5wvc

Structure of the CARD-CARD disk

Method: X-RAY DIFFRACTION

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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 6	Caspase × 3 （A8K7U6） IODIDE ION × 11	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 1–95； UniProt 1–95 Author chain C； PDBConstruct 1–95； UniProt 1–95 Author chain E； PDBConstruct 1–95； UniProt 1–95

Caspase

Homo sapiens

UniProt A8K7U6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Apoptotic protease-activating factor 1 × 3 （O14727） IODIDE ION × 11	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8K7U6_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 24–151； UniProt 1–128 Author chain D； PDBConstruct 24–151； UniProt 1–128 Author chain F； PDBConstruct 24–151； UniProt 1–128

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	5wvc
Deposition date deposition_date	2016-12-24
Structure title title	Structure of the CARD-CARD disk
Keywords keywords	protein-protein interaction, signaling protein complex, APOPTOSIS; APOPTOSIS
Experimental Method method	X-RAY DIFFRACTION

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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.

5wvc__assembly_1__model_1

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

Download this curve (.dat)

5wvc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5wvc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.08 Å
Rg (electron density)	27.35 Å
Total Rg	28.07 Å
Atom count	4796
Residues	590
Excluded volume	85358 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5wvc__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	Apoptotic protease-activating factor 1
Molecular weight formula_weight	10925.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A,E
Atom count atom_count	4796

MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVS

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

Entity 2 Entity 2 polymer

Description description	Caspase
Molecular weight formula_weight	17410.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,B,F

MGSSHHHHHHSSGLVPRGSHMASMDEADRRLLRRCRLRLVEELQVDQLWDVLLSRELFRPHMIEDIQRAGSGSRRDQARQLIIDLETRGSQALPLFISCLEDTGQDMLASFLRTNRQAAKLSKPTLENLTPVVLRPEIRKPEVLRPETPRP

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

Entity 3 Entity 3 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	11

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d5wvca_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.3 — Caspase recruitment domain, CARD

Domain ID domain_id	d5wvcb1
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.3 — Caspase recruitment domain, CARD

Domain ID domain_id	d5wvcb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5wvcc_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.3 — Caspase recruitment domain, CARD

Domain ID domain_id	d5wvcd1
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.3 — Caspase recruitment domain, CARD

Domain ID domain_id	d5wvcd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5wvce_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.3 — Caspase recruitment domain, CARD

Domain ID domain_id	d5wvcf1
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.3 — Caspase recruitment domain, CARD

Domain ID domain_id	d5wvcf2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	5wvcA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	5wvcB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	5wvcC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	5wvcD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	5wvcE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

Domain ID domain_id	5wvcF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

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Unit-cell length a length_a	190.110 Å
Unit-cell length b length_b	190.110 Å
Unit-cell length c length_c	68.828 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.993 Å
Low-resolution limit resolution_low	24.852 Å
R factor r_factor	0.1992
R_work r_work	0.1969
R_free r_free	0.2281

Structure of the CARD-CARD disk

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

Caspase

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

5wvc__assembly_1__model_1

5wvc__assembly_1__model_1 | I(q)

5wvc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of the CARD-CARD disk

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

Caspase

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

5wvc__assembly_1__model_1

5wvc__assembly_1__model_1 | I(q)

5wvc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)