other:Article Title: Substrate binding modes of purine and pyrimidine nucleotides to human ecto-5′-nucleotidase (CD73) and inhibition by their bisphosphonic acid derivatives
Article Snippet: Compound Supplier, Product number, purity Adenosine 5'-monophosphate (AMP) Sigma-Aldrich, 01930, ≥ 99 % 2′-Deoxyadenosine 5′-monophosphate (dAMP) Sigma-Aldrich, D6375, ≥ 98 % Cytidine 5′-monophosphate (CMP) Sigma-Aldrich, C1006, ≥ 99 % 2′-Deoxycytidine 5′-monophosphate (dCMP) Sigma-Aldrich, D7750, ≥ 95% 2′-Deoxyguanosine 5′-monophosphate (dGMP) Sigma-Aldrich, D9500, ≥ 99 % 2'-Deoxyuridine-5'-[(α,β)methyleno]diphosphate, Sodium salt (dUMPCP) Jena Bioscience, NU-428S, ≥ 95 % Guanosin-5'-monophosphat Dinatriumsalz (GMP) Sigma-Aldrich, G8377, ≥ 99 % α,β-Methyleneguanosine 5′-diphosphate sodium salt (GMPCP) Jena Bioscience, NU-414-5, ≥ 95 % Adenosin 5'-[α,β-methylene] diphosphoric acid (AMPCP) Jena Bioscience, NU-420-5, ≥ 95 % Thymidine 5'-Monophosphate Natriumsalz ) dTMP) Sigma-Aldrich, T7004, ≥ 99 % Uridin-5'-Monophosphate Dinatriumsalz Sigma-Aldrich, U6375, ≥ 99 % Inosine 5'-monophosphate Disodiumsalt Sigma-Aldrich, U6375, ≥ 98 % Cytidine-5'-[(α,β)-methyleno]diphosphate, Sodium salt (CMPCP) Jena Bioscience, I4625, ≥ 95 % Table S2a.
Virus:Article Title: Catalytic cycling of human mitochondrial Lon protease.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-6X His tag antibody primary antibody Abcam Ab18184; RRID: AB_444306 anti-rabbit secondary antibody, Alkaline Phosphatase conjugated Sigma-Aldrich A3687; RRID: AB_258103 Bacterial and virus strains E. coli BL21(DE3) cells Merck 69450 E. coli Rosetta DE3 Merck 70954 Chemicals, peptides, and recombinant proteins FITC-casein Sigma-Aldrich SLCD5097 Adenosine-5’-(g-thio)-triphosphate, Tetralithium salt Jena Biosciences Cat# NU-406 Adenosine-5’-[(b,g)-methyleno]triphosphate, Sodium salt Jena Biosciences Cat# NU-422 Adenosine-5’-[(a,b)-imido]diphosphate, Sodium salt Jena Biosciences Cat# NU-448 Adenosine 50-triphosphate, Disodium salt trihydrate Jena Biosciences Cat# NU1010 Adenosine-50-diphosphate, Sodium salt Jena Biosciences Cat# NU-1198 Critical commercial assays ATPase/GTPase activity assay kit Sigma-Aldrich MAK113 Pierce Fluorescent Protease Assay Kit Thermo Scientific Cat# 23266 Deposited data R-state in the presence of ADP and ATP This work PDB: 7NGL EMDB-12315 R-state in the presence of AMPCPP This work PDB: 7OXO EMDB-13102 D1-state This work PDB: 7NGP EMDB-12316 D2-state This work PDB: 7NGQ EMDB-12317 P1a-state This work PDB: 7NFY EMDB-12306 P1b-state This work PDB: 7NG4 EMDB-12307 P1c-state This work PDB: 7NG5 EMDB-12308 P2a-state This work PDB: 7NGC EMDB-12312 P2c-state This work PDB: 7NGF EMDB-12313 Recombinant DNA LONP1 wild type GenScript synthesized Mutants of LONP1 (K529R, E591Q, E801A, T803V, E812A, H841F, H843F, S855A, C520S and double mutant C520S/C637S) GenScript Site directed mutagenesis TFAM, Human_TFAM_NoMTS_pET28 a gift from David Chan Addgene Ngo et al., 2014 Cat##34705 Software and algorithms Relion Nakane et al. (2018) https://github.com/3dem/relion cryoSPARC