4u1l

HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes

Method: X-RAY DIFFRACTION Dmax: 131.1 Å Quality: GOOD

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

HLA class I histocompatibility antigen, B-81 alpha chain

Homo sapiens

UniProt Q31610

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:UNP residues 25-300 Beta-2-microglobulin × 1 (P61769) Protein Nef × 1 (Q90VG9) GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 6 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;291 K;0.1 M TRIS pH 8.0, 15% PEG 4000 and 15% glycerol Resolution 2.06 Å R-free 0.209
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: Trimeric(3) Consistent with protein copy count Chain D; UniProt 25–300 Fragment:UNP residues 25-300 Beta-2-microglobulin × 1 (P61769) Protein Nef × 1 (Q90VG9) GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;291 K;0.1 M TRIS pH 8.0, 15% PEG 4000 and 15% glycerol Resolution 2.06 Å R-free 0.209

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.

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

View Construct and Data Evidence
UniProt name 1B81_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 Fragment:UNP residues 21-119 HLA class I histocompatibility antigen, B-81 alpha chain × 1 (Q31610) Protein Nef × 1 (Q90VG9) GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 6 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;291 K;0.1 M TRIS pH 8.0, 15% PEG 4000 and 15% glycerol Resolution 2.06 Å R-free 0.209
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: Trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Fragment:UNP residues 21-119 HLA class I histocompatibility antigen, B-81 alpha chain × 1 (Q31610) Protein Nef × 1 (Q90VG9) GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;291 K;0.1 M TRIS pH 8.0, 15% PEG 4000 and 15% glycerol Resolution 2.06 Å R-free 0.209

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

Protein Nef

OrganismNot specified

UniProt Q90VG9

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 69–77 Fragment:UNP residues 69-77 HLA class I histocompatibility antigen, B-81 alpha chain × 1 (Q31610) Beta-2-microglobulin × 1 (P61769) GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 6 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;291 K;0.1 M TRIS pH 8.0, 15% PEG 4000 and 15% glycerol Resolution 2.06 Å R-free 0.209
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: Trimeric(3) Consistent with protein copy count Chain F; UniProt 69–77 Fragment:UNP residues 69-77 HLA class I histocompatibility antigen, B-81 alpha chain × 1 (Q31610) Beta-2-microglobulin × 1 (P61769) GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;291 K;0.1 M TRIS pH 8.0, 15% PEG 4000 and 15% glycerol Resolution 2.06 Å R-free 0.209

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.

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

View Construct and Data Evidence
UniProt name Q90VG9_9HIV1
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 69–77 Author chain F; PDBConstruct 1–9; UniProt 69–77

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 4u1l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4u1l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4u1l
Deposition date deposition_date2014-07-15
Structure title titleHLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes
Keywords keywordsImmunoglobulin, HLA, HIV, 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_guinier35.94
Radius of gyration Rg (electron density) rg_electron35.84
Forward intensity I(0) i0142303000.00
Molecular weight molecular_weight91508.0 kDa
Excluded volume excluded_volume112700 ų
Envelope volume envelope_volume152990 ų
Hydration-shell volume shell_volume37196 ų
Envelope diameter envelope_diameter140.9
Shell Rg shell_rg39.65
Envelope Rg envelope_rg36.38
Shape Rg shape_rg35.84
Total Rg total_rg36.09
Total atoms total_atoms6448
Residues n_residues772
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 dmax131.1
Rg (real space) rg_real36.29
Rg uncertainty (real space) rg_real_error1.57
I(0) (real space) i0_real1.4230e+08
I(0) uncertainty (real space) i0_real_error2.6210e+06
Rg (reciprocal space) rg_reciprocal36.07
I(0) (reciprocal space) i0_reciprocal142300000.0000
Solution quality estimate total_estimate0.8227
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.8
Skewness Skewness skewness0.597
Kurtosis Kurtosis kurtosis0.001
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14040000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.694; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.710; Smooth: 0.900

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id4u1lA01
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_id4u1lA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4u1lB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4u1lD01
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_id4u1lD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4u1lE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)