate, min. 99%, p.a., ACS Carl Roth 8043.2 Glycine Serva 23391.02 HEPES PUFFERAN , min. 99.5%, p.-1 kg Carl Roth 9105.3 Iron (III) sulfate hydrate, 80%, pure Carl Roth 0492.1 Isopropanol Carl Roth CP41.1 Leupeptin Sigma-Aldrich L2884-1MG Magnesium chloride hexahydrate, min. 99%, p.a., ACS Carl Roth 2189.1 Magnesium sulfate heptahydrate, R 99%, p.a., ACS Carl Roth P027.1 Methanol Carl Roth 4627.6 Milk powder Carl Roth T145.3 Pefabloc Sigma-Aldrich 11585916001 Pepstatin A Sigma-Aldrich 77170-5MG Peptone ex casein Carl Roth 8986.1 Phosphate buffered saline tablets (PBS) Sigma-Aldrich P4417 Potassium chloride min. 99.5%, 1 kg Carl Roth 6781.1 (Continued on next page) e1 Cell Reports 34, 108727, February 9, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Potassium dihydrogen phosphate, R 99%, p.a., ACS Carl Roth 3904.2 Precision plus protein all blue standards (marker) BIO-RAD 161-0373 Sodium chloride 99,5%, p.a., ACS, ISO Carl Roth 3957.2 Sodium dodecyl sulfate (SDS) Carl Roth 0183.2 Sodium nitrate, R 99%, p.a., ACS, ISO Carl Roth A136.1 TEMED Carl Roth 2367.3 Tris Carl Roth AE15.2 Tris Hydrochloride Carl Roth 9090.2 Tween 20 Carl Roth 9127.1 Tryptone Sigma-Aldrich T7293 Yeast Extract, micro-granulated Carl Roth 2904.3 Critical commercial assays A-KG Dehydrogenase activity assay kit Sigma-Aldrich MAK189-1KT PDH Activity assay kit Sigma-Aldrich MAK183-1KT Deposited data Cryo-EM structure of human E2p core Jiang et al., 2018 PDB: 6CT0 Proteomics data Kastritis et al., 2017 PXD006660 Crosslinking data Kastritis et al., 2017 PXD006626 Crystallographic structure of human E1p Seifert et al., 2007 PDB: 2OZL Cryo-EM structure of human E2o core 10.2210/pdb6H05/pdb PDB: 6H05 Crystallographic structure of cattle E2b core Kato et al., 2006) PDB: 2II3 Crystallographic structure of E3 Szabo et al., 2019 PDB: 6I4R Crystallographic structure of A. vinelandii cubic E2p core Mattevi et al., 1993 PDB: 1EAA Model of C. thermophilum PDHc E2p core from cryo-EM This study PDB: 7BGJ Cryo-EM structure of native PDHc E2p core (icosahedrally-averaged and asymmetric) and native, asymmetric PDHc This study EMDB: EMD-12181 Negative stain reconstructions of PDHc core, Fraction 6, and asymmetric reconstructions from Fractions 5-10 This study EMDB: EMD-12234 Negative stain reconstructions of hybrid BCKDc/OGDHc core, Fraction 6, and asymmetric reconstructions from Fractions 5-11 This study EMDB: EMD-12233 Model of C. thermophilum PDHc E2p core from negative stain This study https://data.sbgrid.org/817 Model of C. thermophilum E1p PDHc This study https://data.sbgrid.org/817 Model of C. thermophilum E2o OGDHc from negative stain This study https://data.sbgrid.org/817 Model of C. thermophilum E2b BCKDHc from negative stain This study https://data.sbgrid.org/817 Model ofC. thermophilum E3BP trimer from cryo-EM This study https://data.sbgrid.org/817) ‘‘SBGRID: 817’’ Model of C. thermophilum E3 This study https://data.sbgrid.org/817 (Continued on next page) Cell Reports 34, 108727, February 9, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw cryo- and negative stain micrographs of a native extract from C. thermophilum used to reconstruct oxo acid dehydrogenase complexes This study EMPIAR: 10625 Experimental models: organisms/strains Chaetomium thermophilum var. thermophilum (Freeze-dried) DSMZ DSM 1495 Software and algorithms 3DFSC Tan et al., 2017 https://3dfsc.salk.edu/ Eman 2.0 Tang et al., 2007 