Punjani et al. (2017) https://guide.cryosparc.com (Continued on next page) Structure 30, 1254–1268.e1–e7, September 1, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Coot Emsley and Cowtan (2004) https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ ChimeraX, Chimera Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ download.html Phenix-1.18 Adams et al., 2010 https://phenix-online.org/download/ Focus Biyani et al., 2017 https://lbem-focus.epfl.ch/about.php lafter Ramlaul et al., 2019 https://www.ccpem.ac.uk/download.php CTFFIND4 Rohou and Grigorieff, 2015 https://grigoriefflab.umassmed.edu/ctffind4 Clustal Omega Sievers et al., 2011 https://www.ebi.ac.uk/Tools/msa/clustalo/ SWISS-MODEL Waterhouse et al., 2018 https://swissmodel.expasy.org I-TASSER Yang et al. 2015 https://zhanggroup.org/I-TASSER/ AlphaFold Jumper et al. 2021 https://alphafold.ebi.ac.uk
Recombinant:Article Title: Catalytic cycling of human mitochondrial Lon protease.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-6X His tag antibody primary antibody Abcam Ab18184; RRID: AB_444306 anti-rabbit secondary antibody, Alkaline Phosphatase conjugated Sigma-Aldrich A3687; RRID: AB_258103 Bacterial and virus strains E. coli BL21(DE3) cells Merck 69450 E. coli Rosetta DE3 Merck 70954 Chemicals, peptides, and recombinant proteins FITC-casein Sigma-Aldrich SLCD5097 Adenosine-5’-(g-thio)-triphosphate, Tetralithium salt Jena Biosciences Cat# NU-406 Adenosine-5’-[(b,g)-methyleno]triphosphate, Sodium salt Jena Biosciences Cat# NU-422 Adenosine-5’-[(a,b)-imido]diphosphate, Sodium salt Jena Biosciences Cat# NU-448 Adenosine 50-triphosphate, Disodium salt trihydrate Jena Biosciences Cat# NU1010 Adenosine-50-diphosphate, Sodium salt Jena Biosciences Cat# NU-1198 Critical commercial assays ATPase/GTPase activity assay kit Sigma-Aldrich MAK113 Pierce Fluorescent Protease Assay Kit Thermo Scientific Cat# 23266 Deposited data R-state in the presence of ADP and ATP This work PDB: 7NGL EMDB-12315 R-state in the presence of AMPCPP This work PDB: 7OXO EMDB-13102 D1-state This work PDB: 7NGP EMDB-12316 D2-state This work PDB: 7NGQ EMDB-12317 P1a-state This work PDB: 7NFY EMDB-12306 P1b-state This work PDB: 7NG4 EMDB-12307 P1c-state This work PDB: 7NG5 EMDB-12308 P2a-state This work PDB: 7NGC EMDB-12312 P2c-state This work PDB: 7NGF EMDB-12313 Recombinant DNA LONP1 wild type GenScript synthesized Mutants of LONP1 (K529R, E591Q, E801A, T803V, E812A, H841F, H843F, S855A, C520S and double mutant C520S/C637S) GenScript Site directed mutagenesis TFAM, Human_TFAM_NoMTS_pET28 a gift from David Chan Addgene Ngo et al., 2014 Cat##34705 Software and algorithms Relion Nakane et al. (2018) https://github.com/3dem/relion cryoSPARC Punjani et al. (2017) https://guide.cryosparc.com (Continued on next page) Structure 30, 1254–1268.e1–e7, September 1, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Coot Emsley and Cowtan (2004) https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ ChimeraX, Chimera Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ download.html Phenix-1.18 