Cytochrome c oxidase subunit 1
OrganismNot specified
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 26 PDB declaration: 26-meric（26） Consistent with protein copy count | Chain A； UniProt 1–514 Chain N； UniProt 1–514 | Non-standard monomer：Yes (specific site not provided by mmCIF) | Cytochrome c oxidase subunit 2 × 2 （P68530） Cytochrome c oxidase subunit 3 × 2 （P00415） Cytochrome c oxidase subunit 4 isoform 1 × 2 （P00423） Cytochrome c oxidase polypeptide Va × 2 （P00426） Cytochrome c oxidase polypeptide Vb × 2 （P00428） Cytochrome c oxidase polypeptide VIa-heart × 2 （P07471） Cytochrome c oxidase subunit VIb isoform 1 × 2 （P00429） Cytochrome c oxidase polypeptide VIc × 2 （P04038） Cytochrome c oxidase polypeptide VIIa-heart × 2 （P07470） Cytochrome c oxidase polypeptide VIIb × 2 （P13183） Cytochrome c oxidase polypeptide VIIc × 2 （P00430） Cytochrome c oxidase polypeptide VIII-heart × 2 （P10175） CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 HEA HEME-A × 4 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 CUA DINUCLEAR COPPER ION × 2 TGL TRISTEAROYLGLYCEROL × 6 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 8 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 UNX UNKNOWN LIGAND × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 ZN ZINC ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions | Resolution 1.80 Å R-free 0.227 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 2DYR | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1OCC STRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE Deposited 1996-04-18 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Not recorded | CU COPPER (II) ION × 6 MG MAGNESIUM ION × 2 HEA HEME-A × 4 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；pH 6.8
|
Resolution 2.80 Å R-free 0.252 |
| 1OCO BOVINE HEART CYTOCHROME C OXIDASE IN CARBON MONOXIDE-BOUND STATE Deposited 1998-07-09 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Not recorded | CU COPPER (II) ION × 6 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 HEA HEME-A × 4 CMO CARBON MONOXIDE × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；pH 6.8
|
Resolution 2.80 Å R-free 0.256 |
| 1OCR BOVINE HEART CYTOCHROME C OXIDASE IN THE FULLY REDUCED STATE Deposited 1998-07-07 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Not recorded | CU COPPER (II) ION × 6 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 HEA HEME-A × 4 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；pH 6.8
|
Resolution 2.35 Å R-free 0.247 |
| 1OCZ BOVINE HEART CYTOCHROME C OXIDASE IN AZIDE-BOUND STATE Deposited 1998-07-13 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Not recorded | CU COPPER (II) ION × 6 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 AZI AZIDE ION × 4 HEA HEME-A × 4 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；pH 6.8
|
Resolution 2.90 Å R-free 0.255 |
| 1V54 Bovine heart cytochrome c oxidase at the fully oxidized state Deposited 2003-11-21 | Different ligand/ion | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 HEA HEME-A × 4 TGL TRISTEAROYLGLYCEROL × 6 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 8 CDL CARDIOLIPIN × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 UNX UNKNOWN LIGAND × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 ZN ZINC ION × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.227 |
| 1V55 Bovine heart cytochrome c oxidase at the fully reduced state Deposited 2003-11-21 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 HEA HEME-A × 4 TGL TRISTEAROYLGLYCEROL × 6 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 8 CDL CARDIOLIPIN × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 UNX UNKNOWN LIGAND × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 ZN ZINC ION × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å R-free 0.230 |
| 2DYS Bovine heart cytochrome C oxidase modified by DCCD Deposited 2006-09-16 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 HEA HEME-A × 4 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 CUA DINUCLEAR COPPER ION × 2 TGL TRISTEAROYLGLYCEROL × 6 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 8 DCW DICYCLOHEXYLUREA × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 UNX UNKNOWN LIGAND × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 ZN ZINC ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å R-free 0.242 |
| 2EIJ Bovine heart cytochrome C oxidase in the fully reduced state Deposited 2007-03-13 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 HEA HEME-A × 4 TGL TRISTEAROYLGLYCEROL × 6 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 CUA DINUCLEAR COPPER ION × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 8 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 ZN ZINC ION × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.90 Å R-free 0.234 |
| 2EIK Cadmium ion binding structure of bovine heart cytochrome C oxidase in the fully reduced state Deposited 2007-03-13 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CD CADMIUM ION × 6 HEA HEME-A × 4 TGL TRISTEAROYLGLYCEROL × 6 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 CUA DINUCLEAR COPPER ION × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 8 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 ZN ZINC ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.10 Å R-free 0.228 |
| 2EIL Cadmium ion binding structure of bovine heart cytochrome C oxidase in the fully oxidized state Deposited 2007-03-13 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CD CADMIUM ION × 3 HEA HEME-A × 4 TGL TRISTEAROYLGLYCEROL × 6 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 CUA DINUCLEAR COPPER ION × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 8 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 ZN ZINC ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.10 Å R-free 0.231 |
| 2EIM Zinc ion binding structure of bovine heart cytochrome C oxidase in the fully reduced state Deposited 2007-03-13 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 ZN ZINC ION × 6 HEA HEME-A × 4 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 CHD CHOLIC ACID × 8 CUA DINUCLEAR COPPER ION × 2 TGL TRISTEAROYLGLYCEROL × 6 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.60 Å R-free 0.256 |
| 2EIN Zinc ion binding structure of bovine heart cytochrome C oxidase in the fully oxidized state Deposited 2007-03-13 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 HEA HEME-A × 4 TGL TRISTEAROYLGLYCEROL × 6 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 ZN ZINC ION × 14 CUA DINUCLEAR COPPER ION × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 8 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.70 Å R-free 0.258 |
| 2OCC BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE Deposited 1998-05-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Not recorded | CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 HEA HEME-A × 2 PER PEROXIDE ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；pH 6.8
|
Resolution 2.30 Å R-free 0.244 |
| 2OCC BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE Deposited 1998-05-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Not recorded | CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 HEA HEME-A × 2 PER PEROXIDE ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；pH 6.8
|
Resolution 2.30 Å R-free 0.244 |
| 2OCC BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE Deposited 1998-05-26 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Not recorded | CU COPPER (II) ION × 6 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 HEA HEME-A × 4 PER PEROXIDE ION × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.8；pH 6.8
|
Resolution 2.30 Å R-free 0.244 |