https://blake.bcm.edu/emanwiki/EMAN2 Fiji Schindelin et al., 2012 https://imagej.net/Fiji Gctf Zhang, 2016 https://www.mrc-lmb.cam.ac.uk/kzhang/ Gen5 BioTek Instruments https://www.biotek.com/products/ software-robotics-software/ gen5-microplatereader-and-imager-software/ Haddock van Zundert et al., 2016 https://alcazar.science.uu.nl/services/ HADDOCK2.2/ Image Lab Software 6.1 BIO-RAD https://www.bio-rad.com/en-us/product/ image-lab-software?ID=KRE6P5E8Z Modeler Eswar et al., 2006 https://salilab.org/modeller/ MotionCor2 Zheng et al., 2017 https://emcore.ucsf.edu/ucsf-software Needle Needleman and Wunsch, 1970 https://www.ebi.ac.uk/Tools/psa/ emboss_needle/ Phenix Afonine et al., 2018 https://www.phenix-online.org Pymol Schrödinger, inc https://pymol.org/2/ Relion 3.0 Zivanov et al., 2018 https://github.com/3dem/relion Scipion 2.0 de la Rosa-Trevı́n et al., 2016 https://scipion-em.github.io/docs/ Segger Pintilie and Chiu, 2012 https://www.cgl.ucsf.edu/chimera/ Sphire-cryolo Wagner and Raunser, 2020 http://sphire.mpg.de/ UCSF Chimera Pettersen et al., 2004 https://www.cgl.ucsf.edu/chimera/ UCSF ChimeraX Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ UNICORN 7 Workstation for ÄKTA pure, pilot, process, Ready To Process WAVE 25 GE Healthcare Europe GmbH https://www.cytivalifesciences.com/en/us/ shop/chromatography/software/ unicorn-7-p-05649 Xmipp Sorzano et al., 2004 https://github.com/I2PC/xmipp
Staining:Article Title: Integrative structure of a 10-megadalton eukaryotic pyruvate dehydrogenase complex from native cell extracts.
Article Snippet: Carl Roth 4621.1 D(+)-Glucose p. a., ACS, anhydrous Carl Roth X997.2 Dextrin for microbiology (from potato starch) Carl Roth 3488.1 di-Potassium hydrogen phosphate trihydrate Carl Roth 6878.1 di-Potassium hydrogen phosphate, R 99%, p.a., anhydrous Carl Roth P749.1 DNase I Sigma-Aldrich 10104159001 E-64 Sigma-Aldrich E3132-1MG EDTA disodium salt dihydrate, min. 99%, p.a., ACS Carl Roth 8043.2 Glycine Serva 23391.02 HEPES PUFFERAN , min. 99.5%, p.-1 kg Carl Roth 9105.3 Iron (III) sulfate hydrate, 80%, pure Carl Roth 0492.1 Isopropanol Carl Roth CP41.1 Leupeptin Sigma-Aldrich L2884-1MG Magnesium chloride hexahydrate, min. 99%, p.a., ACS Carl Roth 2189.1 Magnesium sulfate heptahydrate, R 99%, p.a., ACS Carl Roth P027.1 Methanol Carl Roth 4627.6 Milk powder Carl Roth T145.3 Pefabloc Sigma-Aldrich 11585916001 Pepstatin A Sigma-Aldrich 77170-5MG Peptone ex casein Carl Roth 8986.1 Phosphate buffered saline tablets (PBS) Sigma-Aldrich P4417 Potassium chloride min. 99.5%, 1 kg Carl Roth 6781.1 (Continued on next page) e1 Cell Reports 34, 108727, February 9, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER Potassium dihydrogen phosphate, R 99%, p.a., ACS Carl Roth 3904.2 Precision plus protein all blue standards (marker) BIO-RAD 161-0373 Sodium chloride 99,5%, p.a., ACS, ISO Carl Roth 3957.2 Sodium dodecyl sulfate (SDS) Carl Roth 0183.2 Sodium nitrate, R 99%, p.a., ACS, ISO Carl Roth A136.1 TEMED Carl Roth 2367.3 Tris Carl Roth AE15.2 Tris Hydrochloride Carl Roth 9090.2 Tween 20 Carl Roth 9127.1 Tryptone Sigma-Aldrich T7293 Yeast Extract, micro-granulated Carl Roth 2904.3 Critical commercial assays A-KG Dehydrogenase activity assay kit Sigma-Aldrich MAK189-1KT PDH Activity assay kit Sigma-Aldrich MAK183-1KT Deposited data Cryo-EM structure of human E2p core Jiang et al., 2018 PDB: 6CT0 Proteomics data Kastritis et al., 2017 PXD006660 Crosslinking