4wym

Structural basis of HIV-1 capsid recognition by CPSF6

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid protein p24

Human immunodeficiency virus type 1 group M subtype B

UniProt P12497

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 12 ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6 × 6 (Q16630) Consistent with protein count
2 Protein heterocomplex Heteromer Protein 11 ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6 × 5 (Q16630) Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name POL_HV1N5
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–231; UniProt 133–363 Author chain B; PDBConstruct 1–231; UniProt 133–363 Author chain C; PDBConstruct 1–231; UniProt 133–363 Author chain D; PDBConstruct 1–231; UniProt 133–363 Author chain E; PDBConstruct 1–231; UniProt 133–363 Author chain F; PDBConstruct 1–231; UniProt 133–363 Author chain G; PDBConstruct 1–231; UniProt 133–363 Author chain H; PDBConstruct 1–231; UniProt 133–363 Author chain I; PDBConstruct 1–231; UniProt 133–363 Author chain J; PDBConstruct 1–231; UniProt 133–363 Author chain K; PDBConstruct 1–231; UniProt 133–363 Author chain L; PDBConstruct 1–231; UniProt 133–363

ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6

Homo sapiens

UniProt Q16630

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 12 Capsid protein p24 × 6 (P12497) Consistent with protein count
2 Protein heterocomplex Heteromer Protein 11 Capsid protein p24 × 6 (P12497) Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name CPSF6_HUMAN
Isoform Q16630-2
PDB entities 2
Chains and sequence ranges Author chain M; PDBConstruct 3–17; UniProt 313–327 Author chain N; PDBConstruct 3–17; UniProt 313–327 Author chain O; PDBConstruct 3–17; UniProt 313–327 Author chain P; PDBConstruct 3–17; UniProt 313–327 Author chain Q; PDBConstruct 3–17; UniProt 313–327 Author chain R; PDBConstruct 3–17; UniProt 313–327 Author chain S; PDBConstruct 3–17; UniProt 313–327 Author chain T; PDBConstruct 3–17; UniProt 313–327 Author chain U; PDBConstruct 3–17; UniProt 313–327 Author chain V; PDBConstruct 3–17; UniProt 313–327 Author chain W; PDBConstruct 3–17; UniProt 313–327

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_id4wym
Deposition date deposition_date2014-11-17
Structure title titleStructural basis of HIV-1 capsid recognition by CPSF6
Keywords keywordsCAPSID PROTEIN, HEXAMER, ENGINEERED DISULFIDE BONDS, VIRAL PROTEIN, CPSF6, viral restriction; VIRAL PROTEIN
Experimental Method methodX-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.

4wym__assembly_1__model_1

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

Download this curve (.dat)

4wym__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4wym__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)36.25 Å
Rg (electron density)35.35 Å
Total Rg35.86 Å
Atom count10552
Residues1359
Excluded volume188360 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4wym__assembly_1__model_1 dodecameric (12) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4wym__assembly_2__model_1 undecameric (11) 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 (2)

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6. Fold Classification (SCOP + CATH) 46 domains

SCOP 2.08 (22 domains)

Domain ID domain_idd4wyma1
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain
Domain ID domain_idd4wyma2
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.3 — Retrovirus capsid dimerization domain-like
Family Family familya.28.3.0 — automated matches
Domain ID domain_idd4wymb1
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain
Domain ID domain_idd4wymb2
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.3 — Retrovirus capsid dimerization domain-like
Family Family familya.28.3.0 — automated matches
Domain ID domain_idd4wymc1
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain
Domain ID domain_idd4wymc2
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.3 — Retrovirus capsid dimerization domain-like
Family Family familya.28.3.0 — automated matches
Domain ID domain_idd4wymd1
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain
Domain ID domain_idd4wymd2
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.3 — Retrovirus capsid dimerization domain-like
Family Family familya.28.3.0 — automated matches
Domain ID domain_idd4wyme1
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain
Domain ID domain_idd4wyme2
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.3 — Retrovirus capsid dimerization domain-like
Family Family familya.28.3.0 — automated matches
Domain ID domain_idd4wymf1
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain
Domain ID domain_idd4wymf2
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.3 — Retrovirus capsid dimerization domain-like
Family Family familya.28.3.0 — automated matches
Domain ID domain_idd4wymg1
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain
Domain ID domain_idd4wymg2
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.3 — Retrovirus capsid dimerization domain-like
Family Family familya.28.3.0 — automated matches
Domain ID domain_idd4wymh1
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain
Domain ID domain_idd4wymh2
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.3 — Retrovirus capsid dimerization domain-like
Family Family familya.28.3.0 — automated matches
Domain ID domain_idd4wymi1
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain
Domain ID domain_idd4wymj1
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain
Domain ID domain_idd4wymj2
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.3 — Retrovirus capsid dimerization domain-like
Family Family familya.28.3.0 — automated matches
Domain ID domain_idd4wymk1
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain
Domain ID domain_idd4wymk2
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.3 — Retrovirus capsid dimerization domain-like
Family Family familya.28.3.0 — automated matches
Domain ID domain_idd4wyml1
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain

CATH v4.4 (24 domains)

Domain ID domain_id4wymA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id4wymA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain
Domain ID domain_id4wymB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id4wymB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain
Domain ID domain_id4wymC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id4wymC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain
Domain ID domain_id4wymD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id4wymD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain
Domain ID domain_id4wymE01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id4wymE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain
Domain ID domain_id4wymF01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id4wymF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain
Domain ID domain_id4wymG01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id4wymG02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain
Domain ID domain_id4wymH01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id4wymH02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain
Domain ID domain_id4wymI01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id4wymI02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain
Domain ID domain_id4wymJ01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id4wymJ02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain
Domain ID domain_id4wymK01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id4wymK02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain
Domain ID domain_id4wymL01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id4wymL02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain
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7. Citations (1)