| 2Y69 Bovine heart cytochrome c oxidase re-refined with molecular oxygen Deposited 2011-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Not recorded | HEA HEME-A × 2 CU COPPER (II) ION × 1 OXY OXYGEN MOLECULE × 1 MG MAGNESIUM ION × 1 CHD CHOLIC ACID × 3 CUA DINUCLEAR COPPER ION × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.245 |
| 2Y69 Bovine heart cytochrome c oxidase re-refined with molecular oxygen Deposited 2011-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Not recorded | HEA HEME-A × 2 CU COPPER (II) ION × 1 OXY OXYGEN MOLECULE × 1 MG MAGNESIUM ION × 1 CHD CHOLIC ACID × 3 CUA DINUCLEAR COPPER ION × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.245 |
| 2YBB Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876) Deposited 2011-03-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric |
Chain L
1–514（514 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 MG MAGNESIUM ION × 7 FES FE2/S2 (INORGANIC) CLUSTER × 4 CA CALCIUM ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 5 SMA STIGMATELLIN A × 2 UQ1 UBIQUINONE-1 × 2 HEC HEME C × 2 CDL CARDIOLIPIN × 4 HEA HEME-A × 2 CU COPPER (II) ION × 3 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
10 MM KCL, 15 MM HEPES, RESIDUAL TREHALOSE；pH 7.7；10 MM KCL, 15 MM HEPES, RESIDUAL TREHALOSE
cryo-EM vitrification conditions
Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 70, TEMPERATURE- 95, INSTRUMENT- CUSTOM-MADE HAND PLUNGER, METHOD- ONE- SIDED BLOTTING FOR 26 - 30 SECONDS BEFORE PLUNGING, DETAILS- SAMPLE WAS ADSORBED TO CARBON FILM FOR 30 SECONDS BEFORE BLOTTING
|
Resolution 19.00 Å |
| 2ZXW Bovine heart cytochrome c oxidase at the fully oxidized state (1-s X-ray exposure dataset) Deposited 2009-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 1 PER PEROXIDE ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 HEA HEME-A × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 5 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.50 Å R-free 0.233 |
| 2ZXW Bovine heart cytochrome c oxidase at the fully oxidized state (1-s X-ray exposure dataset) Deposited 2009-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 1 PER PEROXIDE ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 HEA HEME-A × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 3 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.50 Å R-free 0.233 |
| 3ABK Bovine heart cytochrome c oxidase at the NO-bound fully reduced state (50K) Deposited 2009-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 NO NITRIC OXIDE × 1 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 4 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å R-free 0.219 |
| 3ABK Bovine heart cytochrome c oxidase at the NO-bound fully reduced state (50K) Deposited 2009-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 NO NITRIC OXIDE × 1 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 4 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å R-free 0.219 |
| 3ABL Bovine heart cytochrome c oxidase at the fully oxidized state (15-s X-ray exposure dataset) Deposited 2009-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 1 PER PEROXIDE ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 HEA HEME-A × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 4 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.10 Å R-free 0.210 |
| 3ABL Bovine heart cytochrome c oxidase at the fully oxidized state (15-s X-ray exposure dataset) Deposited 2009-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 1 PER PEROXIDE ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 HEA HEME-A × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 4 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.10 Å R-free 0.210 |
| 3ABM Bovine heart cytochrome c oxidase at the fully oxidized state (200-s X-ray exposure dataset) Deposited 2009-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 1 PER PEROXIDE ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 HEA HEME-A × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.214 |
| 3ABM Bovine heart cytochrome c oxidase at the fully oxidized state (200-s X-ray exposure dataset) Deposited 2009-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 1 PER PEROXIDE ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 HEA HEME-A × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.214 |
| 3AG1 Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fully Reduced State at 280 K Deposited 2010-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CMO CARBON MONOXIDE × 1 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 4 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 ZN ZINC ION × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å R-free 0.192 |
| 3AG1 Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fully Reduced State at 280 K Deposited 2010-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CMO CARBON MONOXIDE × 1 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 4 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 ZN ZINC ION × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.20 Å R-free 0.192 |
| 3AG2 Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fully Reduced State at 100 K Deposited 2010-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 CMO CARBON MONOXIDE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 TGL TRISTEAROYLGLYCEROL × 3 EDO 1,2-ETHANEDIOL × 39 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 5 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 6 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；0.2 % decal maltose in 40 mM sodium phosphate buffer, 9.0 % (w/v) protein concentration, PEG 4000 as the precipitant.
|
Resolution 1.80 Å R-free 0.208 |
| 3AG2 Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fully Reduced State at 100 K Deposited 2010-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 CMO CARBON MONOXIDE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 TGL TRISTEAROYLGLYCEROL × 3 EDO 1,2-ETHANEDIOL × 27 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 5 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 5 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；0.2 % decal maltose in 40 mM sodium phosphate buffer, 9.0 % (w/v) protein concentration, PEG 4000 as the precipitant.
|
Resolution 1.80 Å R-free 0.208 |
| 3AG3 Bovine Heart Cytochrome c Oxidase in the Nitric Oxide-bound Fully Reduced State at 100 K Deposited 2010-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 NO NITRIC OXIDE × 1 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 4 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.203 |
| 3AG3 Bovine Heart Cytochrome c Oxidase in the Nitric Oxide-bound Fully Reduced State at 100 K Deposited 2010-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 NO NITRIC OXIDE × 1 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 4 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.203 |
| 3AG4 Bovine Heart Cytochrome c Oxidase in the Cyanide Ion-bound Fully Reduced State at 100 K Deposited 2010-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CYN CYANIDE ION × 1 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.05 Å R-free 0.219 |
| 3AG4 Bovine Heart Cytochrome c Oxidase in the Cyanide Ion-bound Fully Reduced State at 100 K Deposited 2010-03-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CYN CYANIDE ION × 1 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.05 Å R-free 0.219 |
| 3ASN Bovine heart cytochrome C oxidase in the fully oxidized state measured at 1.7470 angstrom wavelength Deposited 2010-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 5 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH；pH 6.8；277 K；40mM sodium phosphate, 0.2% decylmaltoside , pH 6.8, BATCH, temperature 277K
|
Resolution 3.00 Å R-free 0.187 |
| 3ASN Bovine heart cytochrome C oxidase in the fully oxidized state measured at 1.7470 angstrom wavelength Deposited 2010-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 3 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH；pH 6.8；277 K；40mM sodium phosphate, 0.2% decylmaltoside , pH 6.8, BATCH, temperature 277K