Adams et al., 2010 https://phenix-online.org/download/ Focus Biyani et al., 2017 https://lbem-focus.epfl.ch/about.php lafter Ramlaul et al., 2019 https://www.ccpem.ac.uk/download.php CTFFIND4 Rohou and Grigorieff, 2015 https://grigoriefflab.umassmed.edu/ctffind4 Clustal Omega Sievers et al., 2011 https://www.ebi.ac.uk/Tools/msa/clustalo/ SWISS-MODEL Waterhouse et al., 2018 https://swissmodel.expasy.org I-TASSER Yang et al. 2015 https://zhanggroup.org/I-TASSER/ AlphaFold Jumper et al. 2021 https://alphafold.ebi.ac.uk
Activity Assay:Article Title: Catalytic cycling of human mitochondrial Lon protease.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-6X His tag antibody primary antibody Abcam Ab18184; RRID: AB_444306 anti-rabbit secondary antibody, Alkaline Phosphatase conjugated Sigma-Aldrich A3687; RRID: AB_258103 Bacterial and virus strains E. coli BL21(DE3) cells Merck 69450 E. coli Rosetta DE3 Merck 70954 Chemicals, peptides, and recombinant proteins FITC-casein Sigma-Aldrich SLCD5097 Adenosine-5’-(g-thio)-triphosphate, Tetralithium salt Jena Biosciences Cat# NU-406 Adenosine-5’-[(b,g)-methyleno]triphosphate, Sodium salt Jena Biosciences Cat# NU-422 Adenosine-5’-[(a,b)-imido]diphosphate, Sodium salt Jena Biosciences Cat# NU-448 Adenosine 50-triphosphate, Disodium salt trihydrate Jena Biosciences Cat# NU1010 Adenosine-50-diphosphate, Sodium salt Jena Biosciences Cat# NU-1198 Critical commercial assays ATPase/GTPase activity assay kit Sigma-Aldrich MAK113 Pierce Fluorescent Protease Assay Kit Thermo Scientific Cat# 23266 Deposited data R-state in the presence of ADP and ATP This work PDB: 7NGL EMDB-12315 R-state in the presence of AMPCPP This work PDB: 7OXO EMDB-13102 D1-state This work PDB: 7NGP EMDB-12316 D2-state This work PDB: 7NGQ EMDB-12317 P1a-state This work PDB: 7NFY EMDB-12306 P1b-state This work PDB: 7NG4 EMDB-12307 P1c-state This work PDB: 7NG5 EMDB-12308 P2a-state This work PDB: 7NGC EMDB-12312 P2c-state This work PDB: 7NGF EMDB-12313 Recombinant DNA LONP1 wild type GenScript synthesized Mutants of LONP1 (K529R, E591Q, E801A, T803V, E812A, H841F, H843F, S855A, C520S and double mutant C520S/C637S) GenScript Site directed mutagenesis TFAM, Human_TFAM_NoMTS_pET28 a gift from David Chan Addgene Ngo et al., 2014 Cat##34705 Software and algorithms Relion Nakane et al. (2018) https://github.com/3dem/relion cryoSPARC Punjani et al. (2017) https://guide.cryosparc.com (Continued on next page) Structure 30, 1254–1268.e1–e7, September 1, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Coot Emsley and Cowtan (2004) https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ ChimeraX, Chimera Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ download.html Phenix-1.18 Adams et al., 2010 https://phenix-online.org/download/ Focus Biyani et al., 2017 https://lbem-focus.epfl.ch/about.php lafter Ramlaul et al., 2019 https://www.ccpem.ac.uk/download.php CTFFIND4 Rohou and Grigorieff, 2015 https://grigoriefflab.umassmed.edu/ctffind4 Clustal Omega Sievers et al., 2011 https://www.ebi.ac.uk/Tools/msa/clustalo/ SWISS-MODEL Waterhouse et al., 2018 https://swissmodel.expasy.org I-TASSER Yang et al. 2015 https://zhanggroup.org/I-TASSER/ AlphaFold Jumper et al. 2021 https://alphafold.ebi.ac.uk
