SAXSdb — 3j2t

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Apoptotic protease-activating factor 1

Homo sapiens

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 × 14 PDB declaration: tetradecameric（14） Consistent with protein copy count	Chain A； UniProt 1–1248 Chain B； UniProt 1–1248 Chain C； UniProt 1–1248 Chain D； UniProt 1–1248 Chain E； UniProt 1–1248 Chain F； UniProt 1–1248 Chain G； UniProt 1–1248	Not recorded	Cytochrome c × 7 （P62894） 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

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 3J2T	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
3JBT Atomic structure of the Apaf-1 apoptosome Deposited 2015-10-15	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 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 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
5WVE Apaf-1-Caspase-9 holoenzyme Deposited 2016-12-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	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） Chain O 1–102（102 aa） Fragment：CARD domain, UNP residues 1-102 Chain P 1–102（102 aa） Fragment：CARD domain, UNP residues 1-102 Chain Q 1–102（102 aa） Fragment：CARD domain, UNP residues 1-102 Chain R 1–102（102 aa） Fragment：CARD domain, UNP residues 1-102 Chain W 1–102（102 aa） Fragment：CARD domain, UNP residues 1-102 Chain X 1–102（102 aa） Fragment：CARD domain, UNP residues 1-102	Not recorded	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
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
Chains and sequence ranges	Author chain A； PDBConstruct 7–1254； UniProt 1–1248 Author chain B； PDBConstruct 7–1254； UniProt 1–1248 Author chain C； PDBConstruct 7–1254； UniProt 1–1248 Author chain D； PDBConstruct 7–1254； UniProt 1–1248 Author chain E； PDBConstruct 7–1254； UniProt 1–1248 Author chain F； PDBConstruct 7–1254； UniProt 1–1248 Author chain G； PDBConstruct 7–1254； UniProt 1–1248

Cytochrome c

OrganismNot specified

UniProt P62894

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 × 14 PDB declaration: tetradecameric（14） Consistent with protein copy count	Chain H； UniProt 2–105 Chain I； UniProt 2–105 Chain J； UniProt 2–105 Chain K； UniProt 2–105 Chain L； UniProt 2–105 Chain M； UniProt 2–105 Chain N； UniProt 2–105	Not recorded	Apoptotic protease-activating factor 1 × 7 （O14727） 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

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 3J2T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2B4Z Crystal structure of cytochrome C from bovine heart at 1.5 A resolution. Deposited 2005-09-27	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 1–104（104 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROSEEDING；pH 7；277 K；PEG 1000, SODIUM PHOSPHATE, pH 7.0, MICROSEEDING, temperature 277K	Resolution 1.50 Å R-free 0.218
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 conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric	Chain Y 2–105（104 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
5JUY Active human apoptosome with procaspase-9 Deposited 2016-05-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric	Chain H 2–105（104 aa） Chain I 2–105（104 aa） Chain J 2–105（104 aa） Chain K 2–105（104 aa） Chain L 2–105（104 aa） Chain M 2–105（104 aa） Chain N 2–105（104 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
6FF5 X-ray structure of bovine heart cytochrome c at high ionic strength Deposited 2018-01-03	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 2–105（104 aa）	Not recorded	HEC HEME C × 1 NO3 NITRATE ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；3.2-3.4 M ammonium sulfate and 0.4-0.5 M NaNO3	Resolution 1.74 Å R-free 0.203

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYC_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 1–104； UniProt 2–105 Author chain I； PDBConstruct 1–104； UniProt 2–105 Author chain J； PDBConstruct 1–104； UniProt 2–105 Author chain K； PDBConstruct 1–104； UniProt 2–105 Author chain L； PDBConstruct 1–104； UniProt 2–105 Author chain M； PDBConstruct 1–104； UniProt 2–105 Author chain N； PDBConstruct 1–104； UniProt 2–105