|
Resolution 3.00 Å R-free 0.187 |
| 3ASO Bovine heart cytochrome C oxidase in the fully oxidized state measured at 0.9 angstrom wavelength Deposited 2010-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 5 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH；pH 6.8；277 K；40mM sodium phosphate, 0.2% decylmaltoside , pH 6.8, BATCH, temperature 277K
|
Resolution 2.30 Å R-free 0.205 |
| 3ASO Bovine heart cytochrome C oxidase in the fully oxidized state measured at 0.9 angstrom wavelength Deposited 2010-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 3 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH；pH 6.8；277 K；40mM sodium phosphate, 0.2% decylmaltoside , pH 6.8, BATCH, temperature 277K
|
Resolution 2.30 Å R-free 0.205 |
| 3WG7 A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography Deposited 2013-07-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 5 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
Batch；pH 5.7；277 K；40mM sodium phosphate, 0.2% decylmaltoside, pH 5.7, BATCH, temperature 277K, Batch
|
Resolution 1.90 Å R-free 0.230 |
| 3WG7 A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography Deposited 2013-07-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
Batch；pH 5.7；277 K；40mM sodium phosphate, 0.2% decylmaltoside, pH 5.7, BATCH, temperature 277K, Batch
|
Resolution 1.90 Å R-free 0.230 |
| 3X2Q X-ray structure of cyanide-bound bovine heart cytochrome c oxidase in the fully oxidized state at 2.0 angstrom resolution Deposited 2014-12-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CYN CYANIDE ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 3 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 6.8；277 K；40mM Sodium phosphate, 0.2% decylmaltoside, PEG 4000, pH 6.8, batch, temperature 277K
|
Resolution 2.00 Å R-free 0.214 |
| 3X2Q X-ray structure of cyanide-bound bovine heart cytochrome c oxidase in the fully oxidized state at 2.0 angstrom resolution Deposited 2014-12-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CYN CYANIDE ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 3 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
batch；pH 6.8；277 K；40mM Sodium phosphate, 0.2% decylmaltoside, PEG 4000, pH 6.8, batch, temperature 277K
|
Resolution 2.00 Å R-free 0.214 |
| 5B1A Bovine heart cytochrome c oxidase in the fully oxidized state at 1.5 angstrom resolution Deposited 2015-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate
|
Resolution 1.50 Å R-free 0.172 |
| 5B1A Bovine heart cytochrome c oxidase in the fully oxidized state at 1.5 angstrom resolution Deposited 2015-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate
|
Resolution 1.50 Å R-free 0.172 |
| 5B1B Bovine heart cytochrome c oxidase in the fully reduced state at 1.6 angstrom resolution Deposited 2015-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 TGL TRISTEAROYLGLYCEROL × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 EDO 1,2-ETHANEDIOL × 29 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 13 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate, Decylmaltoside
|
Resolution 1.60 Å R-free 0.191 |
| 5B1B Bovine heart cytochrome c oxidase in the fully reduced state at 1.6 angstrom resolution Deposited 2015-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 TGL TRISTEAROYLGLYCEROL × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 EDO 1,2-ETHANEDIOL × 33 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 10 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate, Decylmaltoside
|
Resolution 1.60 Å R-free 0.191 |
| 5B3S Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K) Deposited 2016-03-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CMO CARBON MONOXIDE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 5 EDO 1,2-ETHANEDIOL × 52 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 12 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40mM Sodium phosphate, 0.2% decylmaltoside, 2% EG, PEG 4000
|
Resolution 1.68 Å R-free 0.177 |
| 5B3S Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K) Deposited 2016-03-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CMO CARBON MONOXIDE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 3 EDO 1,2-ETHANEDIOL × 42 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 5 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 4 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 11 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40mM Sodium phosphate, 0.2% decylmaltoside, 2% EG, PEG 4000
|
Resolution 1.68 Å R-free 0.177 |
| 5GPN Architecture of mammalian respirasome Deposited 2016-08-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 84 PDB declaration: 84-meric |
Chain y
1–514（514 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 2 FES FE2/S2 (INORGANIC) CLUSTER × 4 SF4 IRON/SULFUR CLUSTER × 6 FMN FLAVIN MONONUCLEOTIDE × 1 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 ZN ZINC ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 5.40 Å |
| 5IY5 Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom resolution Deposited 2016-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 HEA HEME-A × 2 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 EDO 1,2-ETHANEDIOL × 6 CHD CHOLIC ACID × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 CDL CARDIOLIPIN × 2 UNL UNKNOWN LIGAND × 5 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 HEC HEME C × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 8；277 K；15mM sodium phosphate, pH 8.0, 0.7% fluorinated octylmaltoside, 0.2% decylmaltoside, 3% ethylene glycol, 5% PEG 4000
|
Resolution 2.00 Å R-free 0.207 |
| 5IY5 Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom resolution Deposited 2016-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 HEA HEME-A × 2 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 3 TGL TRISTEAROYLGLYCEROL × 2 CUA DINUCLEAR COPPER ION × 1 EDO 1,2-ETHANEDIOL × 3 CHD CHOLIC ACID × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 CDL CARDIOLIPIN × 2 UNL UNKNOWN LIGAND × 10 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 HEC HEME C × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 8；277 K；15mM sodium phosphate, pH 8.0, 0.7% fluorinated octylmaltoside, 0.2% decylmaltoside, 3% ethylene glycol, 5% PEG 4000
|
Resolution 2.00 Å R-free 0.207 |
| 5LUF Cryo-EM of bovine respirasome Deposited 2016-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 62 PDB declaration: 62-meric |
Chain x
1–514（514 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 2 FES FE2/S2 (INORGANIC) CLUSTER × 3 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 HEA HEME-A × 2 ZN ZINC ION × 1 SF4 IRON/SULFUR CLUSTER × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.7
cryo-EM vitrification conditions
Cryogen ETHANE；10 s blotting
|
Resolution 9.10 Å |
| 5W97 Crystal Structure of CO-bound Cytochrome c Oxidase determined by Serial Femtosecond X-Ray Crystallography at Room Temperature Deposited 2017-06-22 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain a
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 TGL TRISTEAROYLGLYCEROL × 6 CMO CARBON MONOXIDE × 2 CUA DINUCLEAR COPPER ION × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 8 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Potassium Phosphate, decylmaltoside
|
Resolution 2.30 Å R-free 0.252 |
| 5WAU Crystal Structure of CO-bound Cytochrome c Oxidase determined by Synchrotron X-Ray Crystallography at 100 K Deposited 2017-06-27 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain a
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 TGL TRISTEAROYLGLYCEROL × 6 CMO CARBON MONOXIDE × 2 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 8 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；.2 % decylmaltoside and 2.5 % PEG4000
|
Resolution 1.95 Å R-free 0.244 |