Protease Assay:Article Title: Catalytic cycling of human mitochondrial Lon protease.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-6X His tag antibody primary antibody Abcam Ab18184; RRID: AB_444306 anti-rabbit secondary antibody, Alkaline Phosphatase conjugated Sigma-Aldrich A3687; RRID: AB_258103 Bacterial and virus strains E. coli BL21(DE3) cells Merck 69450 E. coli Rosetta DE3 Merck 70954 Chemicals, peptides, and recombinant proteins FITC-casein Sigma-Aldrich SLCD5097 Adenosine-5’-(g-thio)-triphosphate, Tetralithium salt Jena Biosciences Cat# NU-406 Adenosine-5’-[(b,g)-methyleno]triphosphate, Sodium salt Jena Biosciences Cat# NU-422 Adenosine-5’-[(a,b)-imido]diphosphate, Sodium salt Jena Biosciences Cat# NU-448 Adenosine 50-triphosphate, Disodium salt trihydrate Jena Biosciences Cat# NU1010 Adenosine-50-diphosphate, Sodium salt Jena Biosciences Cat# NU-1198 Critical commercial assays ATPase/GTPase activity assay kit Sigma-Aldrich MAK113 Pierce Fluorescent Protease Assay Kit Thermo Scientific Cat# 23266 Deposited data R-state in the presence of ADP and ATP This work PDB: 7NGL EMDB-12315 R-state in the presence of AMPCPP This work PDB: 7OXO EMDB-13102 D1-state This work PDB: 7NGP EMDB-12316 D2-state This work PDB: 7NGQ EMDB-12317 P1a-state This work PDB: 7NFY EMDB-12306 P1b-state This work PDB: 7NG4 EMDB-12307 P1c-state This work PDB: 7NG5 EMDB-12308 P2a-state This work PDB: 7NGC EMDB-12312 P2c-state This work PDB: 7NGF EMDB-12313 Recombinant DNA LONP1 wild type GenScript synthesized Mutants of LONP1 (K529R, E591Q, E801A, T803V, E812A, H841F, H843F, S855A, C520S and double mutant C520S/C637S) GenScript Site directed mutagenesis TFAM, Human_TFAM_NoMTS_pET28 a gift from David Chan Addgene Ngo et al., 2014 Cat##34705 Software and algorithms Relion Nakane et al. (2018) https://github.com/3dem/relion cryoSPARC Punjani et al. (2017) https://guide.cryosparc.com (Continued on next page) Structure 30, 1254–1268.e1–e7, September 1, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Coot Emsley and Cowtan (2004) https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ ChimeraX, Chimera Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ download.html Phenix-1.18 Adams et al., 2010 https://phenix-online.org/download/ Focus Biyani et al., 2017 https://lbem-focus.epfl.ch/about.php lafter Ramlaul et al., 2019 https://www.ccpem.ac.uk/download.php CTFFIND4 Rohou and Grigorieff, 2015 https://grigoriefflab.umassmed.edu/ctffind4 Clustal Omega Sievers et al., 2011 https://www.ebi.ac.uk/Tools/msa/clustalo/ SWISS-MODEL Waterhouse et al., 2018 https://swissmodel.expasy.org I-TASSER Yang et al. 2015 https://zhanggroup.org/I-TASSER/ AlphaFold Jumper et al. 2021 https://alphafold.ebi.ac.uk
