SAXSdb — 4b4n

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

GAG PROTEIN

HUMAN IMMUNODEFICIENCY VIRUS 1

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A9PKC6_9HIV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–146； UniProt 33–178

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 2	GAG PROTEIN × 1 （A9PKC6） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CPSF6_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–15； 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_id	4b4n
Deposition date deposition_date	2012-07-31
Structure title title	CPSF6 defines a conserved capsid interface that modulates HIV-1 replication
Keywords keywords	VIRAL PROTEIN-RNA BINDING PROTEIN COMPLEX, HIV-1, CYCLOPHILIN; VIRAL PROTEIN/RNA BINDING PROTEIN
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.

4b4n__assembly_1__model_1

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

Download this curve (.dat)

4b4n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4b4n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.65 Å
Rg (electron density)	15.43 Å
Total Rg	16.56 Å
Atom count	1178
Residues	151
Excluded volume	21058 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4b4n__assembly_1__model_1`	dimeric （2）	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	GAG PROTEIN
Molecular weight formula_weight	16204.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1285

PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYS

Source Source

Source organism organism	HUMAN IMMUNODEFICIENCY VIRUS 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	SACCHAROMYCES CEREVISIAE

Entity 2 Entity 2 polymer

Description description	CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
Molecular weight formula_weight	1550.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PVLFPGQPFGQPPLG

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	SACCHAROMYCES CEREVISIAE

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4b4na_
Class class	a — All alpha proteins
Fold Fold fold	a.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamily	a.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family family	a.73.1.1 — Retrovirus capsid protein, N-terminal core domain

CATH v4.4 (1 domains)

Domain ID domain_id	4b4nA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily	10 — Human Immunodeficiency Virus Type 1 Capsid Protein

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Unit-cell length a length_a	40.560 Å
Unit-cell length b length_b	46.360 Å
Unit-cell length c length_c	80.820 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.813 Å
Low-resolution limit resolution_low	36.251 Å
R factor r_factor	0.1910
R_work r_work	0.1867
R_free r_free	0.2729

CPSF6 defines a conserved capsid interface that modulates HIV-1 replication

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

GAG PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6

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

4b4n__assembly_1__model_1

4b4n__assembly_1__model_1 | I(q)

4b4n__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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

CPSF6 defines a conserved capsid interface that modulates HIV-1 replication

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

GAG PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6

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

4b4n__assembly_1__model_1

4b4n__assembly_1__model_1 | I(q)

4b4n__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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)