| 5X19 CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center Deposited 2017-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CMO CARBON MONOXIDE × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 17 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 5 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate, 0.2% decyl maltoside, 2% ethylene glycol, PEG 4000
|
Resolution 2.20 Å R-free 0.210 |
| 5X19 CO bound cytochrome c oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center Deposited 2017-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CMO CARBON MONOXIDE × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 6 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate, 0.2% decyl maltoside, 2% ethylene glycol, PEG 4000
|
Resolution 2.20 Å R-free 0.210 |
| 5X1B CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center Deposited 2017-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CMO CARBON MONOXIDE × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 5 EDO 1,2-ETHANEDIOL × 16 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate, 0.2% decyl maltoside, 2% ethylene glycol, PEG 4000
|
Resolution 2.40 Å R-free 0.230 |
| 5X1B CO bound cytochrome c oxidase at 20 nsec after pump laser irradiation to release CO from O2 reduction center Deposited 2017-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CMO CARBON MONOXIDE × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 3 EDO 1,2-ETHANEDIOL × 2 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate, 0.2% decyl maltoside, 2% ethylene glycol, PEG 4000
|
Resolution 2.40 Å R-free 0.230 |
| 5X1F CO bound cytochrome c oxidase without pump laser irradiation at 278K Deposited 2017-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CMO CARBON MONOXIDE × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 17 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 5 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 5 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate, 0.2 % decyl maltoside, 2% ethylene glycol, PEG 4000
|
Resolution 2.20 Å R-free 0.209 |
| 5X1F CO bound cytochrome c oxidase without pump laser irradiation at 278K Deposited 2017-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CMO CARBON MONOXIDE × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 8 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate, 0.2 % decyl maltoside, 2% ethylene glycol, PEG 4000
|
Resolution 2.20 Å R-free 0.209 |
| 5XDQ Bovine heart cytochrome c oxidase in the fully oxidized state with pH 7.3 at 1.77 angstrom resolution Deposited 2017-03-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 PER PEROXIDE ION × 1 EDO 1,2-ETHANEDIOL × 31 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 5 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 3 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.3；277 K；3% polythylene glycol (PEG), 0.35% decal maltose, 0.70% fluorinated octyl-maltoside, 33mM sodium acetate, 25mM Tris-HCL (pH 7.3)
|
Resolution 1.77 Å R-free 0.190 |
| 5XDQ Bovine heart cytochrome c oxidase in the fully oxidized state with pH 7.3 at 1.77 angstrom resolution Deposited 2017-03-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 PER PEROXIDE ION × 1 EDO 1,2-ETHANEDIOL × 25 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 3 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 3 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.3；277 K；3% polythylene glycol (PEG), 0.35% decal maltose, 0.70% fluorinated octyl-maltoside, 33mM sodium acetate, 25mM Tris-HCL (pH 7.3)
|
Resolution 1.77 Å R-free 0.190 |
| 5XDX Bovine heart cytochrome c oxidase in the reduced state with pH 7.3 at 1.99 angstrom resolution Deposited 2017-03-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 19 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.3；277 K；3% PEG 1500, 0.20% decal maltoside, 0.35% fluorinated octyl-maltoside, 25mM Tris-HCL(pH 7.3), 20mM sodium acetate
|
Resolution 1.99 Å R-free 0.203 |
| 5XDX Bovine heart cytochrome c oxidase in the reduced state with pH 7.3 at 1.99 angstrom resolution Deposited 2017-03-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 14 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.3；277 K；3% PEG 1500, 0.20% decal maltoside, 0.35% fluorinated octyl-maltoside, 25mM Tris-HCL(pH 7.3), 20mM sodium acetate
|
Resolution 1.99 Å R-free 0.203 |
| 5XTH Cryo-EM structure of human respiratory supercomplex I1III2IV1 Deposited 2017-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 80 PDB declaration: 80-meric |
Chain x
1–514（514 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 6 FMN FLAVIN MONONUCLEOTIDE × 1 PLX (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL × 12 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 4 CDL CARDIOLIPIN × 14 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 10 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 HEA HEME-A × 2 ZN ZINC ION × 1 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 5XTI Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2 Deposited 2017-06-19 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 138 PDB declaration: 138-meric |
Chain Bx
1–514（514 aa）
Chain x
1–514（514 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 12 FMN FLAVIN MONONUCLEOTIDE × 2 PLX (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL × 21 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 4 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 FES FE2/S2 (INORGANIC) CLUSTER × 6 CDL CARDIOLIPIN × 19 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 14 CU COPPER (II) ION × 6 MG MAGNESIUM ION × 2 HEA HEME-A × 4 ZN ZINC ION × 2 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 17.40 Å |
| 5Z84 The structure of azide-bound cytochrome c oxidase determined using the crystals exposed to 20 mM azide solution for 4 days Deposited 2018-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 AZI AZIDE ION × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 5 EDO 1,2-ETHANEDIOL × 45 CHD CHOLIC ACID × 5 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 5 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate
|
Resolution 1.85 Å R-free 0.189 |
| 5Z84 The structure of azide-bound cytochrome c oxidase determined using the crystals exposed to 20 mM azide solution for 4 days Deposited 2018-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 AZI AZIDE ION × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 3 EDO 1,2-ETHANEDIOL × 32 CHD CHOLIC ACID × 3 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 3 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate
|
Resolution 1.85 Å R-free 0.189 |
| 5Z85 The structure of azide-bound cytochrome c oxidase determined using the another batch crystals exposed to 20 mM azide solution for 2 days Deposited 2018-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 AZI AZIDE ION × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 37 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 3 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG4000, Sodium phosphate
|
Resolution 1.85 Å R-free 0.189 |
| 5Z85 The structure of azide-bound cytochrome c oxidase determined using the another batch crystals exposed to 20 mM azide solution for 2 days Deposited 2018-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 AZI AZIDE ION × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 32 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 3 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG4000, Sodium phosphate
|
Resolution 1.85 Å R-free 0.189 |
| 5Z86 azide-bound cytochrome c oxidase structure determined using the crystals exposed to 20 mM azide solution for 3 days Deposited 2018-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 AZI AZIDE ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 39 TGL TRISTEAROYLGLYCEROL × 3 CHD CHOLIC ACID × 5 CUA DINUCLEAR COPPER ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate
|
Resolution 1.85 Å R-free 0.196 |
