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9prz

HIV-1 CA hexamer from purified viral cores, C6 symmetry

Method: ELECTRON MICROSCOPY Dmax: 73.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid protein p24

Human immunodeficiency virus 1

UniProt Q73368

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 133–363 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.95 Å
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 133–363 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.95 Å
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 133–363 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.95 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9PRZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9PRY HIV-1 CA hexamer from purified viral cores, C1 symmetry Deposited 2025-07-24 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 133–363（231 aa）
Chain B 133–363（231 aa）
Chain C 133–363（231 aa）
Chain D 133–363（231 aa）
Chain E 133–363（231 aa）
Chain L 133–363（231 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9Y7J HIV-1 CA hexamer from purified viral cores bound to lenacapavir, C6 symmetry Deposited 2025-09-10 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 11 PDB declaration: 11-meric
Chain L 133–363（231 aa）
Not recorded QNG Lenacapavir × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POL_HV1B9
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 9prz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9prz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9prz
Deposition date deposition_date2025-07-24
Structure title titleHIV-1 CA hexamer from purified viral cores, C6 symmetry
Keywords keywordscapsid, native purified HIV cores, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.78 Å
Radius of gyration Rg (electron density) rg_electron22.11 Å
Forward intensity I(0) i09628960.00
Molecular weight molecular_weight23064.0 kDa
Excluded volume excluded_volume28854 ų
Envelope volume envelope_volume37039 ų
Hydration-shell volume shell_volume15263 ų
Envelope diameter envelope_diameter73.9 Å
Shell Rg shell_rg27.12 Å
Envelope Rg envelope_rg22.19 Å
Shape Rg shape_rg22.09 Å
Total Rg total_rg22.91 Å
Total atoms total_atoms1615
Residues n_residues206
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax73.9 Å
Rg (real space) rg_real22.95 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real9.6290e+06
I(0) uncertainty (real space) i0_real_error1.3030e+05
Rg (reciprocal space) rg_reciprocal22.92 Å
I(0) (reciprocal space) i0_reciprocal9629000.0000
Solution quality estimate total_estimate0.7841
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.0 Å
Skewness Skewness skewness0.422
Kurtosis Kurtosis kurtosis-0.605
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2048000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.814; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.750; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)