7s8q

Crystal Structure of HLA A*1101 in complex with KTNGNAFIGK, an 10-mer epitope from Influenza B

Method: X-RAY DIFFRACTION Dmax: 106.1 Å Quality: GOOD

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

HLA class I histocompatibility antigen, A alpha chain

Homo sapiens

UniProt U5YJK1

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 25–302 Not recorded Beta-2-microglobulin × 1 (P61769) Nucleoprotein peptide KTNGNAFIGK × 1 (P04666) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;20% PEG 3350, 0.1M BisTris pH 6.5 Resolution 2.08 Å R-free 0.217
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–302 Not recorded Beta-2-microglobulin × 1 (P61769) Nucleoprotein peptide KTNGNAFIGK × 1 (P04666) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;20% PEG 3350, 0.1M BisTris pH 6.5 Resolution 2.08 Å R-free 0.217

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 U5YJK1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–278; UniProt 25–302 Author chain D; PDBConstruct 1–278; UniProt 25–302

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 (U5YJK1) Nucleoprotein peptide KTNGNAFIGK × 1 (P04666) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;20% PEG 3350, 0.1M BisTris pH 6.5 Resolution 2.08 Å R-free 0.217
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 (U5YJK1) Nucleoprotein peptide KTNGNAFIGK × 1 (P04666) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;20% PEG 3350, 0.1M BisTris pH 6.5 Resolution 2.08 Å R-free 0.217

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 KTNGNAFIGK

OrganismNot specified

UniProt P04666

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 511–520 Fragment:UNP residues 511-520 HLA class I histocompatibility antigen, A alpha chain × 1 (U5YJK1) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;20% PEG 3350, 0.1M BisTris pH 6.5 Resolution 2.08 Å R-free 0.217
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 511–520 Fragment:UNP residues 511-520 HLA class I histocompatibility antigen, A alpha chain × 1 (U5YJK1) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;20% PEG 3350, 0.1M BisTris pH 6.5 Resolution 2.08 Å R-free 0.217

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_INBSI
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–10; UniProt 511–520 Author chain F; PDBConstruct 1–10; UniProt 511–520

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 7s8q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7s8q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7s8q
Deposition date deposition_date2021-09-19
Structure title titleCrystal Structure of HLA A*1101 in complex with KTNGNAFIGK, an 10-mer epitope from Influenza B
Keywords keywordsHLA A*1101, influenza B, 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_guinier32.42
Radius of gyration Rg (electron density) rg_electron31.57
Forward intensity I(0) i0137812000.00
Molecular weight molecular_weight89265.0 kDa
Excluded volume excluded_volume109850 ų
Envelope volume envelope_volume143500 ų
Hydration-shell volume shell_volume38327 ų
Envelope diameter envelope_diameter110.5
Shell Rg shell_rg38.11
Envelope Rg envelope_rg31.19
Shape Rg shape_rg31.55
Total Rg total_rg32.16
Total atoms total_atoms6301
Residues n_residues769
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 dmax106.1
Rg (real space) rg_real32.36
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real1.3780e+08
I(0) uncertainty (real space) i0_real_error2.1400e+06
Rg (reciprocal space) rg_reciprocal32.39
I(0) (reciprocal space) i0_reciprocal137800000.0000
Solution quality estimate total_estimate0.8959
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.0
Skewness Skewness skewness0.257
Kurtosis Kurtosis kurtosis-0.435
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13700000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.898

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id7s8qA01
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_id7s8qA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7s8qD01
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_id7s8qD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)