SAXSdb — 5tsv

▼

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

HIV-1 CA protein

Human immunodeficiency virus type 1 group M subtype B (isolate NY5)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Nuclear pore complex protein Nup153 × 3 （P49790） 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 3	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 B； PDBConstruct 1–231； UniProt 133–363

Nuclear pore complex protein Nup153

OrganismNot specified

UniProt P49790

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	HIV-1 CA protein × 6 （P12493） 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NU153_HUMAN
Isoform	P49790-2
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–23； UniProt 1365–1387

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5tsv
Deposition date deposition_date	2016-10-31
Structure title title	HIV-1 CA hexamer with NUP153 peptide - R3 crystal form
Keywords keywords	viral capsid protein, hexamer, FG repeat, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5tsv__assembly_1__model_1

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

Download this curve (.dat)

5tsv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5tsv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.09 Å
Rg (electron density)	35.17 Å
Total Rg	35.65 Å
Atom count	20370
Residues	1314
Excluded volume	182390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5tsv__assembly_1__model_1`	nonameric （9）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	HIV-1 CA protein
Molecular weight formula_weight	25461.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6790

PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

Source Source

Source organism organism	Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11698
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nuclear pore complex protein Nup153
Molecular weight formula_weight	2213.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

TNNSPSGVFTFGANSSTPAASAQ

Entity 3 Entity 3 non-polymer

Description description	2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID
Molecular weight formula_weight	332.3 kDa
Source method src_method	syn
Copy count entity_count	1

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5tsvA01
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	5tsvA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	30 — Retrovirus capsid C-terminal domain

Domain ID domain_id	5tsvB01
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	5tsvB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	30 — Retrovirus capsid C-terminal domain

▶

Unit-cell length a length_a	151.924 Å
Unit-cell length b length_b	151.924 Å
Unit-cell length c length_c	69.646 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	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.502 Å
Low-resolution limit resolution_low	47.824 Å
R factor r_factor	0.2082
R_work r_work	0.2035
R_free r_free	0.2512

HIV-1 CA hexamer with NUP153 peptide - R3 crystal form

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

HIV-1 CA protein

State in the Current Structure

Other States of the Same Protein in the Database

Nuclear pore complex protein Nup153

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

5tsv__assembly_1__model_1

5tsv__assembly_1__model_1 | I(q)

5tsv__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

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

HIV-1 CA hexamer with NUP153 peptide - R3 crystal form

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

HIV-1 CA 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

Nuclear pore complex protein Nup153

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

5tsv__assembly_1__model_1

5tsv__assembly_1__model_1 | I(q)

5tsv__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

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)