| 5Z86 azide-bound cytochrome c oxidase structure determined using the crystals exposed to 20 mM azide solution for 3 days Deposited 2018-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 AZI AZIDE ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 32 TGL TRISTEAROYLGLYCEROL × 3 CHD CHOLIC ACID × 3 CUA DINUCLEAR COPPER ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate
|
Resolution 1.85 Å R-free 0.196 |
| 5ZCO azide-bound cytochrome c oxidase structure determined using the crystals exposed to 2 mM azide solution for 2 days Deposited 2018-02-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 AZI AZIDE ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 26 TGL TRISTEAROYLGLYCEROL × 3 CHD CHOLIC ACID × 5 CUA DINUCLEAR COPPER ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 4 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate
|
Resolution 1.90 Å R-free 0.189 |
| 5ZCO azide-bound cytochrome c oxidase structure determined using the crystals exposed to 2 mM azide solution for 2 days Deposited 2018-02-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 AZI AZIDE ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 19 TGL TRISTEAROYLGLYCEROL × 3 CHD CHOLIC ACID × 3 CUA DINUCLEAR COPPER ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 3 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate
|
Resolution 1.90 Å R-free 0.189 |
| 5ZCP azide-bound cytochrome c oxidase structure determined using the crystals exposed to 20 mM azide solution for 2 days Deposited 2018-02-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 AZI AZIDE ION × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 26 CHD CHOLIC ACID × 5 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate
|
Resolution 1.65 Å R-free 0.197 |
| 5ZCP azide-bound cytochrome c oxidase structure determined using the crystals exposed to 20 mM azide solution for 2 days Deposited 2018-02-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 AZI AZIDE ION × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 19 CHD CHOLIC ACID × 3 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 3 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate
|
Resolution 1.65 Å R-free 0.197 |
| 5ZCQ Azide-bound cytochrome c oxidase structure determined using the crystals exposed to 10 mM azide solution for 2 days Deposited 2018-02-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 AZI AZIDE ION × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 32 CHD CHOLIC ACID × 5 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 5 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate
|
Resolution 1.65 Å R-free 0.182 |
| 5ZCQ Azide-bound cytochrome c oxidase structure determined using the crystals exposed to 10 mM azide solution for 2 days Deposited 2018-02-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 AZI AZIDE ION × 2 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 19 CHD CHOLIC ACID × 3 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 UNX UNKNOWN LIGAND × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate
|
Resolution 1.65 Å R-free 0.182 |
| 6J8M Low-dose structure of bovine heart cytochrome c oxidase in the fully oxidized state determined using 30 keV X-ray Deposited 2019-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 PER PEROXIDE ION × 1 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 5.8；277 K；PEG 4000
|
Resolution 1.90 Å R-free 0.199 |
| 6J8M Low-dose structure of bovine heart cytochrome c oxidase in the fully oxidized state determined using 30 keV X-ray Deposited 2019-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 PER PEROXIDE ION × 1 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 5.8；277 K；PEG 4000
|
Resolution 1.90 Å R-free 0.199 |
| 6JUW BOVINE HEART CYTOCHROME C OXIDASE IN CATALITIC INTERMEDIATES AT 1.80 ANGSTROM RESOLUTION Deposited 2019-04-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 4 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 25 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 TGL TRISTEAROYLGLYCEROL × 6 EDO 1,2-ETHANEDIOL × 80 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 9 CDL CARDIOLIPIN × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 ZN ZINC ION × 2 PO4 PHOSPHATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate buffer
|
Resolution 1.80 Å R-free 0.188 |
| 6JY3 Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State Deposited 2019-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 CDL CARDIOLIPIN × 3 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 CQX (2S,3S,4S,5S,6R)-2-(2-decoxyethoxy)-6-(hydroxymethyl)oxane-3,4,5-triol × 8 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；277 K；sodium phosphate, PEG 4000, DM
|
Resolution 1.85 Å R-free 0.192 |
| 6JY4 Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Reduced State Deposited 2019-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 CQX (2S,3S,4S,5S,6R)-2-(2-decoxyethoxy)-6-(hydroxymethyl)oxane-3,4,5-triol × 7 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 CDL CARDIOLIPIN × 3 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 1 ZN ZINC ION × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；277 K；sodium phosphate, PEG 4000, DM
|
Resolution 1.95 Å R-free 0.205 |
| 6NKN Time-resolved SFX structure of the PR intermediate of cytochrome c oxidase at room temperature Deposited 2019-01-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 HEA HEME-A × 4 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 TGL TRISTEAROYLGLYCEROL × 6 O OXYGEN ATOM × 2 OH HYDROXIDE ION × 2 CUA DINUCLEAR COPPER ION × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 8 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 ZN ZINC ION × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；36 hour crystallization in a cold room with stirring
|
Resolution 2.50 Å R-free 0.217 |
| 6NMF SFX structure of reduced cytochrome c oxidase at room temperature Deposited 2019-01-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 TGL TRISTEAROYLGLYCEROL × 6 CDL CARDIOLIPIN × 4 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 8 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；36 hour crystallization in a cold room with stirring
|
Resolution 2.80 Å R-free 0.232 |
| 6NMP SFX structure of oxidized cytochrome c oxidase at room temperature Deposited 2019-01-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 HEA HEME-A × 4 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 TGL TRISTEAROYLGLYCEROL × 6 PER PEROXIDE ION × 2 CUA DINUCLEAR COPPER ION × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 8 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；36 hour crystallization in a cold room with stirring
|
Resolution 2.90 Å R-free 0.244 |
| 7COH Dimeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State Deposited 2020-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CDL CARDIOLIPIN × 3 CHD CHOLIC ACID × 3 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 21 PER PEROXIDE ION × 1 LFA EICOSANE × 13 EDO 1,2-ETHANEDIOL × 14 CUA DINUCLEAR COPPER ION × 1 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate pH 6.8, 0.2% decylmaltoside, 1% polyethylene glycol 4000, 2% ethylene glycol
|
Resolution 1.30 Å R-free 0.170 |
| 7COH Dimeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State Deposited 2020-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CDL CARDIOLIPIN × 3 CHD CHOLIC ACID × 3 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 21 PER PEROXIDE ION × 1 LFA EICOSANE × 13 EDO 1,2-ETHANEDIOL × 15 CUA DINUCLEAR COPPER ION × 1 UNX UNKNOWN LIGAND × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate pH 6.8, 0.2% decylmaltoside, 1% polyethylene glycol 4000, 2% ethylene glycol
|
Resolution 1.30 Å R-free 0.170 |