data Kastritis et al., 2017 PXD006626 Crystallographic structure of human E1p Seifert et al., 2007 PDB: 2OZL Cryo-EM structure of human E2o core 10.2210/pdb6H05/pdb PDB: 6H05 Crystallographic structure of cattle E2b core Kato et al., 2006) PDB: 2II3 Crystallographic structure of E3 Szabo et al., 2019 PDB: 6I4R Crystallographic structure of A. vinelandii cubic E2p core Mattevi et al., 1993 PDB: 1EAA Model of C. thermophilum PDHc E2p core from cryo-EM This study PDB: 7BGJ Cryo-EM structure of native PDHc E2p core (icosahedrally-averaged and asymmetric) and native, asymmetric PDHc This study EMDB: EMD-12181 Negative stain reconstructions of PDHc core, Fraction 6, and asymmetric reconstructions from Fractions 5-10 This study EMDB: EMD-12234 Negative stain reconstructions of hybrid BCKDc/OGDHc core, Fraction 6, and asymmetric reconstructions from Fractions 5-11 This study EMDB: EMD-12233 Model of C. thermophilum PDHc E2p core from negative stain This study https://data.sbgrid.org/817 Model of C. thermophilum E1p PDHc This study https://data.sbgrid.org/817 Model of C. thermophilum E2o OGDHc from negative stain This study https://data.sbgrid.org/817 Model of C. thermophilum E2b BCKDHc from negative stain This study https://data.sbgrid.org/817 Model ofC. thermophilum E3BP trimer from cryo-EM This study https://data.sbgrid.org/817) ‘‘SBGRID: 817’’ Model of C. thermophilum E3 This study https://data.sbgrid.org/817 (Continued on next page) Cell Reports 34, 108727, February 9, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw cryo- and negative stain micrographs of a native extract from C. thermophilum used to reconstruct oxo acid dehydrogenase complexes This study EMPIAR: 10625 Experimental models: organisms/strains Chaetomium thermophilum var. thermophilum (Freeze-dried) DSMZ DSM 1495 Software and algorithms 3DFSC Tan et al., 2017 https://3dfsc.salk.edu/ Eman 2.0 Tang et al., 2007 https://blake.bcm.edu/emanwiki/EMAN2 Fiji Schindelin et al., 2012 https://imagej.net/Fiji Gctf Zhang, 2016 https://www.mrc-lmb.cam.ac.uk/kzhang/ Gen5 BioTek Instruments https://www.biotek.com/products/ software-robotics-software/ gen5-microplatereader-and-imager-software/ Haddock van Zundert et al., 2016 https://alcazar.science.uu.nl/services/ HADDOCK2.2/ Image Lab Software 6.1 BIO-RAD https://www.bio-rad.com/en-us/product/ image-lab-software?ID=KRE6P5E8Z Modeler Eswar et al., 2006 https://salilab.org/modeller/ MotionCor2 Zheng et al., 2017 https://emcore.ucsf.edu/ucsf-software Needle Needleman and Wunsch, 1970 https://www.ebi.ac.uk/Tools/psa/ emboss_needle/ Phenix Afonine et al., 2018 https://www.phenix-online.org Pymol Schrödinger, inc https://pymol.org/2/ Relion 3.0 Zivanov et al., 2018 https://github.com/3dem/relion Scipion 2.0 de la Rosa-Trevı́n et al., 2016 https://scipion-em.github.io/docs/ Segger Pintilie and Chiu, 2012 https://www.cgl.ucsf.edu/chimera/ Sphire-cryolo Wagner and Raunser, 2020 http://sphire.mpg.de/ UCSF Chimera Pettersen et al., 2004 https://www.cgl.ucsf.edu/chimera/ UCSF ChimeraX Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ UNICORN 7 Workstation for ÄKTA pure, pilot, process, Ready To Process WAVE 25 GE Healthcare Europe GmbH https://www.cytivalifesciences.com/en/us/ shop/chromatography/software/ unicorn-7-p-05649 Xmipp Sorzano et al., 2004 https://github.com/I2PC/xmipp
Starch:Article Title: Cryo-EM and artificial intelligence visualize endogenous protein community members.
