8emk

Crystal structure of HLA-B*35:01-NP3 epitope from 1957 H2N2 influenza strain

Method: X-RAY DIFFRACTION Dmax: 75.1 Å Quality: EXCELLENT

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

MHC class I antigen

Homo sapiens

UniProt F4NBT2

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 Not recorded Beta-2-microglobulin × 1 (P61769) Nucleoprotein NP3 epitope × 1 (P26072) NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;297 K;PEG, NA ACETATE Resolution 1.67 Å R-free 0.206

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.

9 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F4NBT2_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 Fragment:UNP residues 21-119 MHC class I antigen × 1 (F4NBT2) Nucleoprotein NP3 epitope × 1 (P26072) NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;297 K;PEG, NA ACETATE Resolution 1.67 Å R-free 0.206

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

Nucleoprotein NP3 epitope

OrganismNot specified

UniProt P26072

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 418–426 Fragment:residues 418-426 MHC class I antigen × 1 (F4NBT2) Beta-2-microglobulin × 1 (P61769) NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;297 K;PEG, NA ACETATE Resolution 1.67 Å R-free 0.206

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_I57A5
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 418–426

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 8emk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8emk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8emk
Deposition date deposition_date2022-09-27
Structure title titleCrystal structure of HLA-B*35:01-NP3 epitope from 1957 H2N2 influenza strain
Keywords keywordsHLA B*3501, NP418 EPITOPE, INFLUENZA, INFLUENZA A, T CELL IMMUNITY, HOST-VIRUS INTERACTION, 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_guinier24.02
Radius of gyration Rg (electron density) rg_electron22.88
Forward intensity I(0) i035852400.00
Molecular weight molecular_weight44727.0 kDa
Excluded volume excluded_volume55279 ų
Envelope volume envelope_volume67674 ų
Hydration-shell volume shell_volume24737 ų
Envelope diameter envelope_diameter77.5
Shell Rg shell_rg29.76
Envelope Rg envelope_rg22.97
Shape Rg shape_rg22.86
Total Rg total_rg23.73
Total atoms total_atoms3159
Residues n_residues384
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 dmax75.1
Rg (real space) rg_real23.95
Rg uncertainty (real space) rg_real_error0.48
I(0) (real space) i0_real3.5850e+07
I(0) uncertainty (real space) i0_real_error4.8100e+05
Rg (reciprocal space) rg_reciprocal23.97
I(0) (reciprocal space) i0_reciprocal35850000.0000
Solution quality estimate total_estimate0.9112
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.3
Skewness Skewness skewness0.238
Kurtosis Kurtosis kurtosis-0.482
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8480000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)