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5wve

Apaf-1-Caspase-9 holoenzyme

Method: ELECTRON MICROSCOPY Dmax: 241.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Apoptotic protease-activating factor 1

Homo sapiens

UniProt O14727

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 × 25 PDB declaration: 25-meric（25） Consistent with protein copy count Chain A； UniProt 1–1248 Chain C； UniProt 1–1248 Chain E； UniProt 1–1248 Chain G； UniProt 1–1248 Chain I； UniProt 1–1248 Chain K； UniProt 1–1248 Chain M； UniProt 1–1248 Chain O； UniProt 1–102 Chain P； UniProt 1–102 Chain Q； UniProt 1–102 Chain R； UniProt 1–102 Chain W； UniProt 1–102 Chain X； UniProt 1–102 Fragment：CARD domain, UNP residues 1-102 Cytochrome c × 7 （P00004） Caspase × 5 （A8K7U6） DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 7 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.40 Å

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 5WVE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C15 SOLUTION STRUCTURE OF APAF-1 CARD Deposited 1999-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–97（97 aa） Fragment：CASPASE RECRUITMENT DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 1；Pressure AMBIENT
NMR sample composition 1MM 15N LABELED APAF-1 CARD, 20 MM PHOSPHATE BUFFER, 50 MM NACL
NMR sample composition 1MM 13C LABELED APAF-1 CARD, 20 MM PHOSPHATE BUFFER, 50 MM NACL
NMR sample composition 1MM NON-LABELED APAF-1 CARD, 20 MM PHOSPHATE BUFFER, 50 MM NACL
NMR sample composition 1MM 13C,15N LABELED, 80%DEUTERATED APAF-1 CARD, 20 MM PHOSPHATE BUFFER, 50 MM NACL
Resolution not provided
1CWW SOLUTION STRUCTURE OF THE CASPASE RECRUITMENT DOMAIN (CARD) FROM APAF-1 Deposited 1999-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–97（97 aa） Fragment：CASPASE RECRUITMENT DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；30 K
NMR measurement conditions pH 6.7；30 K
NMR measurement conditions pH 6.7；30 K
NMR sample composition UNLABELLED 1.5MM APAF-1 CARD 20MM SODIUM PHOSPHATE PH 6.7 75MM NACL 2MM DITHIOTHREITOL
NMR sample composition U-15N 1.5MM APAF-1 CARD 20MM SODIUM PHOSPHATE PH 6.7 75MM NACL 2MM DITHIOTHREITOL
NMR sample composition U-15N; U-13C 1.5MM APAF-1 CARD 20MM SODIUM PHOSPHATE PH 6.7 75MM NACL 2MM DITHIOTHREITOL
Resolution not provided
1CY5 CRYSTAL STRUCTURE OF THE APAF-1 CARD Deposited 1999-08-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–97（97 aa） Fragment：CASPASE RECRUITMENT DOMAIN
Not recorded ZN ZINC ION × 5 BME BETA-MERCAPTOETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；HANGING DROP VAPOR DIFFUSION WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTIONS. PROTEIN SOLUTION: 5-20 MG/ML PROTEIN IN 0.02 MOLAR TRIS (PH 8.0-8.5) , 0.1-0.2 MOLAR SODIUM CHLORIDE. 0.005 MOLAR 2-MERCAPTOETHANOL RESERVOIR SOLUTION: 8-20% (W/V) PEG 8000, 0.2 MOLAR TRIS (PH 7.5-8.0), 0.05-0.2 MOLAR ZINC ACETATE., VAPOR DIFFUSION, HANGING DROP, temperature 17K
Resolution 1.30 Å R-free 0.199
1Z6T Structure of the apoptotic protease-activating factor 1 bound to ADP Deposited 2005-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–591（591 aa） Fragment：Apaf-1, residues 1-591
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.1；276 K；HEPES, ammonium acetate, PEG-3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 276K, pH 7.10
Resolution 2.21 Å R-free 0.244
1Z6T Structure of the apoptotic protease-activating factor 1 bound to ADP Deposited 2005-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–591（591 aa） Fragment：Apaf-1, residues 1-591
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.1；276 K；HEPES, ammonium acetate, PEG-3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 276K, pH 7.10
Resolution 2.21 Å R-free 0.244
1Z6T Structure of the apoptotic protease-activating factor 1 bound to ADP Deposited 2005-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–591（591 aa） Fragment：Apaf-1, residues 1-591
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.1；276 K；HEPES, ammonium acetate, PEG-3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 276K, pH 7.10
Resolution 2.21 Å R-free 0.244
1Z6T Structure of the apoptotic protease-activating factor 1 bound to ADP Deposited 2005-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–591（591 aa） Fragment：Apaf-1, residues 1-591
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.1；276 K；HEPES, ammonium acetate, PEG-3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 276K, pH 7.10