| 7CP5 Bovine heart cytochrome c oxidase in a catalytic intermediate of E at 1.76 angstrom resolution Deposited 2020-08-06 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 4 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 PER PEROXIDE ION × 2 EDO 1,2-ETHANEDIOL × 71 TGL TRISTEAROYLGLYCEROL × 6 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 6 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 23 CDL CARDIOLIPIN × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 ZN ZINC ION × 2 PO4 PHOSPHATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.7；277 K；PEG 4000, SODIUM PHOSPHATE BUFFER
|
Resolution 1.76 Å R-free 0.189 |
| 7D5W Bovine heart cytochrome c oxidase in a catalytic intermediate of O at 1.84 angstrom resolution Deposited 2020-09-28 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 4 TGL TRISTEAROYLGLYCEROL × 6 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 PER PEROXIDE ION × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 EDO 1,2-ETHANEDIOL × 80 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 23 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 8 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 ZN ZINC ION × 2 PO4 PHOSPHATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.7；277 K；PEG 4000, SODIUM PHOSPHATE BUFFER
|
Resolution 1.84 Å R-free 0.184 |
| 7D5X Bovine heart cytochrome c oxidase in a catalytic intermediate, IO10, at 1.74 angstrom resolution Deposited 2020-09-28 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 4 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 OXY OXYGEN MOLECULE × 2 EDO 1,2-ETHANEDIOL × 81 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 23 TGL TRISTEAROYLGLYCEROL × 6 CUA DINUCLEAR COPPER ION × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 7 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 ZN ZINC ION × 2 PO4 PHOSPHATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.7；277 K；PEG 4000, Sodium Phosphate Buffer
|
Resolution 1.74 Å R-free 0.184 |
| 7DGQ Activity optimized supercomplex state1 Deposited 2020-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 80 PDB declaration: 80-meric |
Chain C3
1–514（514 aa）
|
Not recorded | PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 FES FE2/S2 (INORGANIC) CLUSTER × 3 CDL CARDIOLIPIN × 3 FMN FLAVIN MONONUCLEOTIDE × 1 SF4 IRON/SULFUR CLUSTER × 6 CU COPPER (II) ION × 3 HEA HEME-A × 2 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 2 UQ2 UBIQUINONE-2 × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.00 Å |
| 7DGR Activity optimized supercomplex state2 Deposited 2020-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 80 PDB declaration: 80-meric |
Chain A9
1–514（514 aa）
|
Not recorded | FES FE2/S2 (INORGANIC) CLUSTER × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 4 CDL CARDIOLIPIN × 3 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 FMN FLAVIN MONONUCLEOTIDE × 1 SF4 IRON/SULFUR CLUSTER × 6 ZN ZINC ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 2 HEA HEME-A × 2 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 7DGS Activity optimized supercomplex state3 Deposited 2020-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 80 PDB declaration: 80-meric |
Chain A9
1–514（514 aa）
|
Not recorded | FES FE2/S2 (INORGANIC) CLUSTER × 3 CDL CARDIOLIPIN × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 5 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 FMN FLAVIN MONONUCLEOTIDE × 1 SF4 IRON/SULFUR CLUSTER × 6 ZN ZINC ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 2 HEA HEME-A × 2 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.80 Å |
| 7DKF Activity optimized supercomplex state4 Deposited 2020-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 80 PDB declaration: 80-meric |
Chain A3
1–514（514 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 4 HEC HEME C × 2 FES FE2/S2 (INORGANIC) CLUSTER × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 3 CDL CARDIOLIPIN × 1 FMN FLAVIN MONONUCLEOTIDE × 1 SF4 IRON/SULFUR CLUSTER × 6 ZN ZINC ION × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 HEA HEME-A × 2 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.30 Å |
| 7EV7 Bovine heart cytochrome c oxidase in the carbon monoxide-bound fully reduced state at a 50 K Deposited 2021-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 CMO CARBON MONOXIDE × 1 EDO 1,2-ETHANEDIOL × 71 TGL TRISTEAROYLGLYCEROL × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 6 CUA DINUCLEAR COPPER ION × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 5 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate buffer
|
Resolution 1.70 Å R-free 0.178 |
| 7EV7 Bovine heart cytochrome c oxidase in the carbon monoxide-bound fully reduced state at a 50 K Deposited 2021-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 CMO CARBON MONOXIDE × 1 EDO 1,2-ETHANEDIOL × 64 TGL TRISTEAROYLGLYCEROL × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 5 CUA DINUCLEAR COPPER ION × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 6 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate buffer
|
Resolution 1.70 Å R-free 0.178 |
| 7THU Structure of reduced bovine cytochrome c oxidase at 1.93 Angstrom resolution obtained by synchrotron X-rays Deposited 2022-01-12 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 HEA HEME-A × 4 EDO 1,2-ETHANEDIOL × 91 TGL TRISTEAROYLGLYCEROL × 6 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 10 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 6 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 ZN ZINC ION × 2 SAC N-ACETYL-SERINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Postassium phosphate, Decylmaltoside
|
Resolution 1.93 Å R-free 0.212 |
| 7TIE Structure of oxidized bovine cytochrome c oxidase at 1.90 Angstrom resolution obtained by synchrotron X-rays Deposited 2022-01-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 HEA HEME-A × 4 EDO 1,2-ETHANEDIOL × 91 TGL TRISTEAROYLGLYCEROL × 6 OH HYDROXIDE ION × 2 CUA DINUCLEAR COPPER ION × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 10 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 6 ZN ZINC ION × 2 SAC N-ACETYL-SERINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Potassium phosphate, Decylmaltoside
|
Resolution 1.90 Å R-free 0.215 |
| 7TIH Structure of oxidized bovine cytochrome c oxidase with reduced metal centers induced by synchrotron X-ray exposure Deposited 2022-01-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 HEA HEME-A × 4 EDO 1,2-ETHANEDIOL × 84 OH HYDROXIDE ION × 2 CUA DINUCLEAR COPPER ION × 2 TGL TRISTEAROYLGLYCEROL × 6 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 10 CDL CARDIOLIPIN × 4 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 6 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 ZN ZINC ION × 2 SAC N-ACETYL-SERINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Potassium phosphate, Decylmaltoside
|
Resolution 2.35 Å R-free 0.235 |
| 7TII Annealed structure of oxidized bovine cytochrome c oxidase with reduced metal centers induced by synchrotron X-ray exposure Deposited 2022-01-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 EDO 1,2-ETHANEDIOL × 8 OH HYDROXIDE ION × 2 TGL TRISTEAROYLGLYCEROL × 6 CUA DINUCLEAR COPPER ION × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 CHD CHOLIC ACID × 8 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 ZN ZINC ION × 2 SAC N-ACETYL-SERINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Potassium Phosphate, Decylmaltoside
|
Resolution 2.45 Å R-free 0.253 |
| 7VUW Bovine heart cytochrome c oxidase in the cyanide-bound fully oxidized state at 50 K Deposited 2021-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CYN CYANIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 142 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, SODIUM PHOSPHATE BUFFER
|
Resolution 1.60 Å R-free 0.175 |
| 7VUW Bovine heart cytochrome c oxidase in the cyanide-bound fully oxidized state at 50 K Deposited 2021-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CYN CYANIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 107 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 3 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 10 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, SODIUM PHOSPHATE BUFFER
