4u1n

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

Method: X-RAY DIFFRACTION Dmax: 75.3 Å Quality: EXCELLENT

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

HLA class I histocompatibility antigen, B-42 alpha chain

Homo sapiens

UniProt P30480

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 25–301 Not recorded Beta-2-microglobulin × 1 (P61769) Protein Nef × 1 (Q90VG9) EDO 1,2-ETHANEDIOL × 12 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;291 K;10% PEG 6000, 10mM magnesium chloride Resolution 1.77 Å R-free 0.199

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 1B42_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–278; UniProt 25–301

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-42 alpha chain × 1 (P30480) Protein Nef × 1 (Q90VG9) EDO 1,2-ETHANEDIOL × 12 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;291 K;10% PEG 6000, 10mM magnesium chloride Resolution 1.77 Å R-free 0.199

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 1998 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

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:RESIDUES 69-77 HLA class I histocompatibility antigen, B-42 alpha chain × 1 (P30480) Beta-2-microglobulin × 1 (P61769) EDO 1,2-ETHANEDIOL × 12 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;291 K;10% PEG 6000, 10mM magnesium chloride Resolution 1.77 Å R-free 0.199

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 5 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

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 4u1n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4u1n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4u1n
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_guinier24.10
Radius of gyration Rg (electron density) rg_electron22.97
Forward intensity I(0) i038851900.00
Molecular weight molecular_weight45954.0 kDa
Excluded volume excluded_volume56573 ų
Envelope volume envelope_volume68277 ų
Hydration-shell volume shell_volume24830 ų
Envelope diameter envelope_diameter79.5
Shell Rg shell_rg29.90
Envelope Rg envelope_rg23.10
Shape Rg shape_rg22.96
Total Rg total_rg23.80
Total atoms total_atoms3239
Residues n_residues387
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 dmax75.3
Rg (real space) rg_real24.04
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real3.8850e+07
I(0) uncertainty (real space) i0_real_error4.3970e+05
Rg (reciprocal space) rg_reciprocal24.06
I(0) (reciprocal space) i0_reciprocal38850000.0000
Solution quality estimate total_estimate0.9105
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.4
Skewness Skewness skewness0.255
Kurtosis Kurtosis kurtosis-0.466
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10560000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.992

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id4u1nA01
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_id4u1nA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4u1nB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)