Resolution 2.21 Å R-free 0.244
2P1H Rapid Folding and Unfolding of Apaf-1 CARD Deposited 2007-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–92（92 aa） Fragment：CARD domain (Residues 1-92)
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；291 K；200 mM Tris-HCl, pH 6.1, 200 mM zinc acetate, 17% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.59 Å R-free 0.297
2YGS CARD DOMAIN FROM APAF-1 Deposited 1999-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–92（92 aa） Fragment：CASPASE RECRUITMENT DOMAIN (CARD)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.0
Resolution 1.60 Å R-free 0.236
3J2T An improved model of the human apoptosome Deposited 2012-12-23 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 1–1248（1248 aa）
Chain B 1–1248（1248 aa）
Chain C 1–1248（1248 aa）
Chain D 1–1248（1248 aa）
Chain E 1–1248（1248 aa）
Chain F 1–1248（1248 aa）
Chain G 1–1248（1248 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 7 ELECTRON MICROSCOPY
cryo-EM buffer low salt HEPES buffer；pH 7.5；20mM HEPES, 10mM KCl, 1.5mM MgCl2, 1mM EDTA, 1mM EGTA, 1mM DTT
cryo-EM vitrification conditions Blot for 2 seconds before plunging；77 K；Cryogen ETHANE；Blot for 2 seconds before plunging (FEI VITROBOT MARK III)
Resolution 9.50 Å
3JBT Atomic structure of the Apaf-1 apoptosome Deposited 2015-10-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain A 1–1248（1248 aa）
Chain C 1–1248（1248 aa）
Chain E 1–1248（1248 aa）
Chain G 1–1248（1248 aa）
Chain I 1–1248（1248 aa）
Chain K 1–1248（1248 aa）
Chain M 1–1248（1248 aa）
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 7 ELECTRON MICROSCOPY
cryo-EM buffer 20 mM HEPES (pH 7.5), 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM DTT；pH 7.5；20 mM HEPES (pH 7.5), 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM DTT
cryo-EM vitrification conditions Blot for 2.5 seconds before plunging；Cryogen ETHANE
Resolution 3.80 Å
3YGS APAF-1 CARD IN COMPLEX WITH PRODOMAIN OF PROCASPASE-9 Deposited 1999-05-08 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 × 2 PDB declaration: dimeric
Chain C 1–95（95 aa） Fragment：CASPASE RECRUITMENT DOMAIN (CARD)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 2.50 Å R-free 0.299
4RHW Crystal structure of Apaf-1 CARD and caspase-9 CARD complex Deposited 2014-10-03 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 × 6 PDB declaration: hexameric
Chain A 1–97（97 aa） Fragment：card domain
Chain B 1–97（97 aa） Fragment：card domain
Chain C 1–97（97 aa） Fragment：card domain
Chain D 1–97（97 aa） Fragment：card domain
Not recorded SO4 SULFATE ION × 7 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；13% PEG 3000, 0.2M ammonium sulfate, 0.1M MES (pH5.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.10 Å R-free 0.226
5JUY Active human apoptosome with procaspase-9 Deposited 2016-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 1–1248（1248 aa）
Chain B 1–1248（1248 aa）
Chain C 1–1248（1248 aa）
Chain D 1–1248（1248 aa）
Chain E 1–1248（1248 aa）
Chain F 1–1248（1248 aa）
Chain G 1–1248（1248 aa）
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 HEC HEME C × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Buffer A
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
5WVC Structure of the CARD-CARD disk Deposited 2016-12-24 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 × 6 PDB declaration: hexameric
Chain A 1–95（95 aa） Fragment：UNP RESIDUES 1-95
Chain C 1–95（95 aa） Fragment：UNP RESIDUES 1-95
Chain E 1–95（95 aa） Fragment：UNP RESIDUES 1-95
Not recorded IOD IODIDE ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M NH4I, 20% PEG 3350
Resolution 2.99 Å R-free 0.228
8XQK The Crystal Structure of Apaf from Biortus. Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–97（97 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6M Na/KPO4 pH6.5
Resolution 2.85 Å R-free 0.283
8XQK The Crystal Structure of Apaf from Biortus. Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–97（97 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6M Na/KPO4 pH6.5
Resolution 2.85 Å R-free 0.283
8XQK The Crystal Structure of Apaf from Biortus. Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–97（97 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6M Na/KPO4 pH6.5
Resolution 2.85 Å R-free 0.283
8XQK The Crystal Structure of Apaf from Biortus. Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–97（97 aa）
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6M Na/KPO4 pH6.5
Resolution 2.85 Å R-free 0.283

