3w39

Crystal structure of HLA-B*5201 in complexed with HIV immunodominant epitope (TAFTIPSI)

Method: X-RAY DIFFRACTION Dmax: 102.2 Å Quality: GOOD

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

HLA class I histocompatibility antigen, B-52 alpha chain

Homo sapiens

UniProt P30490

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 25–300 Fragment:EXTRACELLULAR RESIDUES 25-300 Beta-2-microglobulin × 1 (P61769) peptid from Gag-Pol polyprotein × 1 (P12499) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.10 Å R-free 0.347
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–300 Fragment:EXTRACELLULAR RESIDUES 25-300 Beta-2-microglobulin × 1 (P61769) peptid from Gag-Pol polyprotein × 1 (P12499) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.10 Å R-free 0.347

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name 1B52_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–277; UniProt 25–300 Author chain D; PDBConstruct 2–277; UniProt 25–300

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, B-52 alpha chain × 1 (P30490) peptid from Gag-Pol polyprotein × 1 (P12499) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.10 Å R-free 0.347
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, B-52 alpha chain × 1 (P30490) peptid from Gag-Pol polyprotein × 1 (P12499) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.10 Å R-free 0.347

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

peptid from Gag-Pol polyprotein

OrganismNot specified

UniProt P12499

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 716–723 Not recorded HLA class I histocompatibility antigen, B-52 alpha chain × 1 (P30490) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.10 Å R-free 0.347
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 716–723 Not recorded HLA class I histocompatibility antigen, B-52 alpha chain × 1 (P30490) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.10 Å R-free 0.347

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.

17 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POL_HV1Z2
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–8; UniProt 716–723 Author chain F; PDBConstruct 1–8; UniProt 716–723

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 3w39

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3w39
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3w39
Deposition date deposition_date2012-12-13
Structure title titleCrystal structure of HLA-B*5201 in complexed with HIV immunodominant epitope (TAFTIPSI)
Keywords keywordsClass I Major Histocompatibility Complex, MHC, Membrane, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.67
Radius of gyration Rg (electron density) rg_electron30.88
Forward intensity I(0) i0136229000.00
Molecular weight molecular_weight89327.0 kDa
Excluded volume excluded_volume110160 ų
Envelope volume envelope_volume141770 ų
Hydration-shell volume shell_volume39051 ų
Envelope diameter envelope_diameter110.4
Shell Rg shell_rg37.43
Envelope Rg envelope_rg30.57
Shape Rg shape_rg30.86
Total Rg total_rg31.47
Total atoms total_atoms6312
Residues n_residues768
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 dmax102.2
Rg (real space) rg_real31.64
Rg uncertainty (real space) rg_real_error0.74
I(0) (real space) i0_real1.3620e+08
I(0) uncertainty (real space) i0_real_error2.0350e+06
Rg (reciprocal space) rg_reciprocal31.66
I(0) (reciprocal space) i0_reciprocal136200000.0000
Solution quality estimate total_estimate0.8963
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.8
Skewness Skewness skewness0.316
Kurtosis Kurtosis kurtosis-0.366
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15820000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.887

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3w39d1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd3w39d2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd3w39d3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id3w39A01
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_id3w39A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3w39B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3w39D01
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_id3w39D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3w39E00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)