8enh

Cross-reactive 3180 TCR recognition of HLA-B*35:01-NP7 epitope from 2002 H3N2 influenza strain

Method: X-RAY DIFFRACTION Dmax: 206.9 Å Quality: GOOD

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Nucleoprotein NP7 epitope × 1 3180 TCR alpha chain × 1 3180 TCR alpha chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;297 K;PEG, ACETATE Resolution 2.50 Å R-free 0.230
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Nucleoprotein NP7 epitope × 1 3180 TCR alpha chain × 1 3180 TCR alpha chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;297 K;PEG, ACETATE Resolution 2.50 Å R-free 0.230
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain K; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Nucleoprotein NP7 epitope × 1 3180 TCR alpha chain × 1 3180 TCR alpha chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;297 K;PEG, ACETATE Resolution 2.50 Å R-free 0.230
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain P; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) Nucleoprotein NP7 epitope × 1 3180 TCR alpha chain × 1 3180 TCR alpha chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;297 K;PEG, ACETATE Resolution 2.50 Å R-free 0.230

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 16 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 Author chain F; PDBConstruct 1–276; UniProt 25–300 Author chain K; PDBConstruct 1–276; UniProt 25–300 Author chain P; 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (F4NBT2) Nucleoprotein NP7 epitope × 1 3180 TCR alpha chain × 1 3180 TCR alpha chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;297 K;PEG, ACETATE Resolution 2.50 Å R-free 0.230
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (F4NBT2) Nucleoprotein NP7 epitope × 1 3180 TCR alpha chain × 1 3180 TCR alpha chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;297 K;PEG, ACETATE Resolution 2.50 Å R-free 0.230
3 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain L; UniProt 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (F4NBT2) Nucleoprotein NP7 epitope × 1 3180 TCR alpha chain × 1 3180 TCR alpha chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;297 K;PEG, ACETATE Resolution 2.50 Å R-free 0.230
4 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain Q; UniProt 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (F4NBT2) Nucleoprotein NP7 epitope × 1 3180 TCR alpha chain × 1 3180 TCR alpha chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;297 K;PEG, ACETATE Resolution 2.50 Å R-free 0.230

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 1995 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 G; PDBConstruct 2–100; UniProt 21–119 Author chain L; PDBConstruct 2–100; UniProt 21–119 Author chain Q; PDBConstruct 2–100; UniProt 21–119

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 8enh

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8enh
Deposition date deposition_date2022-09-30
Structure title titleCross-reactive 3180 TCR recognition of HLA-B*35:01-NP7 epitope from 2002 H3N2 influenza strain
Keywords keywordsHLA B*3501, NP418 EPITOPE, T CELL IMMUNITY, GLYCOPROTEIN, HOST-VIRUS INTERACTION, IMMUNE RESPONSE, 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_guinier59.51
Radius of gyration Rg (electron density) rg_electron59.55
Forward intensity I(0) i02122970000.00
Molecular weight molecular_weight374920.0 kDa
Excluded volume excluded_volume463830 ų
Envelope volume envelope_volume717420 ų
Hydration-shell volume shell_volume102800 ų
Envelope diameter envelope_diameter229.2
Shell Rg shell_rg59.09
Envelope Rg envelope_rg58.38
Shape Rg shape_rg59.57
Total Rg total_rg59.50
Total atoms total_atoms26439
Residues n_residues3298
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 dmax206.9
Rg (real space) rg_real59.70
Rg uncertainty (real space) rg_real_error1.93
I(0) (real space) i0_real2.1230e+09
I(0) uncertainty (real space) i0_real_error4.5150e+07
Rg (reciprocal space) rg_reciprocal59.33
I(0) (reciprocal space) i0_reciprocal2122000000.0000
Solution quality estimate total_estimate0.8672
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary63.6
Skewness Skewness skewness0.407
Kurtosis Kurtosis kurtosis-0.276
Angular range angular_range— – 0.1300 −1
Current regularization parameter α current_alpha0.0011
Highest regularization parameter α highest_alpha132100000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.742

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)