Article Snippet: Carl Roth Cat#6908.4 Acrylamide/Bis solution, 37.5:1 Serva Cat#10688.01 Agar-Agar, bacteriological highly pure Carl Roth Cat#2266.3 Ammonium acetate, R97%, p.a., ACS Carl Roth Cat#7869.2 Ammonium persulfate Serva Cat#13376.02 Aprotinin from bovine lung Merck Cat#A1153-1MG Bestatin, 10MG Merck Cat#10874515001 Clarity Western ECL substrate BIO-RAD Cat#170-5060 D-Sucrose, R99,5%, p.a. .. Carl Roth Cat#4621.1 D(+)-Glucose p. a., ACS, anhydrous Carl Roth Cat#X997.2 Dextrin for microbiology (from potato starch) Carl Roth Cat#3488.1 di-Potassium hydrogen phosphate trihydrate Carl Roth Cat#6878.1 di-Potassium hydrogen phosphate, R99%, p.a., anhydrous Carl Roth Cat#P749.1 DNAse I Merck Cat#10104159001 E-64 Merck Cat#E3132-1MG EDTA disodium salt dihydrate, min. 99%, p.a., ACS Carl Roth Cat#8043.2 Glycine Serva Cat#23391.02 HEPES PUFFERAN , min. 99.5%, p.-1 kg Carl Roth Cat#9105.3 Iron (III) sulphate hydrate, 80%, pure Carl Roth Cat#0492.1 Isopropanol Carl Roth Cat#CP41.1 Leupeptin Merck Cat#L2884-1MG Magnesium chloride hexahydrate, min. 99%, p.a., ACS Carl Roth Cat#2189.1 Magnesium sulphate heptahydrate, R99%, p.a., ACS Carl Roth Cat#P027.1 Methanol Carl Roth Cat#4627.6 Milk powder Carl Roth Cat#T145.3 Pefabloc Merck Cat#11585916001 Pepstatin A Merck Cat#77170-5MG Peptone ex casein Carl Roth Cat#8986.1 Phosphate buffered saline tablets (PBS) Merck Cat#P4417 Potassium chloride min. 99.5%, -1 kg Carl Roth Cat#6781.1 Potassium dihydrogen phosphate, R99%, p.a., ACS Carl Roth Cat#3904.2 Precision plus protein all blue standards (marker) BIO-RAD Cat161-0373 Sodium chloride 99,5%, p.a., ACS, ISO Carl Roth Cat#3957.2 Sodium dodecyl sulfate (SDS) Carl Roth Cat#0183.2 Sodium nitrate, R99%, p.a., ACS, ISO Carl Roth Cat#A136.1 TEMED Carl Roth Cat#2367.3 Tris Carl Roth Cat#AE15.2 (Continued on next page) e1 Structure 30, 575–589.e1–e6, April 7, 2022 .. Closed dimer (C2) of human ATM (Ataxia telangiectasia mutated) (Baretic et al., 2017) EMDB: EMD-3668 Cryo-EM structure of CSN-N8-CRL4ADDB2 at 8.3 A resolution (Cavadini et al., 2016) EMDB: EMD-3316 Experimental models: Organisms/strains Chaetomium thermophilum var. thermophilum (Freeze Dried) DSMZ DSM 1495 Software and algorithms Image Lab Software 6.1 BIO-RAD https://www.bio-rad.com/de-de/product/ image-lab-software UNICORN 7 Workstation for ÄKTA pure, pilot, process, Ready to Process WAVE 25 GE Healthcare Europe GmbH https://www.gelifesciences.com/en/us/ shop/chromatography/software/unicorn7-p-05649 UCSF ChimeraX (Pettersen et al., 2021) https://www.rbvi.ucsf.edu/chimerax/ Omokage Search (Suzuki et al., 2015) https://pdbj.org/emnavi/omo-search.php RELION (Zivanov et al., 2018) https://github.com/3dem/relion PHENIX (Liebschner et al., 2019) https://www.phenix-online.org Pymol Schrödinger, inc https://pymol.org/ cryoSPARC Structura Biotechnology Inc. https://cryosparc.com/ Topaz (Bepler et al., 2020) https://emgweb.nysbc.org/topaz.html MODELLER (Webb and Sali, 2016) https://salilab.org/modeller/ COOT (Emsley and Cowtan, 2004) https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ AlphaFold2 (Jumper et al., 2021) https://github.com/deepmind/alphafold ColabFold (Mirdita et al., 2021) https://colab.research.google.com/ github/sokrypton/ColabFold/blob/main/ AlphaFold2.ipynb FindMySequence (Chojnowski et al., 2022) https://gitlab.com/gchojnowski/findmy sequence ARP/wARP (Chojnowski et al., 2021) https://www.embl-hamburg.de/ARP/ BoxPlotR (Spitzer et al., 2014) http://shiny.chemgrid.org/boxplotr/ Data Analysis ToolPak/MS Excel Microsoft Corporation https://office.microsoft.com/excel
Milk:Article Title: Cryo-EM and artificial intelligence visualize endogenous protein community members.
Article Snippet: Carl Roth Cat#6908.4 Acrylamide/Bis solution, 37.5:1 Serva Cat#10688.01 Agar-Agar, bacteriological highly pure Carl Roth Cat#2266.3 Ammonium acetate, R97%, p.a., ACS Carl Roth Cat#7869.2 Ammonium persulfate Serva Cat#13376.02 Aprotinin from bovine lung Merck Cat#A1153-1MG Bestatin, 10MG Merck Cat#10874515001 Clarity Western ECL substrate BIO-RAD Cat#170-5060 D-Sucrose, R99,5%, p.a. .. Carl Roth Cat#4621.1 D(+)-Glucose p. a., ACS, anhydrous Carl Roth Cat#X997.2 Dextrin for microbiology (from potato starch) Carl Roth Cat#3488.1 di-Potassium hydrogen phosphate trihydrate Carl Roth Cat#6878.1 di-Potassium hydrogen phosphate, R99%, p.a., anhydrous Carl Roth Cat#P749.1 DNAse I Merck Cat#10104159001 E-64 Merck Cat#E3132-1MG EDTA disodium salt dihydrate, min. 99%, p.a., ACS Carl Roth Cat#8043.2 Glycine Serva Cat#23391.02 HEPES PUFFERAN , min. 99.5%, p.