Synthesized:Article Title: Catalytic cycling of human mitochondrial Lon protease.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-6X His tag antibody primary antibody Abcam Ab18184; RRID: AB_444306 anti-rabbit secondary antibody, Alkaline Phosphatase conjugated Sigma-Aldrich A3687; RRID: AB_258103 Bacterial and virus strains E. coli BL21(DE3) cells Merck 69450 E. coli Rosetta DE3 Merck 70954 Chemicals, peptides, and recombinant proteins FITC-casein Sigma-Aldrich SLCD5097 Adenosine-5’-(g-thio)-triphosphate, Tetralithium salt Jena Biosciences Cat# NU-406 Adenosine-5’-[(b,g)-methyleno]triphosphate, Sodium salt Jena Biosciences Cat# NU-422 Adenosine-5’-[(a,b)-imido]diphosphate, Sodium salt Jena Biosciences Cat# NU-448 Adenosine 50-triphosphate, Disodium salt trihydrate Jena Biosciences Cat# NU1010 Adenosine-50-diphosphate, Sodium salt Jena Biosciences Cat# NU-1198 Critical commercial assays ATPase/GTPase activity assay kit Sigma-Aldrich MAK113 Pierce Fluorescent Protease Assay Kit Thermo Scientific Cat# 23266 Deposited data R-state in the presence of ADP and ATP This work PDB: 7NGL EMDB-12315 R-state in the presence of AMPCPP This work PDB: 7OXO EMDB-13102 D1-state This work PDB: 7NGP EMDB-12316 D2-state This work PDB: 7NGQ EMDB-12317 P1a-state This work PDB: 7NFY EMDB-12306 P1b-state This work PDB: 7NG4 EMDB-12307 P1c-state This work PDB: 7NG5 EMDB-12308 P2a-state This work PDB: 7NGC EMDB-12312 P2c-state This work PDB: 7NGF EMDB-12313 Recombinant DNA LONP1 wild type GenScript synthesized Mutants of LONP1 (K529R, E591Q, E801A, T803V, E812A, H841F, H843F, S855A, C520S and double mutant C520S/C637S) GenScript Site directed mutagenesis TFAM, Human_TFAM_NoMTS_pET28 a gift from David Chan Addgene Ngo et al., 2014 Cat##34705 Software and algorithms Relion Nakane et al. (2018) https://github.com/3dem/relion cryoSPARC Punjani et al. (2017) https://guide.cryosparc.com (Continued on next page) Structure 30, 1254–1268.e1–e7, September 1, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Coot Emsley and Cowtan (2004) https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ ChimeraX, Chimera Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ download.html Phenix-1.18 Adams et al., 2010 https://phenix-online.org/download/ Focus Biyani et al., 2017 https://lbem-focus.epfl.ch/about.php lafter Ramlaul et al., 2019 https://www.ccpem.ac.uk/download.php CTFFIND4 Rohou and Grigorieff, 2015 https://grigoriefflab.umassmed.edu/ctffind4 Clustal Omega Sievers et al., 2011 https://www.ebi.ac.uk/Tools/msa/clustalo/ SWISS-MODEL Waterhouse et al., 2018 https://swissmodel.expasy.org I-TASSER Yang et al. 2015 https://zhanggroup.org/I-TASSER/ AlphaFold Jumper et al. 2021 https://alphafold.ebi.ac.uk
Mutagenesis:Article Title: Catalytic cycling of human mitochondrial Lon protease.