13 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name APAF_HUMAN
Isoform —
PDB entities 1, 3
Chains and sequence ranges Author chain A； PDBConstruct 1–1248； UniProt 1–1248 Author chain C； PDBConstruct 1–1248； UniProt 1–1248 Author chain E； PDBConstruct 1–1248； UniProt 1–1248 Author chain G； PDBConstruct 1–1248； UniProt 1–1248 Author chain I； PDBConstruct 1–1248； UniProt 1–1248 Author chain K； PDBConstruct 1–1248； UniProt 1–1248 Author chain M； PDBConstruct 1–1248； UniProt 1–1248 Author chain O； PDBConstruct 1–102； UniProt 1–102 Author chain P； PDBConstruct 1–102； UniProt 1–102 Author chain Q； PDBConstruct 1–102； UniProt 1–102 Author chain R； PDBConstruct 1–102； UniProt 1–102 Author chain W； PDBConstruct 1–102； UniProt 1–102 Author chain X； PDBConstruct 1–102； UniProt 1–102

Cytochrome c

Equus caballus

UniProt P00004

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 × 25 PDB declaration: 25-meric（25） Consistent with protein copy count Chain B； UniProt 1–105 Chain D； UniProt 1–105 Chain F； UniProt 1–105 Chain H； UniProt 1–105 Chain J； UniProt 1–105 Chain L； UniProt 1–105 Chain N； UniProt 1–105 Not recorded Apoptotic protease-activating factor 1 × 7 （O14727） Apoptotic protease-activating factor 1 × 6 （O14727） Caspase × 5 （A8K7U6） DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 7 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.40 Å

