9j4v

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

Method: X-RAY DIFFRACTION Dmax: 135.2 Å Quality: REASONABLE

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

HLA class I histocompatibility antigen, B alpha chain

Homo sapiens

UniProt P01889

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 25–299 Not recorded Beta-2-microglobulin × 1 (P61769) Nucleoprotein × 1 (P0DTC9) P6G HEXAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.1 HEPES (pH 7.5), 0.2 M ammonium acetate, and 24% (w/v) PEG 3350 Resolution 1.98 Å R-free 0.243
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 25–299 Not recorded Beta-2-microglobulin × 1 (P61769) Nucleoprotein × 1 (P0DTC9) PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.1 HEPES (pH 7.5), 0.2 M ammonium acetate, and 24% (w/v) PEG 3350 Resolution 1.98 Å R-free 0.243

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.

35 other PDB entries and 52 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HLAB_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–276; UniProt 25–299 Author chain C; 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, B alpha chain × 1 (P01889) Nucleoprotein × 1 (P0DTC9) P6G HEXAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.1 HEPES (pH 7.5), 0.2 M ammonium acetate, and 24% (w/v) PEG 3350 Resolution 1.98 Å R-free 0.243
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, B alpha chain × 1 (P01889) Nucleoprotein × 1 (P0DTC9) PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.1 HEPES (pH 7.5), 0.2 M ammonium acetate, and 24% (w/v) PEG 3350 Resolution 1.98 Å R-free 0.243

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 D; 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 105–113 Not recorded HLA class I histocompatibility antigen, B alpha chain × 1 (P01889) Beta-2-microglobulin × 1 (P61769) P6G HEXAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.1 HEPES (pH 7.5), 0.2 M ammonium acetate, and 24% (w/v) PEG 3350 Resolution 1.98 Å R-free 0.243
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 105–113 Not recorded HLA class I histocompatibility antigen, B alpha chain × 1 (P01889) Beta-2-microglobulin × 1 (P61769) PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.1 HEPES (pH 7.5), 0.2 M ammonium acetate, and 24% (w/v) PEG 3350 Resolution 1.98 Å R-free 0.243

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 220 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NCAP_SARS2
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–9; UniProt 105–113 Author chain F; PDBConstruct 1–9; UniProt 105–113

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 9j4v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9j4v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9j4v
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 keywordsHLA-B7 SARS-CoV-2, Nuleocapside, 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_guinier35.83
Radius of gyration Rg (electron density) rg_electron36.02
Forward intensity I(0) i0135823000.00
Molecular weight molecular_weight89853.0 kDa
Excluded volume excluded_volume110630 ų
Envelope volume envelope_volume146480 ų
Hydration-shell volume shell_volume37145 ų
Envelope diameter envelope_diameter142.7
Shell Rg shell_rg37.95
Envelope Rg envelope_rg36.62
Shape Rg shape_rg35.99
Total Rg total_rg36.25
Total atoms total_atoms6354
Residues n_residues768
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 dmax135.2
Rg (real space) rg_real36.38
Rg uncertainty (real space) rg_real_error1.65
I(0) (real space) i0_real1.3580e+08
I(0) uncertainty (real space) i0_real_error2.8790e+06
Rg (reciprocal space) rg_reciprocal36.04
I(0) (reciprocal space) i0_reciprocal135800000.0000
Solution quality estimate total_estimate0.7349
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.8
Skewness Skewness skewness0.732
Kurtosis Kurtosis kurtosis0.103
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17580000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.449; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.470; Smooth: 0.735

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)