7uc5

Crystal Structure of HLA A*0301 in complex with ILRGSVAHK, a 9-mer epitope from Influenza A

Method: X-RAY DIFFRACTION Dmax: 108.5 Å Quality: REASONABLE

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

HLA class I histocompatibility antigen, A alpha chain

Homo sapiens

UniProt P04439

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) Nucleoprotein peptide × 1 (P26079) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.6;277 K;0.2 Ammonium Sulfate, 0.1 Bis-Tris propane pH 6.5, 22% PEG 3350 Resolution 1.95 Å R-free 0.229
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–301 Not recorded Beta-2-microglobulin × 1 (P61769) Nucleoprotein peptide × 1 (P26079) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.6;277 K;0.2 Ammonium Sulfate, 0.1 Bis-Tris propane pH 6.5, 22% PEG 3350 Resolution 1.95 Å R-free 0.229

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.

53 other PDB entries and 77 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HLAA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–277; UniProt 25–301 Author chain D; PDBConstruct 1–277; 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 Fragment:UNP residues 21-119 HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Nucleoprotein peptide × 1 (P26079) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.6;277 K;0.2 Ammonium Sulfate, 0.1 Bis-Tris propane pH 6.5, 22% PEG 3350 Resolution 1.95 Å R-free 0.229
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, A alpha chain × 1 (P04439) Nucleoprotein peptide × 1 (P26079) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.6;277 K;0.2 Ammonium Sulfate, 0.1 Bis-Tris propane pH 6.5, 22% PEG 3350 Resolution 1.95 Å R-free 0.229

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

Nucleoprotein peptide

OrganismNot specified

UniProt P26079

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 265–273 Fragment:ILRGSVAHK HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Beta-2-microglobulin × 1 (P61769) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.6;277 K;0.2 Ammonium Sulfate, 0.1 Bis-Tris propane pH 6.5, 22% PEG 3350 Resolution 1.95 Å R-free 0.229
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 265–273 Fragment:ILRGSVAHK HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Beta-2-microglobulin × 1 (P61769) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.6;277 K;0.2 Ammonium Sulfate, 0.1 Bis-Tris propane pH 6.5, 22% PEG 3350 Resolution 1.95 Å R-free 0.229

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 NCAP_I46A1
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 265–273 Author chain F; PDBConstruct 1–9; UniProt 265–273

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 7uc5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7uc5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7uc5
Deposition date deposition_date2022-03-16
Structure title titleCrystal Structure of HLA A*0301 in complex with ILRGSVAHK, a 9-mer epitope from Influenza A
Keywords keywordsHLA A*0301, influenza virus, TCR, T cell, 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_guinier33.38
Radius of gyration Rg (electron density) rg_electron32.64
Forward intensity I(0) i0139669000.00
Molecular weight molecular_weight89645.0 kDa
Excluded volume excluded_volume110150 ų
Envelope volume envelope_volume146060 ų
Hydration-shell volume shell_volume37692 ų
Envelope diameter envelope_diameter115.9
Shell Rg shell_rg39.02
Envelope Rg envelope_rg32.12
Shape Rg shape_rg32.62
Total Rg total_rg33.21
Total atoms total_atoms6321
Residues n_residues770
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 dmax108.5
Rg (real space) rg_real33.37
Rg uncertainty (real space) rg_real_error0.83
I(0) (real space) i0_real1.3970e+08
I(0) uncertainty (real space) i0_real_error2.1680e+06
Rg (reciprocal space) rg_reciprocal33.38
I(0) (reciprocal space) i0_reciprocal139700000.0000
Solution quality estimate total_estimate0.6799
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.2
Skewness Skewness skewness0.298
Kurtosis Kurtosis kurtosis-0.407
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16760000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 0.078; Positv: 1.000; Valcen: 0.979; Smooth: 0.841

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7uc5A01
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_id7uc5A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7uc5D01
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_id7uc5D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)