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 5WVE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AKK SOLUTION STRUCTURE OF OXIDIZED HORSE HEART CYTOCHROME C, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 7；293 K
Resolution not provided
1CRC CYTOCHROME C AT LOW IONIC STRENGTH Deposited 1995-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEC HEME C × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.08 Å
1CRC CYTOCHROME C AT LOW IONIC STRENGTH Deposited 1995-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–104（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEC HEME C × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.08 Å
1FI7 Solution structure of the imidazole complex of cytochrome C Deposited 2000-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded IMD IMIDAZOLE × 1 HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 5.7；313 K；Pressure 1
NMR sample composition 6mM cytochrome c, 1.2M Imidazole | H2O
NMR sample composition 6mM cytochrome c, 1.2M Imidazole | D2O
Resolution not provided
1FI9 SOLUTION STRUCTURE OF THE IMIDAZOLE COMPLEX OF CYTOCHROME C Deposited 2000-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded IMD IMIDAZOLE × 1 HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 5.7；313 K；Pressure 1
NMR sample composition 6mM cytochrome c, 1.2M imidazole | H2O
NMR sample composition 6mM cytochrome c, 1.2M imidazole | D2O
Resolution not provided
1GIW SOLUTION STRUCTURE OF REDUCED HORSE HEART CYTOCHROME C, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1998-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 100 mM PHOSPHATE；Pressure 1013
NMR sample composition H2O
Resolution not provided
1HRC HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF HORSE HEART CYTOCHROME C Deposited 1994-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEC HEME C × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1I5T SOLUTION STRUCTURE OF CYANOFERRICYTOCHROME C Deposited 2001-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded CYN CYANIDE ION × 1 HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 7；303 K
NMR sample composition 5mM cytochrome c,50mM potassium cyanide | 90% H2O/10% D2O
NMR sample composition 5mM cytochrome c, 50mM potassium cyanide | D2O
Resolution not provided
1LC1 Solution Structure Of Reduced Horse Heart Cytochrome c in 30% Acetonitrile Solution, NMR Minimized Average Structure Deposited 2002-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 50mM；Pressure 1
NMR sample composition 5mM FERROCYTOCHROME C 1H; 50mM PHOSPHATE BUFFER; 70% H2O, 30% CD3CN | 70% H2O, 30% CD3CN
Resolution not provided
1LC2 Solution Structure Of Reduced Horse Heart Cytochrome c in 30% Acetonitrile Solution, NMR 30 Structures Deposited 2002-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 50mM；Pressure 1
NMR sample composition 5mM FERROCYTOCHROME C 1H; 50mM PHOSPHATE BUFFER; 70% H2O, 30% CD3CN | 70% H2O, 30% CD3CN
Resolution not provided
1M60 Solution Structure of Zinc-substituted cytochrome c Deposited 2002-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded HES ZINC SUBSTITUTED HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；293 K；Pressure 1
NMR sample composition 5mM Zn-cytc | 90% H2O, 10% D2O; 90% D2O, 10% D2O
Resolution not provided
1OCD CYTOCHROME C (OXIDIZED) FROM EQUUS CABALLUS, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-07-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 5.7；293 K
NMR sample composition [U-15N] 7-10 mM cytochrome c, 50 mM potassium phosphate | 90% H2O/10% D2O
NMR sample composition [U-13C; U-15N] 15 mM cytochrome c, 50 mM potassium phosphate | 90% H2O/10% D2O
Resolution not provided
1U75 Electron Transfer Complex between Horse Heart Cytochrome c and Zinc-Porphyrin Substituted Cytochrome c Peroxidase Deposited 2004-08-02 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 × 3 PDB declaration: trimeric
Chain B 1–104（104 aa）
Not recorded PO4 PHOSPHATE ION × 2 ZNH PROTOPORPHYRIN IX CONTAINING ZN × 2 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.55 Å R-free 0.306
1WEJ IGG1 FAB FRAGMENT (OF E8 ANTIBODY) COMPLEXED WITH HORSE CYTOCHROME C AT 1.8 A RESOLUTION Deposited 1998-03-26 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 × 3 PDB declaration: trimeric
Chain F 1–104（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；50MM ZINC ACETATE BUFFER, PH 6.4, 25% (W/V) PEG 4000.
Resolution 1.80 Å R-free 0.256
1WEJ IGG1 FAB FRAGMENT (OF E8 ANTIBODY) COMPLEXED WITH HORSE CYTOCHROME C AT 1.8 A RESOLUTION Deposited 1998-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–104（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.4；50MM ZINC ACETATE BUFFER, PH 6.4, 25% (W/V) PEG 4000.
Resolution 1.80 Å R-free 0.256