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-6X His tag antibody primary antibody Abcam Ab18184; RRID: AB_444306 anti-rabbit secondary antibody, Alkaline Phosphatase conjugated Sigma-Aldrich A3687; RRID: AB_258103 Bacterial and virus strains E. coli BL21(DE3) cells Merck 69450 E. coli Rosetta DE3 Merck 70954 Chemicals, peptides, and recombinant proteins FITC-casein Sigma-Aldrich SLCD5097 Adenosine-5’-(g-thio)-triphosphate, Tetralithium salt Jena Biosciences Cat# NU-406 Adenosine-5’-[(b,g)-methyleno]triphosphate, Sodium salt Jena Biosciences Cat# NU-422 Adenosine-5’-[(a,b)-imido]diphosphate, Sodium salt Jena Biosciences Cat# NU-448 Adenosine 50-triphosphate, Disodium salt trihydrate Jena Biosciences Cat# NU1010 Adenosine-50-diphosphate, Sodium salt Jena Biosciences Cat# NU-1198 Critical commercial assays ATPase/GTPase activity assay kit Sigma-Aldrich MAK113 Pierce Fluorescent Protease Assay Kit Thermo Scientific Cat# 23266 Deposited data R-state in the presence of ADP and ATP This work PDB: 7NGL EMDB-12315 R-state in the presence of AMPCPP This work PDB: 7OXO EMDB-13102 D1-state This work PDB: 7NGP EMDB-12316 D2-state This work PDB: 7NGQ EMDB-12317 P1a-state This work PDB: 7NFY EMDB-12306 P1b-state This work PDB: 7NG4 EMDB-12307 P1c-state This work PDB: 7NG5 EMDB-12308 P2a-state This work PDB: 7NGC EMDB-12312 P2c-state This work PDB: 7NGF EMDB-12313 Recombinant DNA LONP1 wild type GenScript synthesized Mutants of LONP1 (K529R, E591Q, E801A, T803V, E812A, H841F, H843F, S855A, C520S and double mutant C520S/C637S) GenScript Site directed mutagenesis TFAM, Human_TFAM_NoMTS_pET28 a gift from David Chan Addgene Ngo et al., 2014 Cat##34705 Software and algorithms Relion Nakane et al. (2018) https://github.com/3dem/relion cryoSPARC Punjani et al. (2017) https://guide.cryosparc.com (Continued on next page) Structure 30, 1254–1268.e1–e7, September 1, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Coot Emsley and Cowtan (2004) https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ ChimeraX, Chimera Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ download.html Phenix-1.18 Adams et al., 2010 https://phenix-online.org/download/ Focus Biyani et al., 2017 https://lbem-focus.epfl.ch/about.php lafter Ramlaul et al., 2019 https://www.ccpem.ac.uk/download.php CTFFIND4 Rohou and Grigorieff, 2015 https://grigoriefflab.umassmed.edu/ctffind4 Clustal Omega Sievers et al., 2011 https://www.ebi.ac.uk/Tools/msa/clustalo/ SWISS-MODEL Waterhouse et al., 2018 https://swissmodel.expasy.org I-TASSER Yang et al. 2015 https://zhanggroup.org/I-TASSER/ AlphaFold Jumper et al. 2021 https://alphafold.ebi.ac.uk
Software:Article Title: Catalytic cycling of human mitochondrial Lon protease.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-6X His tag antibody primary antibody Abcam Ab18184; RRID: AB_444306 anti-rabbit secondary antibody, Alkaline Phosphatase conjugated Sigma-Aldrich A3687; RRID: AB_258103 Bacterial and virus strains E. coli BL21(DE3) cells Merck 69450 E. coli Rosetta DE3 Merck 70954 Chemicals, peptides, and recombinant proteins FITC-casein Sigma-Aldrich SLCD5097 Adenosine-5’-(g-thio)-triphosphate, Tetralithium salt Jena Biosciences Cat# NU-406 Adenosine-5’-[(b,g)-methyleno]triphosphate, Sodium salt Jena Biosciences Cat# NU-422 Adenosine-5’-[(a,b)-imido]diphosphate, Sodium salt Jena Biosciences Cat# NU-448 Adenosine 50-triphosphate, Disodium salt trihydrate Jena Biosciences Cat# NU1010 Adenosine-50-diphosphate, Sodium salt Jena Biosciences Cat# NU-1198 Critical commercial