9k2u

Crystal structure of HLA-C*1202 in complex with IY11V9A peptide

Method: X-RAY DIFFRACTION Dmax: 76.0 Å Quality: EXCELLENT

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

MHC class I antigen

Homo sapiens

UniProt A0A165EYK7

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 26–300 Not recorded Beta-2-microglobulin × 1 (P61769) peptide from p51 RT × 1 (O89290) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2M Sodium bromide, 20% (w/v) PEG 3350 Resolution 2.10 Å R-free 0.247

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 A0A165EYK7_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–275; UniProt 26–300

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 MHC class I antigen × 1 (A0A165EYK7) peptide from p51 RT × 1 (O89290) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2M Sodium bromide, 20% (w/v) PEG 3350 Resolution 2.10 Å R-free 0.247

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

peptide from p51 RT

OrganismNot specified

UniProt O89290

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 891–901 Not recorded MHC class I antigen × 1 (A0A165EYK7) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2M Sodium bromide, 20% (w/v) PEG 3350 Resolution 2.10 Å R-free 0.247

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 POL_HV193
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–11; UniProt 891–901

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 9k2u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9k2u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9k2u
Deposition date deposition_date2024-10-18
最后修订 last_revision2025-09-17
Structure title titleCrystal structure of HLA-C*1202 in complex with IY11V9A peptide
Keywords keywordsCD8+ T cells, HIV-1, escape mutant, KIR2DL2, TCR, HLA, 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_electron22.91
Forward intensity I(0) i035692700.00
Molecular weight molecular_weight44384.0 kDa
Excluded volume excluded_volume54733 ų
Envelope volume envelope_volume66868 ų
Hydration-shell volume shell_volume24476 ų
Envelope diameter envelope_diameter79.8
Shell Rg shell_rg29.67
Envelope Rg envelope_rg22.99
Shape Rg shape_rg22.89
Total Rg total_rg23.75
Total atoms total_atoms3140
Residues n_residues380
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 dmax76.0
Rg (real space) rg_real24.02
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real3.5690e+07
I(0) uncertainty (real space) i0_real_error4.6100e+05
Rg (reciprocal space) rg_reciprocal24.04
I(0) (reciprocal space) i0_reciprocal35690000.0000
Solution quality estimate total_estimate0.9084
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.5
Skewness Skewness skewness0.257
Kurtosis Kurtosis kurtosis-0.466
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7699000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.987

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)