2FRC CYTOCHROME C (REDUCED) FROM EQUUS CABALLUS, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 5.7；293 K
Resolution not provided
2GIW SOLUTION STRUCTURE OF REDUCED HORSE HEART CYTOCHROME C, NMR, 40 STRUCTURES Deposited 1998-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–104（104 aa）
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 100 mM PHOSPHATE；Pressure 1013
NMR sample composition H2O
Resolution not provided
2N3B Structure of oxidized horse heart cytochrome c encapsulated in reverse micelles Deposited 2015-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–105（104 aa）
Not recorded HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Pressure ambient
NMR sample composition 0.15 mM [U-100% 13C; U-100% 15N] protein, 1.5 M H2O, 25 mM sodium phosphate, 105 mM 1-decanoyl-rac-glycerol, 45 mM lauryldimethylamine-N-oxide, 8 mM hexanol, 8.67 M [U-99% 2H] pentane, Deuterated pentane | Deuterated pentane
NMR sample composition 0.15 mM [U-100% 15N] protein, 1.5 M H2O, 25 mM sodium phosphate, 105 mM 1-decanoyl-rac-glycerol, 45 mM lauryldimethylamine-N-oxide, 8 mM hexanol, 8.67 M [U-99% 2H] pentane, Deuterated pentane | Deuterated pentane
Resolution not provided
2PCB CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C Deposited 1993-04-14 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 × 2 PDB declaration: dimeric
Chain B 1–104（104 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
3JBT Atomic structure of the Apaf-1 apoptosome Deposited 2015-10-15 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain B 1–105（105 aa）
Chain D 1–105（105 aa）
Chain F 1–105（105 aa）
Chain H 1–105（105 aa）
Chain J 1–105（105 aa）
Chain L 1–105（105 aa）
Chain N 1–105（105 aa）
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 7 ELECTRON MICROSCOPY
cryo-EM buffer 20 mM HEPES (pH 7.5), 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM DTT；pH 7.5；20 mM HEPES (pH 7.5), 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM DTT
cryo-EM vitrification conditions Blot for 2.5 seconds before plunging；Cryogen ETHANE
Resolution 3.80 Å
3NBS Crystal structure of dimeric cytochrome c from horse heart Deposited 2010-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–105（104 aa）
Chain B 2–105（104 aa）
Not recorded HEC HEME C × 2 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；30% PEG 200, 0.1M Tris-HCl, 0.2M ammonium phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.20 Å R-free 0.273
3NBS Crystal structure of dimeric cytochrome c from horse heart Deposited 2010-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 2–105（104 aa）
Chain D 2–105（104 aa）
Not recorded HEC HEME C × 2 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；30% PEG 200, 0.1M Tris-HCl, 0.2M ammonium phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.20 Å R-free 0.273
3NBT Crystal structure of trimeric cytochrome c from horse heart Deposited 2010-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 2–105（104 aa）
Chain E 2–105（104 aa）
Chain F 2–105（104 aa）
Not recorded HEC HEME C × 3 PG4 TETRAETHYLENE GLYCOL × 3 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；30% PEG 200, 0.1M Tris-HCl, 0.2M ammonium phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.10 Å R-free 0.254
3NBT Crystal structure of trimeric cytochrome c from horse heart Deposited 2010-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 2–105（104 aa）
Chain C 2–105（104 aa）
Chain D 2–105（104 aa）
Not recorded HEC HEME C × 3 PG4 TETRAETHYLENE GLYCOL × 3 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；30% PEG 200, 0.1M Tris-HCl, 0.2M ammonium phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.10 Å R-free 0.254
3O1Y Electron transfer complexes: Experimental mapping of the redox-dependent cytochrome c electrostatic surface Deposited 2010-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–105（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEC HEME C × 1 NO3 NITRATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；High concentration of NaNO3 and 10% Ditionite in the wells, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.75 Å R-free 0.248
3O1Y Electron transfer complexes: Experimental mapping of the redox-dependent cytochrome c electrostatic surface Deposited 2010-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–105（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEC HEME C × 1 NO3 NITRATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；High concentration of NaNO3 and 10% Ditionite in the wells, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.75 Å R-free 0.248
3O1Y Electron transfer complexes: Experimental mapping of the redox-dependent cytochrome c electrostatic surface Deposited 2010-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 2–105（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEC HEME C × 1 NO3 NITRATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；High concentration of NaNO3 and 10% Ditionite in the wells, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.75 Å R-free 0.248
