3vxo

HLA-A24 in complex with HIV-1 Nef134-10(2F)

Method: X-RAY DIFFRACTION Dmax: 116.9 Å Quality: GOOD

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

HLA class I histocompatibility antigen, A-24 alpha chain

Homo sapiens

UniProt P05534

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 25–298 Fragment:UNP residues 25-298 Beta-2-microglobulin × 1 (P61769) 10-mer peptide from Protein Nef × 1 (Q9YYU3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG 8000, 200mM ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.61 Å R-free 0.242
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–298 Fragment:UNP residues 25-298 Beta-2-microglobulin × 1 (P61769) 10-mer peptide from Protein Nef × 1 (Q9YYU3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG 8000, 200mM ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.61 Å R-free 0.242

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.

28 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1A24_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–275; UniProt 25–298 Author chain D; PDBConstruct 2–275; UniProt 25–298

Beta-2-microglobulin

Homo sapiens

UniProt P61769

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) 10-mer peptide from Protein Nef × 1 (Q9YYU3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG 8000, 200mM ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.61 Å R-free 0.242
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) 10-mer peptide from Protein Nef × 1 (Q9YYU3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG 8000, 200mM ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.61 Å R-free 0.242

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.

1313 other PDB entries and 1997 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B2MG_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–100; UniProt 21–119 Author chain E; PDBConstruct 2–100; UniProt 21–119

10-mer peptide from Protein Nef

OrganismNot specified

UniProt Q9YYU3

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 143–152 Not recorded HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG 8000, 200mM ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.61 Å R-free 0.242
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 143–152 Not recorded HLA class I histocompatibility antigen, A-24 alpha chain × 1 (P05534) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;20% PEG 8000, 200mM ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.61 Å R-free 0.242

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.

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9YYU3_9HIV1
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–10; UniProt 143–152 Author chain F; PDBConstruct 1–10; UniProt 143–152

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 3vxo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3vxo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3vxo
Deposition date deposition_date2012-09-20
Structure title titleHLA-A24 in complex with HIV-1 Nef134-10(2F)
Keywords keywordsHIV-1, NEF, IMMUNE SYSTEM, HLA-A24, MHC CLASS I, IMMUNOGLOBURIN DOMAIN, MHC, IMMUNE ESPONSE; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.19
Radius of gyration Rg (electron density) rg_electron34.89
Forward intensity I(0) i0133506000.00
Molecular weight molecular_weight89005.0 kDa
Excluded volume excluded_volume109770 ų
Envelope volume envelope_volume148550 ų
Hydration-shell volume shell_volume37496 ų
Envelope diameter envelope_diameter120.6
Shell Rg shell_rg39.05
Envelope Rg envelope_rg34.24
Shape Rg shape_rg34.88
Total Rg total_rg35.22
Total atoms total_atoms6284
Residues n_residues766
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax116.9
Rg (real space) rg_real35.36
Rg uncertainty (real space) rg_real_error1.19
I(0) (real space) i0_real1.3350e+08
I(0) uncertainty (real space) i0_real_error2.1640e+06
Rg (reciprocal space) rg_reciprocal35.26
I(0) (reciprocal space) i0_reciprocal133500000.0000
Solution quality estimate total_estimate0.8764
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.4
Skewness Skewness skewness0.419
Kurtosis Kurtosis kurtosis-0.519
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13410000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.887

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id3vxoA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id3vxoA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3vxoB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3vxoD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id3vxoD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3vxoE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)