|
Resolution 1.60 Å R-free 0.175 |
| 7VVR Bovine cytochrome c oxidese in CN-bound mixed valence state at 50 K Deposited 2021-11-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CYN CYANIDE ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 48 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 5 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 8 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG4000, Sodium phosphate buffer
|
Resolution 1.65 Å R-free 0.176 |
| 7VVR Bovine cytochrome c oxidese in CN-bound mixed valence state at 50 K Deposited 2021-11-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 CYN CYANIDE ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 42 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CHD CHOLIC ACID × 5 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 4 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 5 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG4000, Sodium phosphate buffer
|
Resolution 1.65 Å R-free 0.176 |
| 7W3E Bovine cytochrome c oxidese in CN-bound fully reduced state at 50 K Deposited 2021-11-25 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 4 CYN CYANIDE ION × 2 TGL TRISTEAROYLGLYCEROL × 5 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 7 EDO 1,2-ETHANEDIOL × 46 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 8 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 13 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate buffer
|
Resolution 1.45 Å R-free 0.182 |
| 7W3E Bovine cytochrome c oxidese in CN-bound fully reduced state at 50 K Deposited 2021-11-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 CYN CYANIDE ION × 1 TGL TRISTEAROYLGLYCEROL × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 27 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 3 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 4 CDL CARDIOLIPIN × 3 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 9 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, Sodium phosphate buffer
|
Resolution 1.45 Å R-free 0.182 |
| 7XMA Crystal structure of Bovine heart cytochrome c oxidase, apo structure with DMSO Deposited 2022-04-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 CDL CARDIOLIPIN × 2 CHD CHOLIC ACID × 3 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；sodium phosphate, PEG4000, decyl maltoside, ethylene glycol, DMSO
|
Resolution 2.20 Å R-free 0.213 |
| 7XMA Crystal structure of Bovine heart cytochrome c oxidase, apo structure with DMSO Deposited 2022-04-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 CDL CARDIOLIPIN × 2 CHD CHOLIC ACID × 3 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；sodium phosphate, PEG4000, decyl maltoside, ethylene glycol, DMSO
|
Resolution 2.20 Å R-free 0.213 |
| 7XMB Crystal structure of Bovine heart cytochrome c oxidase, the structure complexed with an allosteric inhibitor T113 Deposited 2022-04-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PER PEROXIDE ION × 1 TGL TRISTEAROYLGLYCEROL × 3 J6X 2-(4-methyl-1,3-thiazol-2-yl)-1-benzothiophen-3-ol × 1 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 4 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；sodium phosphate, PEG4000, decyl maltoside, ethylene glycol, DMSO, T113
|
Resolution 2.20 Å R-free 0.204 |
| 7XMB Crystal structure of Bovine heart cytochrome c oxidase, the structure complexed with an allosteric inhibitor T113 Deposited 2022-04-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PER PEROXIDE ION × 1 TGL TRISTEAROYLGLYCEROL × 3 J6X 2-(4-methyl-1,3-thiazol-2-yl)-1-benzothiophen-3-ol × 1 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 3 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；sodium phosphate, PEG4000, decyl maltoside, ethylene glycol, DMSO, T113
|
Resolution 2.20 Å R-free 0.204 |
| 7Y44 Re-refinement of damage free X-ray structure of bovine cytochrome c oxidase at 1.9 angstrom resolution Deposited 2022-06-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 19 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 13 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 4 CDL CARDIOLIPIN × 2 CHD CHOLIC ACID × 5 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 5.7；277 K；40mM sodium phosphate buffer, 0.2% decylmaltoside, 1% PEG 4000, 2% ethylene glycol
|
Resolution 1.90 Å R-free 0.227 |
| 7Y44 Re-refinement of damage free X-ray structure of bovine cytochrome c oxidase at 1.9 angstrom resolution Deposited 2022-06-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 30 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 10 TGL TRISTEAROYLGLYCEROL × 3 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 CDL CARDIOLIPIN × 2 CHD CHOLIC ACID × 6 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 5.7；277 K；40mM sodium phosphate buffer, 0.2% decylmaltoside, 1% PEG 4000, 2% ethylene glycol
|
Resolution 1.90 Å R-free 0.227 |
| 7YPY Bovine heart cytochrome c oxidase in fully oxidized state at 1.5 angstrom resolution Deposited 2022-08-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 5 TGL TRISTEAROYLGLYCEROL × 3 EDO 1,2-ETHANEDIOL × 56 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 15 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；Sodium phosphate buffer, PEG 4000
|
Resolution 1.50 Å R-free 0.177 |
| 7YPY Bovine heart cytochrome c oxidase in fully oxidized state at 1.5 angstrom resolution Deposited 2022-08-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 3 TGL TRISTEAROYLGLYCEROL × 3 EDO 1,2-ETHANEDIOL × 45 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 11 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 5 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 CDL CARDIOLIPIN × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；Sodium phosphate buffer, PEG 4000
|
Resolution 1.50 Å R-free 0.177 |
| 8D4T Mammalian CIV with GDN bound Deposited 2022-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–513（513 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 HEA HEME-A × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.10 Å |
| 8GBT Time-resolve SFX structure of a photoproduct of carbon monoxide complex of bovine cytochrome c oxidase Deposited 2023-02-28 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 TGL TRISTEAROYLGLYCEROL × 6 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 CMO CARBON MONOXIDE × 2 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 8 OH HYDROXIDE ION × 2 CDL CARDIOLIPIN × 4 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 ZN ZINC ION × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 SAC N-ACETYL-SERINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG4000, Sodium Phosphate, decylmaltoside
|
Resolution 2.80 Å R-free 0.269 |
| 8GCQ SFX structure of oxidized cytochrome c oxidase at 2.38 Angstrom resolution Deposited 2023-03-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 8 HEA HEME-A × 4 OH HYDROXIDE ION × 2 CUA DINUCLEAR COPPER ION × 2 TGL TRISTEAROYLGLYCEROL × 6 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 2 CHD CHOLIC ACID × 10 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 6 CDL CARDIOLIPIN × 4 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 6 ZN ZINC ION × 2 SAC N-ACETYL-SERINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG4000, Sodium Phosphate, decylmaltoside
|
Resolution 2.38 Å R-free 0.266 |
| 8GVM The structure of azide-bound cytochrome C oxidase determined using the crystals exposed to 20 mm azide solution for 4 days Deposited 2022-09-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 AZI AZIDE ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 5 EDO 1,2-ETHANEDIOL × 39 TGL TRISTEAROYLGLYCEROL × 3 CHD CHOLIC ACID × 5 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 5 CDL CARDIOLIPIN × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, SODIUM PHOSPHATE BUFFER PH 6.8