-1 kg Carl Roth Cat#9105.3 Iron (III) sulphate hydrate, 80%, pure Carl Roth Cat#0492.1 Isopropanol Carl Roth Cat#CP41.1 Leupeptin Merck Cat#L2884-1MG Magnesium chloride hexahydrate, min. 99%, p.a., ACS Carl Roth Cat#2189.1 Magnesium sulphate heptahydrate, R99%, p.a., ACS Carl Roth Cat#P027.1 Methanol Carl Roth Cat#4627.6 Milk powder Carl Roth Cat#T145.3 Pefabloc Merck Cat#11585916001 Pepstatin A Merck Cat#77170-5MG Peptone ex casein Carl Roth Cat#8986.1 Phosphate buffered saline tablets (PBS) Merck Cat#P4417 Potassium chloride min. 99.5%, -1 kg Carl Roth Cat#6781.1 Potassium dihydrogen phosphate, R99%, p.a., ACS Carl Roth Cat#3904.2 Precision plus protein all blue standards (marker) BIO-RAD Cat161-0373 Sodium chloride 99,5%, p.a., ACS, ISO Carl Roth Cat#3957.2 Sodium dodecyl sulfate (SDS) Carl Roth Cat#0183.2 Sodium nitrate, R99%, p.a., ACS, ISO Carl Roth Cat#A136.1 TEMED Carl Roth Cat#2367.3 Tris Carl Roth Cat#AE15.2 (Continued on next page) e1 Structure 30, 575–589.e1–e6, April 7, 2022 .. Closed dimer (C2) of human ATM (Ataxia telangiectasia mutated) (Baretic et al., 2017) EMDB: EMD-3668 Cryo-EM structure of CSN-N8-CRL4ADDB2 at 8.3 A resolution (Cavadini et al., 2016) EMDB: EMD-3316 Experimental models: Organisms/strains Chaetomium thermophilum var. thermophilum (Freeze Dried) DSMZ DSM 1495 Software and algorithms Image Lab Software 6.1 BIO-RAD https://www.bio-rad.com/de-de/product/ image-lab-software UNICORN 7 Workstation for ÄKTA pure, pilot, process, Ready to Process WAVE 25 GE Healthcare Europe GmbH https://www.gelifesciences.com/en/us/ shop/chromatography/software/unicorn7-p-05649 UCSF ChimeraX (Pettersen et al., 2021) https://www.rbvi.ucsf.edu/chimerax/ Omokage Search (Suzuki et al., 2015) https://pdbj.org/emnavi/omo-search.php RELION (Zivanov et al., 2018) https://github.com/3dem/relion PHENIX (Liebschner et al., 2019) https://www.phenix-online.org Pymol Schrödinger, inc https://pymol.org/ cryoSPARC Structura Biotechnology Inc. https://cryosparc.com/ Topaz (Bepler et al., 2020) https://emgweb.nysbc.org/topaz.html MODELLER (Webb and Sali, 2016) https://salilab.org/modeller/ COOT (Emsley and Cowtan, 2004) https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ AlphaFold2 (Jumper et al., 2021) https://github.com/deepmind/alphafold ColabFold (Mirdita et al., 2021) https://colab.research.google.com/ github/sokrypton/ColabFold/blob/main/ AlphaFold2.ipynb FindMySequence (Chojnowski et al., 2022) https://gitlab.com/gchojnowski/findmy sequence ARP/wARP (Chojnowski et al., 2021) https://www.embl-hamburg.de/ARP/ BoxPlotR (Spitzer et al., 2014) http://shiny.chemgrid.org/boxplotr/ Data Analysis ToolPak/MS Excel Microsoft Corporation https://office.microsoft.com/excel
Saline:Article Title: Cryo-EM and artificial intelligence visualize endogenous protein community members.
