SAXSdb — 5l93

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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 (isolate NY5)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 18	No other associated polymer	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 1–224； UniProt 148–371 Author chain B； PDBConstruct 1–224； UniProt 148–371 Author chain C； PDBConstruct 1–224； UniProt 148–371

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	5l93
Deposition date deposition_date	2016-06-09
Structure title title	An atomic model of HIV-1 CA-SP1 reveals structures regulating assembly and maturation
Keywords keywords	HIV-1 capsid SP1, 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.

5l93__assembly_1__model_1

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

Download this curve (.dat)

5l93__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5l93__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.78 Å
Rg (electron density)	55.06 Å
Total Rg	55.27 Å
Atom count	31212
Residues	4032
Excluded volume	555760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5l93__assembly_1__model_1`	octadecameric （18）	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 (1)

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5l93A01
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	5l93A02
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	5l93B01
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	5l93B02
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	5l93C01
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	5l93C02
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

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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	1

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

Resolution resolution	3.900 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	128733

Description description	Capsid protein p24
Molecular weight formula_weight	24789.4 kDa
Source method src_method	man
Copy count entity_count	3

An atomic model of HIV-1 CA-SP1 reveals structures regulating assembly and maturation

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

Capsid protein p24

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

5l93__assembly_1__model_1

5l93__assembly_1__model_1 | I(q)

5l93__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5202

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

An atomic model of HIV-1 CA-SP1 reveals structures regulating assembly and maturation

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

Capsid protein p24

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

5l93__assembly_1__model_1

5l93__assembly_1__model_1 | I(q)

5l93__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)