|
Resolution 1.85 Å R-free 0.188 |
| 8GVM The structure of azide-bound cytochrome C oxidase determined using the crystals exposed to 20 mm azide solution for 4 days Deposited 2022-09-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 AZI AZIDE ION × 2 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 3 EDO 1,2-ETHANEDIOL × 28 TGL TRISTEAROYLGLYCEROL × 3 CHD CHOLIC ACID × 3 CUA DINUCLEAR COPPER ION × 1 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 CDL CARDIOLIPIN × 3 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG 4000, SODIUM PHOSPHATE BUFFER PH 6.8
|
Resolution 1.85 Å R-free 0.188 |
| 8H8R Bovine Heart Cytochrome c Oxidase in the Calcium-bound Fully Oxidized State Deposited 2022-10-24 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 PER PEROXIDE ION × 2 LFA EICOSANE × 26 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 42 EDO 1,2-ETHANEDIOL × 29 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 6 UNX UNKNOWN LIGAND × 2 CDL CARDIOLIPIN × 6 ZN ZINC ION × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate buffer, pH 6.8
0.2% (w/v) decyl-maltoside
1% (w/v) polyethylene glycol 4000
|
Resolution 1.70 Å R-free 0.153 |
| 8H8S Bovine Heart Cytochrome c Oxidase in the Calcium-bound Fully Reduced State Deposited 2022-10-24 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 CA CALCIUM ION × 2 CDL CARDIOLIPIN × 6 LFA EICOSANE × 26 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 42 EDO 1,2-ETHANEDIOL × 29 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 6 UNX UNKNOWN LIGAND × 2 ZN ZINC ION × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate buffer, pH 6.8
0.2% (w/v) decyl-maltoside
1% (w/v) polyethylene glycol 4000
|
Resolution 1.70 Å R-free 0.156 |
| 8IJN Bovine Heart Cytochrome c Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K Deposited 2023-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 NO NITRIC OXIDE × 1 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 7 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 2 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG4000, Sodium phosphate buffer
|
Resolution 1.80 Å R-free 0.192 |
| 8IJN Bovine Heart Cytochrome c Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K Deposited 2023-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 NO NITRIC OXIDE × 1 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 TGL TRISTEAROYLGLYCEROL × 3 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 EDO 1,2-ETHANEDIOL × 15 CUA DINUCLEAR COPPER ION × 1 CHD CHOLIC ACID × 4 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 3 CDL CARDIOLIPIN × 2 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 4 PSC (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；PEG4000, Sodium phosphate buffer
|
Resolution 1.80 Å R-free 0.192 |
| 9IKF Bovine Heart Cytochrome c Oxidase in the Carbon Dioxide-bound Fully Oxidized State Deposited 2024-06-27 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PER PEROXIDE ION × 2 CDL CARDIOLIPIN × 6 CO2 CARBON DIOXIDE × 2 LFA EICOSANE × 26 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 42 EDO 1,2-ETHANEDIOL × 29 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 6 UNX UNKNOWN LIGAND × 2 ZN ZINC ION × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000
|
Resolution 1.75 Å R-free 0.167 |
| 9IKG Bovine Heart Cytochrome c Oxidase in the Carbon Dioxide-bound Fully Reduced State Deposited 2024-06-27 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CO2 CARBON DIOXIDE × 2 LFA EICOSANE × 26 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 42 EDO 1,2-ETHANEDIOL × 29 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 6 UNX UNKNOWN LIGAND × 2 CDL CARDIOLIPIN × 6 ZN ZINC ION × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000
|
Resolution 1.85 Å R-free 0.170 |
| 9IKH Bovine Heart Cytochrome c Oxidase in the Nitrous Oxide-bound Fully Oxidized State Deposited 2024-06-27 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PER PEROXIDE ION × 2 N2O NITROUS OXIDE × 2 LFA EICOSANE × 26 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 42 EDO 1,2-ETHANEDIOL × 29 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 6 UNX UNKNOWN LIGAND × 2 CDL CARDIOLIPIN × 6 ZN ZINC ION × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000
|
Resolution 1.75 Å R-free 0.174 |
| 9IKI Bovine Heart Cytochrome c Oxidase in the Nitrous Oxide-bound Fully Reduced State Deposited 2024-06-27 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 N2O NITROUS OXIDE × 2 LFA EICOSANE × 26 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 42 EDO 1,2-ETHANEDIOL × 29 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 6 UNX UNKNOWN LIGAND × 2 CDL CARDIOLIPIN × 6 ZN ZINC ION × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000
|
Resolution 1.75 Å R-free 0.189 |
| 9KUK Bovine Heart Cytochrome c Oxidase in the Xenon-bound Fully Oxidized State under Aerobic Condition Deposited 2024-12-04 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PER PEROXIDE ION × 2 CDL CARDIOLIPIN × 6 LFA EICOSANE × 26 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 42 EDO 1,2-ETHANEDIOL × 29 XE XENON × 14 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 6 UNX UNKNOWN LIGAND × 2 ZN ZINC ION × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000
|
Resolution 1.80 Å R-free 0.156 |
| 9KUL Bovine Heart Cytochrome c Oxidase in the Xenon-bound Fully Oxidized State under Anaerobic Condition Deposited 2024-12-04 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PER PEROXIDE ION × 2 CDL CARDIOLIPIN × 6 LFA EICOSANE × 26 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 42 EDO 1,2-ETHANEDIOL × 29 XE XENON × 14 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 6 UNX UNKNOWN LIGAND × 2 ZN ZINC ION × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000
|
Resolution 1.80 Å R-free 0.155 |
| 9KUM Bovine Heart Cytochrome c Oxidase in the Xenon-bound Fully Reduced State Deposited 2024-12-04 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CDL CARDIOLIPIN × 6 LFA EICOSANE × 26 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 42 EDO 1,2-ETHANEDIOL × 29 XE XENON × 16 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 6 UNX UNKNOWN LIGAND × 2 ZN ZINC ION × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；277 K；40 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000
|
Resolution 1.80 Å R-free 0.169 |
| 9M56 Bovine Heart Cytochrome c Oxidase in the Fully Reduced State Deposited 2025-03-05 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric |
Chain A
1–514（514 aa）
Chain N
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 4 CU COPPER (II) ION × 2 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CDL CARDIOLIPIN × 6 LFA EICOSANE × 26 DMU DECYL-BETA-D-MALTOPYRANOSIDE × 42 EDO 1,2-ETHANEDIOL × 29 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 4 CUA DINUCLEAR COPPER ION × 2 CHD CHOLIC ACID × 6 UNX UNKNOWN LIGAND × 2 ZN ZINC ION × 2 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 6.8；277 K；40 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000
|
Resolution 1.60 Å R-free 0.155 |
| 9W2Z Cryo-EM structure of complex IV on the bovine heart submitochondrial particles, IV-A Deposited 2025-07-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric |
Chain A
1–514（514 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | HEA HEME-A × 2 CU COPPER (II) ION × 1 MG MAGNESIUM ION × 1 PER PEROXIDE ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 2 CUA DINUCLEAR COPPER ION × 1 NA SODIUM ION × 1 ZN ZINC ION × 1 PEK (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.61 Å |
91 other PDB entries and 133 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | COX1_BOVIN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–514； UniProt 1–514 Author chain N； PDBConstruct 1–514； UniProt 1–514 |