9j4u

Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors

Method: X-RAY DIFFRACTION Dmax: 130.2 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt Q8WLS4

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 25–299 Not recorded Beta-2-microglobulin × 1 (P61769) LLL epitope specific TCR APHLA × 1 LLL epitope specific TCR BETA × 1 Nucleoprotein × 1 (P0DTC9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.2 M potassium sodium tartrate tetrahydrate, and 20% (w/v) PEG 3350 Resolution 2.17 Å R-free 0.239

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.

10 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8WLS4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–276; UniProt 25–299

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 Not recorded MHC class I antigen × 1 (Q8WLS4) LLL epitope specific TCR APHLA × 1 LLL epitope specific TCR BETA × 1 Nucleoprotein × 1 (P0DTC9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.2 M potassium sodium tartrate tetrahydrate, and 20% (w/v) PEG 3350 Resolution 2.17 Å R-free 0.239

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

OrganismNot specified

UniProt P0DTC9

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 C; UniProt 222–230 Not recorded MHC class I antigen × 1 (Q8WLS4) Beta-2-microglobulin × 1 (P61769) LLL epitope specific TCR APHLA × 1 LLL epitope specific TCR BETA × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.2 M potassium sodium tartrate tetrahydrate, and 20% (w/v) PEG 3350 Resolution 2.17 Å R-free 0.239

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.

96 other PDB entries and 221 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NCAP_SARS2
Isoform
PDB entities 5
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 222–230

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 9j4u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9j4u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9j4u
Deposition date deposition_date2024-08-10
Structure title titleStructural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
Keywords keywordsTCR, T cell receptor, sars-cov-2, nuleocapside, hla-a2, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.94
Radius of gyration Rg (electron density) rg_electron37.20
Forward intensity I(0) i0139816000.00
Molecular weight molecular_weight92411.0 kDa
Excluded volume excluded_volume114270 ų
Envelope volume envelope_volume151950 ų
Hydration-shell volume shell_volume37257 ų
Envelope diameter envelope_diameter135.0
Shell Rg shell_rg39.01
Envelope Rg envelope_rg37.43
Shape Rg shape_rg37.19
Total Rg total_rg37.35
Total atoms total_atoms6525
Residues n_residues817
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 dmax130.2
Rg (real space) rg_real37.49
Rg uncertainty (real space) rg_real_error1.75
I(0) (real space) i0_real1.3980e+08
I(0) uncertainty (real space) i0_real_error2.3130e+06
Rg (reciprocal space) rg_reciprocal37.15
I(0) (reciprocal space) i0_reciprocal139800000.0000
Solution quality estimate total_estimate0.7749
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.3
Skewness Skewness skewness0.645
Kurtosis Kurtosis kurtosis-0.197
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17500000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.634; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.519; Smooth: 0.651

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)