4lnr

The structure of HLA-B*35:01 in complex with the peptide (RPQVPLRPMTY)

Method: X-RAY DIFFRACTION Dmax: 75.5 Å Quality: EXCELLENT

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

HLA class I histocompatibility antigen, B-35 alpha chain

Homo sapiens

UniProt P30685

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) Peptide from Protein Nef × 1 (Q9YYU8) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;0.1M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.00 Å R-free 0.208

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.

33 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1B35_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; 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-35 alpha chain × 1 (P30685) Peptide from Protein Nef × 1 (Q9YYU8) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;0.1M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.00 Å R-free 0.208

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 1–99; UniProt 21–119

Peptide from Protein Nef

OrganismNot specified

UniProt Q9YYU8

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 71–81 Not recorded HLA class I histocompatibility antigen, B-35 alpha chain × 1 (P30685) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;291 K;0.1M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.00 Å R-free 0.208

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.

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9YYU8_9HIV1
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–11; UniProt 71–81

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 4lnr

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4lnr
Deposition date deposition_date2013-07-12
Structure title titleThe structure of HLA-B*35:01 in complex with the peptide (RPQVPLRPMTY)
Keywords keywordsheterotrimer, ligand for T cell receptor, 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_guinier24.08
Radius of gyration Rg (electron density) rg_electron22.92
Forward intensity I(0) i036795900.00
Molecular weight molecular_weight44979.0 kDa
Excluded volume excluded_volume55513 ų
Envelope volume envelope_volume67846 ų
Hydration-shell volume shell_volume24775 ų
Envelope diameter envelope_diameter78.9
Shell Rg shell_rg29.74
Envelope Rg envelope_rg23.00
Shape Rg shape_rg22.90
Total Rg total_rg23.80
Total atoms total_atoms3178
Residues n_residues386
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 dmax75.5
Rg (real space) rg_real24.00
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real3.6800e+07
I(0) uncertainty (real space) i0_real_error4.8910e+05
Rg (reciprocal space) rg_reciprocal24.02
I(0) (reciprocal space) i0_reciprocal36800000.0000
Solution quality estimate total_estimate0.9095
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.5
Skewness Skewness skewness0.240
Kurtosis Kurtosis kurtosis-0.478
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8115000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.986

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id4lnrA01
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_id4lnrA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4lnrB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)