3O20 Electron transfer complexes:experimental mapping of the Redox-dependent Cytochrome C electrostatic surface Deposited 2010-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–105（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEC HEME C × 1 NO3 NITRATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；Excess of NaNO3 and 10% of Ditionite, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.90 Å R-free 0.276
3O20 Electron transfer complexes:experimental mapping of the Redox-dependent Cytochrome C electrostatic surface Deposited 2010-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–105（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEC HEME C × 1 NO3 NITRATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；Excess of NaNO3 and 10% of Ditionite, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.90 Å R-free 0.276
3O20 Electron transfer complexes:experimental mapping of the Redox-dependent Cytochrome C electrostatic surface Deposited 2010-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 2–105（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEC HEME C × 1 NO3 NITRATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；300 K；Excess of NaNO3 and 10% of Ditionite, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.90 Å R-free 0.276
3WC8 Dimeric horse cytochrome c obtained by refolding with desalting method Deposited 2013-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–105（104 aa）
Not recorded HEC HEME C × 2 PO4 PHOSPHATE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；100mM Tris-HCl buffer, 200mM (NH4)2HPO4, 40%(v/v) PEG200, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.80 Å R-free 0.208
3WUI Dimeric horse cytochrome c formed by refolding from molten globule state Deposited 2014-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–105（104 aa）
Not recorded HEC HEME C × 2 PG4 TETRAETHYLENE GLYCOL × 2 PO4 PHOSPHATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；100mM Tris-HCl buffer, 200mM (NH4)2HPO4, 40%(v/v) PEG 200, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.80 Å R-free 0.227
4NFG K13R mutant of horse cytochrome c and yeast cytochrome c peroxidase complex Deposited 2013-10-31 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 × 2 PDB declaration: dimeric
Chain B 2–105（104 aa）
Mutation：K13R HEM PROTOPORPHYRIN IX CONTAINING FE × 1 UNX UNKNOWN LIGAND × 1 HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；15% PEG 3350, 150 mM NaCl, 0.5 mM 1:1 ratio of horse cytochrome c and yeast cytochrome c peroxidase, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.11 Å R-free 0.236
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–105（104 aa）
Not recorded HEC HEME C × 1 CPT Cisplatin × 1 NO3 NITRATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 2.19 Å R-free 0.282
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–105（104 aa）
Not recorded HEC HEME C × 1 CPT Cisplatin × 1 NO3 NITRATE ION × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 2.19 Å R-free 0.282
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 2–105（104 aa）
Not recorded HEC HEME C × 1 NO3 NITRATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 2.19 Å R-free 0.282
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 2–105（104 aa）
Not recorded HEC HEME C × 1 CPT Cisplatin × 1 NO3 NITRATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 2.19 Å R-free 0.282
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 2–105（104 aa）
Not recorded HEC HEME C × 1 CPT Cisplatin × 1 NO3 NITRATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 2.19 Å R-free 0.282
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 2–105（104 aa）
Not recorded HEC HEME C × 1 CPT Cisplatin × 1 NO3 NITRATE ION × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 2.19 Å R-free 0.282
4RSZ The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c Deposited 2014-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 2–105（104 aa）
Chain B 2–105（104 aa）
Chain C 2–105（104 aa）
Chain D 2–105（104 aa）
Chain E 2–105（104 aa）
Chain F 2–105（104 aa）
Not recorded HEC HEME C × 6 CPT Cisplatin × 5 NO3 NITRATE ION × 16 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；A new crystal form of horse heart cytochrome c that co-crystallized with nitrate and sulphate ions has been obtained. Crystallization was prepared by using the hanging-drop vapour diffusion method in Linbro plates and a reservoir contained 3.5 M ammonium sulphate, 0.6 M sodium nitrate. The droplets consisted of 1 microliter protein (30 mg/mL in water) and 1 microliter of reservoir. They were equilibrated against a 500 microliters reservoir solution at 20 C. These conditions produced well shaped red crystals after 1 month. These crystals have been soaked for 24 h in a solution consisting of 0.005 M cisplatin in 2.0 M ammonium sulphate and 0.4 M sodium nitrate. To prepare this solution, Cisplatin was first dissolved in 5 mM sodium acetate buffer at pH 5.0. , VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 2.19 Å R-free 0.282