assays ATPase/GTPase activity assay kit Sigma-Aldrich MAK113 Pierce Fluorescent Protease Assay Kit Thermo Scientific Cat# 23266 Deposited data R-state in the presence of ADP and ATP This work PDB: 7NGL EMDB-12315 R-state in the presence of AMPCPP This work PDB: 7OXO EMDB-13102 D1-state This work PDB: 7NGP EMDB-12316 D2-state This work PDB: 7NGQ EMDB-12317 P1a-state This work PDB: 7NFY EMDB-12306 P1b-state This work PDB: 7NG4 EMDB-12307 P1c-state This work PDB: 7NG5 EMDB-12308 P2a-state This work PDB: 7NGC EMDB-12312 P2c-state This work PDB: 7NGF EMDB-12313 Recombinant DNA LONP1 wild type GenScript synthesized Mutants of LONP1 (K529R, E591Q, E801A, T803V, E812A, H841F, H843F, S855A, C520S and double mutant C520S/C637S) GenScript Site directed mutagenesis TFAM, Human_TFAM_NoMTS_pET28 a gift from David Chan Addgene Ngo et al., 2014 Cat##34705 Software and algorithms Relion Nakane et al. (2018) https://github.com/3dem/relion cryoSPARC Punjani et al. (2017) https://guide.cryosparc.com (Continued on next page) Structure 30, 1254–1268.e1–e7, September 1, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Coot Emsley and Cowtan (2004) https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot/ ChimeraX, Chimera Goddard et al., 2018 https://www.rbvi.ucsf.edu/chimerax/ download.html Phenix-1.18 Adams et al., 2010 https://phenix-online.org/download/ Focus Biyani et al., 2017 https://lbem-focus.epfl.ch/about.php lafter Ramlaul et al., 2019 https://www.ccpem.ac.uk/download.php CTFFIND4 Rohou and Grigorieff, 2015 https://grigoriefflab.umassmed.edu/ctffind4 Clustal Omega Sievers et al., 2011 https://www.ebi.ac.uk/Tools/msa/clustalo/ SWISS-MODEL Waterhouse et al., 2018 https://swissmodel.expasy.org I-TASSER Yang et al. 2015 https://zhanggroup.org/I-TASSER/ AlphaFold Jumper et al. 2021 https://alphafold.ebi.ac.uk
Incubation:Article Title: Active nematic pumps.
Article Snippet: .. Tubulin (8 mg mL-1) was incubated at 37 ◦C for 30 min in aqueous M2B buffer (80 mM Pipes (piperazine-N,N’-bis(2-ethanesulfonic acid)), 1 mM EGTA (ethylene glycol-bis( -aminoethyl ether)-N,N,N’,N’-tetraacetic acid), 2 mM MgCl2) (Sigma; P1851, E3889, and M4880, respectively) prepared with Milli-Q water and supplemented with the antioxidant agent dithiothrethiol (DTT) (Sigma 43815) and GMPCPP (guanosine-5’-[( , )-methyleno]triphosphate) (Jena Biosciences, NU-405) up to a concentration of 1 mM and 0.6 mM, respectively. ..
Concentration Assay:Article Title: Active nematic pumps.
Article Snippet: .. Tubulin (8 mg mL-1) was incubated at 37 ◦C for 30 min in aqueous M2B buffer (80 mM Pipes (piperazine-N,N’-bis(2-ethanesulfonic acid)), 1 mM EGTA (ethylene glycol-bis( -aminoethyl ether)-N,N,N’,N’-tetraacetic acid), 2 mM MgCl2) (Sigma; P1851, E3889, and M4880, respectively) prepared with Milli-Q water and supplemented with the antioxidant agent dithiothrethiol (DTT) (Sigma 43815) and GMPCPP (guanosine-5’-[( , )-methyleno]triphosphate) (Jena Biosciences, NU-405) up to a concentration of 1 mM and 0.6 mM, respectively. ..
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