SAXSdb — 8ejl

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

HIV-1 capsid 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 30	Cleavage and polyadenylation specificity factor subunit 6 × 10 （Q16630）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Cleavage and polyadenylation specificity factor subunit 6 × 2 （Q16630）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Cleavage and polyadenylation specificity factor subunit 6 × 2 （Q16630）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GAG_HV1N5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–231； UniProt 133–363 Author chain L； PDBConstruct 1–231； UniProt 133–363 Author chain M； PDBConstruct 1–231； UniProt 133–363 Author chain N； PDBConstruct 1–231； UniProt 133–363

Cleavage and polyadenylation specificity factor subunit 6

OrganismNot specified

UniProt Q16630

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 30	HIV-1 capsid protein × 20 （P12493）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	HIV-1 capsid protein × 4 （P12493）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	HIV-1 capsid protein × 4 （P12493）	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 Y； PDBConstruct 3–17； UniProt 313–327 Author chain Z； 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_id	8ejl
Deposition date deposition_date	2022-09-17
Structure title title	Structure of HIV-1 capsid declination in complex with CPSF6-FG peptide
Keywords keywords	HIV-1, capsid, declination, pentamer, hexamer, VIRAL PROTEIN; VIRAL PROTEIN
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.

8ejl__assembly_1__model_1

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

Download this curve (.dat)

8ejl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ejl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.68 Å
Rg (electron density)	55.50 Å
Total Rg	55.42 Å
Atom count	22155
Residues	3095
Excluded volume	395390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ejl__assembly_1__model_1`	30-meric （30）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8ejl__assembly_2__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`8ejl__assembly_3__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	HIV-1 capsid protein
Molecular weight formula_weight	25630.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M,N,A
Atom count atom_count	4431

PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Cleavage and polyadenylation specificity factor subunit 6
Molecular weight formula_weight	1709.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y,Z

GTPVLFPGQPFGQPPLG

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8ejlA01
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

Domain ID domain_id	8ejlL01
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	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	—

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

Resolution resolution	3.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	166463

Structure of HIV-1 capsid declination in complex with CPSF6-FG peptide

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

HIV-1 capsid 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

8ejl__assembly_1__model_1

8ejl__assembly_1__model_1 | I(q)

8ejl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of HIV-1 capsid declination in complex with CPSF6-FG peptide

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

HIV-1 capsid 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

8ejl__assembly_1__model_1

8ejl__assembly_1__model_1 | I(q)

8ejl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)