SAXSdb — 5juy

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	Cytochrome c × 7 （P62894） Caspase-9 × 4 （P55211） ;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ; × 7 HEME C × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APAF_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1248； UniProt 1–1248 Author chain B； PDBConstruct 1–1248； UniProt 1–1248 Author chain C； PDBConstruct 1–1248； UniProt 1–1248 Author chain D； PDBConstruct 1–1248； UniProt 1–1248 Author chain E； PDBConstruct 1–1248； UniProt 1–1248 Author chain F； PDBConstruct 1–1248； UniProt 1–1248 Author chain G； PDBConstruct 1–1248； UniProt 1–1248

Cytochrome c

OrganismNot specified

UniProt P62894

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	Apoptotic protease-activating factor 1 × 7 （O14727） Caspase-9 × 4 （P55211） ;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ; × 7 HEME C × 7	Consistent with protein count

Other States of the Same Protein in the Database

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

Caspase-9

Homo sapiens

UniProt P55211

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	Apoptotic protease-activating factor 1 × 7 （O14727） Cytochrome c × 7 （P62894） ;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ; × 7 HEME C × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CASP9_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain O； PDBConstruct 1–95； UniProt 1–95 Author chain P； PDBConstruct 1–95； UniProt 1–95 Author chain Q； PDBConstruct 1–95； UniProt 1–95 Author chain R； PDBConstruct 1–95； UniProt 1–95

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	5juy
Deposition date deposition_date	2016-05-10
Structure title title	Active human apoptosome with procaspase-9
Keywords keywords	Apaf-1, apoptosis, programmed cell death, AAA+ ATPase; APOPTOSIS
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5juy__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5juy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5juy__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	96.29 Å
Rg (electron density)	96.29 Å
Total Rg	95.95 Å
Atom count	76058
Residues	9461
Excluded volume	1352700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5juy__assembly_1__model_1`	octadecameric （18）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Apoptotic protease-activating factor 1
Molecular weight formula_weight	142023.7 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	76058

MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLCEGGVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDILQEFVNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQFQRYHQPHTLSPDQEDCMYWYNFLAYHMASAKMHKELCALMFSLDWIKAKTELVGPAHLIHEFVEYRHILDEKDCAVSENFQEFLSLNGHLLGRQPFPNIVQLGLCEPETSEVYQQAKLQAKQEVDNGMLYLEWINKKNITNLSRLVVRPHTDAVYHACFSEDGQRIASCGADKTLQVFKAETGEKLLEIKAHEDEVLCCAFSTDDRFIATCSVDKKVKIWNSMTGELVHTYDEHSEQVNCCHFTNSSHHLLLATGSSDCFLKLWDLNQKECRNTMFGHTNSVNHCRFSPDDKLLASCSADGTLKLWDATSANERKSINVKQFFLNLEDPQEDMEVIVKCCSWSADGARIMVAAKNKIFLFDIHTSGLLGEIHTGHHSTIQYCDFSPQNHLAVVALSQYCVELWNTDSRSKVADCRGHLSWVHGVMFSPDGSSFLTSSDDQTIRLWETKKVCKNSAVMLKQEVDVVFQENEVMVLAVDHIRRLQLINGRTGQIDYLTEAQVSCCCLSPHLQYIAFGDENGAIEILELVNNRIFQSRFQHKKTVWHIQFTADEKTLISSSDDAEIQVWNWQLDKCIFLRGHQETVKDFRLLKNSRLLSWSFDGTVKVWNIITGNKEKDFVCHQGTVLSCDISHDATKFSSTSADKTAKIWSFDLLLPLHELRGHNGCVRCSAFSVDSTLLATGDDNGEIRIWNVSNGELLHLCAPLSEEGAATHGGWVTDLCFSPDGKMLISAGGYIKWWNVVTGESSQTFYTNGTNLKKIHVSPDFKTYVTVDNLGILYILQTLE

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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 polymer

Description description	Caspase-9
Molecular weight formula_weight	11140.7 kDa
EC 编号 ec_number	3.4.22.62
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,P,Q,R

MDEADRRLLRRCRLRLVEELQVDQLWDALLSRELFRPHMIEDIQRAGSGSRRDQARQLIIDLETRGSQALPLFISCLEDTGQDMLASFLRTNRQA

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 4 Entity 4 non-polymer

Description description	;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	491.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	7

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Resolution resolution	4.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	92867

Active human apoptosome with procaspase-9

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

Caspase-9

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5juy__assembly_1__model_1

5juy__assembly_1__model_1 | I(q)

5juy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Active human apoptosome with procaspase-9

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Caspase-9

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5juy__assembly_1__model_1

5juy__assembly_1__model_1 | I(q)

5juy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)