Article Snippet: Carl Roth Cat#6908.4 Acrylamide/Bis solution, 37.5:1 Serva Cat#10688.01 Agar-Agar, bacteriological highly pure Carl Roth Cat#2266.3 Ammonium acetate, R97%, p.a., ACS Carl Roth Cat#7869.2 Ammonium persulfate Serva Cat#13376.02 Aprotinin from bovine lung Merck Cat#A1153-1MG Bestatin, 10MG Merck Cat#10874515001 Clarity Western ECL substrate BIO-RAD Cat#170-5060 D-Sucrose, R99,5%, p.a. .. Carl Roth Cat#4621.1 D(+)-Glucose p. a., ACS, anhydrous Carl Roth Cat#X997.2 Dextrin for microbiology (from potato starch) Carl Roth Cat#3488.1 di-Potassium hydrogen phosphate trihydrate Carl Roth Cat#6878.1 di-Potassium hydrogen phosphate, R99%, p.a., anhydrous Carl Roth Cat#P749.1 DNAse I Merck Cat#10104159001 E-64 Merck Cat#E3132-1MG EDTA disodium salt dihydrate, min. 99%, p.a., ACS Carl Roth Cat#8043.2 Glycine Serva Cat#23391.02 HEPES PUFFERAN , min. 99.5%, p.-1 kg Carl Roth Cat#9105.3 Iron (III) sulphate hydrate, 80%, pure Carl Roth Cat#0492.1 Isopropanol Carl Roth Cat#CP41.1 Leupeptin Merck Cat#L2884-1MG Magnesium chloride hexahydrate, min. 99%, p.a., ACS Carl Roth Cat#2189.1 Magnesium sulphate heptahydrate, R99%, p.a., ACS Carl Roth Cat#P027.1 Methanol Carl Roth Cat#4627.6 Milk powder Carl Roth Cat#T145.3 Pefabloc Merck Cat#11585916001 Pepstatin A Merck Cat#77170-5MG Peptone ex casein Carl Roth Cat#8986.1 Phosphate buffered saline tablets (PBS) Merck Cat#P4417 Potassium chloride min. 99.5%, -1 kg Carl Roth Cat#6781.1 Potassium dihydrogen phosphate, R99%, p.a., ACS Carl Roth Cat#3904.2 Precision plus protein all blue standards (marker) BIO-RAD Cat161-0373 Sodium chloride 99,5%, p.a., ACS, ISO Carl Roth Cat#3957.2 Sodium dodecyl sulfate (SDS) Carl Roth Cat#0183.2 Sodium nitrate, R99%, p.a., ACS, ISO Carl Roth Cat#A136.1 TEMED Carl Roth Cat#2367.3 Tris Carl Roth Cat#AE15.2 (Continued on next page) e1 Structure 30, 575–589.e1–e6, April 7, 2022 .. Closed dimer (C2) of human ATM (Ataxia telangiectasia mutated) (Baretic et al., 2017) EMDB: EMD-3668 Cryo-EM structure of CSN-N8-CRL4ADDB2 at 8.3 A resolution (Cavadini et al., 2016) EMDB: EMD-3316 Experimental models: Organisms/strains Chaetomium thermophilum var. thermophilum (Freeze Dried) DSMZ DSM 1495 Software and algorithms Image Lab Software 6.1 BIO-RAD https://www.bio-rad.com/de-de/product/ image-lab-software UNICORN 7 Workstation for ÄKTA pure, pilot, process, Ready to Process WAVE 25 GE Healthcare Europe GmbH https://www.gelifesciences.com/en/us/ shop/chromatography/software/unicorn7-p-05649 UCSF ChimeraX (Pettersen et al., 2021) https://www.rbvi.ucsf.edu/chimerax/ Omokage Search (Suzuki et al., 2015) https://pdbj.org/emnavi/omo-search.php RELION (Zivanov et al., 2018) https://github.com/3dem/relion PHENIX (Liebschner et al., 2019) https://www.phenix-online.org Pymol Schrödinger, inc https://pymol.org/ cryoSPARC Structura Biotechnology Inc. https://cryosparc.com/ Topaz (Bepler et al., 2020) https://emgweb.nysbc.org/topaz.html MODELLER (Webb and Sali, 2016) https://salilab.org/modeller/ COOT (Emsley and Cowtan, 2004) https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ AlphaFold2 (Jumper et al., 2021) https://github.com/deepmind/alphafold ColabFold (Mirdita et al., 2021) https://colab.research.google.com/ github/sokrypton/ColabFold/blob/main/ AlphaFold2.ipynb FindMySequence (Chojnowski et al., 2022) https://gitlab.com/gchojnowski/findmy sequence ARP/wARP (Chojnowski et al., 2021) https://www.embl-hamburg.de/ARP/ BoxPlotR (Spitzer et al., 2014) http://shiny.chemgrid.org/boxplotr/ Data Analysis ToolPak/MS Excel Microsoft Corporation https://office.microsoft.com/excel
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