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 method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain 1 2–105（104 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 method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain 2 2–105（104 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
5ZKV Solution structure of molten globule state of L94G mutant of horse cytochrome-c Deposited 2018-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–105（104 aa）
Mutation：L94G HEC HEME C × 1 SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.03 M cacodylate buffer containing 0.1 M NaCl；Pressure 1
NMR sample composition 2 mM [U-99% 13C; U-99% 15N] Molten globule of L94G mutant of horse cytochrome-c, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6K9I High-resolution three-dimensional structure of horse heart cytochrome C at room temperature Deposited 2019-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–105（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；1.0-1.5M sodium chloride, 2.7-3.2M ammonium sulfate, 0.1M sodium phosphate
Resolution 1.80 Å R-free 0.199
6K9J 0.98 A three-dimensional structure of horse heart cytochrome C at 110K Deposited 2019-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–105（104 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) HEC HEME C × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；1.0-1.5M sodium chloride, 2.7-3.2M ammonium sulfate, 0.1M sodium phosphate
Resolution 0.98 Å R-free 0.153
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AaA 2–105（104 aa）
Not recorded ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride
Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain BaB 2–105（104 aa）
Not recorded ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride
Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain CaC 2–105（104 aa）
Not recorded ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride
Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain DaD 2–105（104 aa）
Not recorded ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride
Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain EaE 2–105（104 aa）
Not recorded ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride
Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain FaF 2–105（104 aa）
Not recorded ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride
Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain GaG 2–105（104 aa）
Not recorded ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride
Resolution 2.50 Å R-free 0.237
6SUV Horse cytochrome c complexed by octa-anionic calixarene Deposited 2019-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain HaH 2–105（104 aa）
Not recorded ACE ACETYL GROUP × 1 HEC HEME C × 1 LVQ octa-anionic calixarene × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；56% PEG 3350, 0.05 M sodium cacodylate pH 5.5 and 0.0017 M gadolinium chloride
Resolution 2.50 Å R-free 0.237
8ZXR Crystal structure of Ssr1698 in complex with heme c Deposited 2024-06-14 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 × 2 PDB declaration: dimeric
Chain B 12–22（11 aa）
Not recorded NI NICKEL (II) ION × 1 CL CHLORIDE ION × 2 HEC HEME C × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Sodium acetate, Sodium formate, Glycerol
Resolution 1.60 Å R-free 0.218
8ZXR Crystal structure of Ssr1698 in complex with heme c Deposited 2024-06-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 12–22（11 aa）
Not recorded NI NICKEL (II) ION × 6 CL CHLORIDE ION × 12 HEC HEME C × 6 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Sodium acetate, Sodium formate, Glycerol
Resolution 1.60 Å R-free 0.218
8ZXR Crystal structure of Ssr1698 in complex with heme c Deposited 2024-06-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 12–22（11 aa）
Not recorded NI NICKEL (II) ION × 3 CL CHLORIDE ION × 6 HEC HEME C × 3 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Sodium acetate, Sodium formate, Glycerol
Resolution 1.60 Å R-free 0.218
8ZXR Crystal structure of Ssr1698 in complex with heme c Deposited 2024-06-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 12–22（11 aa）
Not recorded NI NICKEL (II) ION × 2 CL CHLORIDE ION × 4 HEC HEME C × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Sodium acetate, Sodium formate, Glycerol
Resolution 1.60 Å R-free 0.218