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3j2t
Deposition date deposition_date	2012-12-23
Structure title title	An improved model of the human apoptosome
Keywords keywords	Apoptosis protease activating factor-1, Apaf-1, cytochrome c, APOPTOSIS; APOPTOSIS
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	97.31 Å
Radius of gyration Rg (electron density) rg_electron	97.31 Å
Forward intensity I(0) i0	13835600000.00
Molecular weight molecular_weight	999430.0 kDa
Excluded volume excluded_volume	1248500 Å³
Envelope volume envelope_volume	2175900 Å³
Hydration-shell volume shell_volume	187690 Å³
Envelope diameter envelope_diameter	298.4 Å
Shell Rg shell_rg	88.60 Å
Envelope Rg envelope_rg	93.66 Å
Shape Rg shape_rg	97.37 Å
Total Rg total_rg	97.01 Å
Total atoms total_atoms	70189
Residues n_residues	8736
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	245.6 Å
Rg (real space) rg_real	93.87 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	1.3310e+10
I(0) uncertainty (real space) i0_real_error	2.8990e+08
Rg (reciprocal space) rg_reciprocal	96.35 Å
I(0) (reciprocal space) i0_reciprocal	13790000000.0000
Solution quality estimate total_estimate	0.9141
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	92.1 Å
Skewness Skewness skewness	0.108
Kurtosis Kurtosis kurtosis	-0.780
Angular range angular_range	— – 0.0800 Å⁻¹
Current regularization parameter α current_alpha	0.5435
Highest regularization parameter α highest_alpha	330300000.0000
Real-space data points n_real_points	17
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.997; Stabil: 0.972; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Apoptotic protease-activating factor 1
Molecular weight formula_weight	144095.8 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	70189

HHHHHHMDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLCEGGVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDILQEFVNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQFQRYHQPHTLSPDQEDCMYWYNFLAYHMASAKMHKELCALMFSLDWIKAKTELVGPAHLIHEFVEYRHILDEKDCAVSENFQEFLSLNGHLLGRQPFPNIVQLGLCEPETSEVYQQAKLQAKQEVDNGMLYLEWINKKNITNLSRLVVRPHTDAVYHACFSEDGQRIASCGADKTLQVFKAETGEKLLEIKAHEDEVLCCAFSTDDRFIATCSVDKKVKIWNSMTGELVHTYDEHSEQVNCCHFTNSSHHLLLATGSSDCFLKLWDLNQKECRNTMFGHTNSVNHCRFSPDDKLLASCSADGTLKLWDATSANERKSINVKQFFLNLEDPQEDMEVIVKCCSWSADGARIMVAAKNKIFLFDIHTSGLLGEIHTGHHSTIQYCDFSPQNHLAVVALSQYCVELWNTDSRSKVADCRGHLSWVHGVMFSPDGSSFLTSSDDQTIRLWETKKVCKNSAVMLKQEVDVVFQENEVMVLAVDHIRRLQLINGRTGQIDYLTEAQVSCCCLSPHLQYIAFGDENGAIEILELVNNRIFQSRFQHKKTVWHIQFTADEKTLISSSDDAEIQVWNWQLDKCIFLRGHQETVKDFRLLKNSRLLSWSFDGTVKVWNIITGNKEKDFVCHQGTVLSCDISHDATKFSSTSADKTAKIWSFDLLLPLHELRGHNGCVRCSAFSVDSTLLATGDDNGEIRIWNVSNGELLHLCAPLSEEGAATHGGWVTDLCFSPDGKMLISAGGYIKWWNVVTGESSQTFYTNGTNLKKIHVSPDFKTYVTVDNLGILYILQTLEHHHHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Cytochrome c
Molecular weight formula_weight	11595.4 kDa
Source method src_method	nat
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I,J,K,L,M,N

GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFSYTDANKNKGITWGEETLMEYLENPKKYIPGTKMIFAGIKKKGEREDLIAYLKKATNE

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	7

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8. Citations (2)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	9.50 Å
Resolution测定方法 resolution_method	Projection Matching
颗粒数 num_particles	34000

fit	/app/data/saxs_computation/j2/3j2t/3j2t.fit
pddf	/app/data/pr_computation/j2/3j2t/3j2t.pr.out
profile	/app/data/saxs_computation/j2/3j2t/3j2t.dat

An improved model of the human apoptosome

1. Protein Identity and Related Structures Protein Identity & Related Structures

Apoptotic protease-activating factor 1

State in the Current Structure

Other States of the Same Protein in the Database

Cytochrome c

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)