SAXSdb — 8vc0

▼

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

Capsid protein p24

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	;N-[(1S)-1-{(3M)-3-{4-chloro-3-[(cyclopropanesulfonyl)amino]-1-(2,2-difluoroethyl)-1H-indazol-7-yl}-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl}-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-3-(difluoromethyl)-5,5-difluoro-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide ; × 5	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 5	;N-[(1S)-1-{(3M)-3-{4-chloro-3-[(cyclopropanesulfonyl)amino]-1-(2,2-difluoroethyl)-1H-indazol-7-yl}-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl}-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-3-(difluoromethyl)-5,5-difluoro-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide ; × 5	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

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	8vc0
Deposition date deposition_date	2023-12-13
Last revision last_revision	2025-03-19
Structure title title	HIV-1 CA crosslinked pentamer in complex with GS-CA1
Keywords keywords	pentamer, capsid, HIV, 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.

8vc0__assembly_1__model_1

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

Download this curve (.dat)

8vc0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8vc0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.74 Å
Rg (electron density)	31.54 Å
Total Rg	32.08 Å
Atom count	13945
Residues	992
Excluded volume	128860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8vc0__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8vc0__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Capsid protein p24
Molecular weight formula_weight	25476.3 kDa
Mutation mutation	N21C, A22C, W184A, M185A
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	28350

PIVQNLQGQMVHQAISPRTLCCWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

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 non-polymer

Description description	;N-[(1S)-1-{(3M)-3-{4-chloro-3-[(cyclopropanesulfonyl)amino]-1-(2,2-difluoroethyl)-1H-indazol-7-yl}-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl}-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-3-(difluoromethyl)-5,5-difluoro-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide ;
Molecular weight formula_weight	958.3 kDa
Source method src_method	syn
Copy count entity_count	10

▶

Unit-cell length a length_a	137.403 Å
Unit-cell length b length_b	149.456 Å
Unit-cell length c length_c	157.109 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	40

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	3.460 Å
Low-resolution limit resolution_low	42.180 Å
R factor r_factor	0.2601
R_work r_work	0.2572
R_free r_free	0.3151

HIV-1 CA crosslinked pentamer in complex with GS-CA1

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

8vc0__assembly_1__model_1

8vc0__assembly_1__model_1 | I(q)

8vc0__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

7. Citations (1)

HIV-1 CA crosslinked pentamer in complex with GS-CA1

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

8vc0__assembly_1__model_1

8vc0__assembly_1__model_1 | I(q)

8vc0__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

7. Citations (1)