32 other PDB entries and 57 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYC_HORSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–105； UniProt 1–105 Author chain D； PDBConstruct 1–105； UniProt 1–105 Author chain F； PDBConstruct 1–105； UniProt 1–105 Author chain H； PDBConstruct 1–105； UniProt 1–105 Author chain J； PDBConstruct 1–105； UniProt 1–105 Author chain L； PDBConstruct 1–105； UniProt 1–105 Author chain N； PDBConstruct 1–105； UniProt 1–105

Caspase

Homo sapiens

UniProt A8K7U6

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 × 25 PDB declaration: 25-meric（25） Consistent with protein copy count Chain S； UniProt 1–100 Chain T； UniProt 1–100 Chain U； UniProt 1–100 Chain V； UniProt 1–100 Chain Y； UniProt 1–100 Fragment：CARD domain, UNP residues 1-100 Apoptotic protease-activating factor 1 × 7 （O14727） Cytochrome c × 7 （P00004） Apoptotic protease-activating factor 1 × 6 （O14727） DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 7 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.40 Å

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 5WVE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5WVC Structure of the CARD-CARD disk Deposited 2016-12-24 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 × 6 PDB declaration: hexameric
Chain B 1–128（128 aa） Fragment：UNP RESIDUES 1-128
Chain D 1–128（128 aa） Fragment：UNP RESIDUES 1-128
Chain F 1–128（128 aa） Fragment：UNP RESIDUES 1-128
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) IOD IODIDE ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M NH4I, 20% PEG 3350
Resolution 2.99 Å R-free 0.228

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A8K7U6_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain S； PDBConstruct 1–100； UniProt 1–100 Author chain T； PDBConstruct 1–100； UniProt 1–100 Author chain U； PDBConstruct 1–100； UniProt 1–100 Author chain V； PDBConstruct 1–100； UniProt 1–100 Author chain Y； PDBConstruct 1–100； UniProt 1–100

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5wve

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5wve
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5wve
Deposition date deposition_date2016-12-24
Structure title titleApaf-1-Caspase-9 holoenzyme
Keywords keywordsapoptosis holoenzyme, APOPTOSIS; APOPTOSIS
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier94.74 Å
Radius of gyration Rg (electron density) rg_electron94.79 Å
Forward intensity I(0) i017460000000.00
Molecular weight molecular_weight1119800.0 kDa
Excluded volume excluded_volume1398000 ų
Envelope volume envelope_volume2324400 ų
Hydration-shell volume shell_volume205950 ų
Envelope diameter envelope_diameter297.0 Å
Shell Rg shell_rg88.00 Å
Envelope Rg envelope_rg92.16 Å
Shape Rg shape_rg94.88 Å
Total Rg total_rg94.44 Å
Total atoms total_atoms78605
Residues n_residues9766
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax241.9 Å
Rg (real space) rg_real91.16 Å
Rg uncertainty (real space) rg_real_error0.72 Å
I(0) (real space) i0_real1.6800e+10
I(0) uncertainty (real space) i0_real_error3.3780e+08
Rg (reciprocal space) rg_reciprocal94.21 Å
I(0) (reciprocal space) i0_reciprocal17430000000.0000
Solution quality estimate total_estimate0.9174
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary105.8 Å
Skewness Skewness skewness0.140
Kurtosis Kurtosis kurtosis-0.639
Angular range angular_range— – 0.0800 Å−1
Current regularization parameter α current_alpha0.4320
Highest regularization parameter α highest_alpha386900000.0000
Real-space data points n_real_points17
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 1.000; Stabil: 0.975; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)