7wt5

Crystal structure of HLA-A*2450 complexed with 8-mer model peptide

Method: X-RAY DIFFRACTION Dmax: 121.6 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt A0A109QAI7

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 24–300 Not recorded Beta-2-microglobulin × 1 (P61769) 8-mer model peptide × 1 ZN ZINC ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 35 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;277 K;100mM Tris, 20 % PEG 8000 Resolution 2.10 Å R-free 0.228
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 24–300 Not recorded Beta-2-microglobulin × 1 (P61769) 8-mer model peptide × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;277 K;100mM Tris, 20 % PEG 8000 Resolution 2.10 Å R-free 0.228

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 A0A109QAI7_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–277; UniProt 24–300 Author chain D; PDBConstruct 1–277; UniProt 24–300

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 20–119 Not recorded MHC class I antigen × 1 (A0A109QAI7) 8-mer model peptide × 1 ZN ZINC ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 35 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;277 K;100mM Tris, 20 % PEG 8000 Resolution 2.10 Å R-free 0.228
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 20–119 Not recorded MHC class I antigen × 1 (A0A109QAI7) 8-mer model peptide × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;277 K;100mM Tris, 20 % PEG 8000 Resolution 2.10 Å R-free 0.228

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 1–100; UniProt 20–119 Author chain E; PDBConstruct 1–100; UniProt 20–119

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 7wt5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7wt5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7wt5
Deposition date deposition_date2022-02-03
Structure title titleCrystal structure of HLA-A*2450 complexed with 8-mer model peptide
Keywords keywordsMHC class I, antigen presentation, 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_guinier36.29
Radius of gyration Rg (electron density) rg_electron36.00
Forward intensity I(0) i0129259000.00
Molecular weight molecular_weight88113.0 kDa
Excluded volume excluded_volume108820 ų
Envelope volume envelope_volume150250 ų
Hydration-shell volume shell_volume35899 ų
Envelope diameter envelope_diameter129.6
Shell Rg shell_rg40.82
Envelope Rg envelope_rg35.54
Shape Rg shape_rg36.00
Total Rg total_rg36.35
Total atoms total_atoms6196
Residues n_residues733
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 dmax121.6
Rg (real space) rg_real36.49
Rg uncertainty (real space) rg_real_error1.34
I(0) (real space) i0_real1.2930e+08
I(0) uncertainty (real space) i0_real_error2.5110e+06
Rg (reciprocal space) rg_reciprocal36.37
I(0) (reciprocal space) i0_reciprocal129200000.0000
Solution quality estimate total_estimate0.8669
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.2
Skewness Skewness skewness0.393
Kurtosis Kurtosis kurtosis-0.520
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13460000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.831; Smooth: 0.811

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7wt5A01
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_id7wt5A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7wt5D01
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_id7wt5D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)