7lgt

HLA-B*07:02 in complex with 229E-derived coronavirus nucleocapsid peptide N75-83

Method: X-RAY DIFFRACTION Dmax: 107.5 Å Quality: GOOD

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 25–302 Not recorded Beta-2-microglobulin × 1 (P61769) Nucleoprotein peptide N75-83 × 1 (P15130) ZN ZINC ION × 7 NA SODIUM ION × 1 CL CHLORIDE ION × 8 K POTASSIUM ION × 8 BR BROMIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;18% PEG 3350, 0.2 M KI Resolution 1.97 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 25–302 Not recorded Beta-2-microglobulin × 1 (P61769) Nucleoprotein peptide N75-83 × 1 (P15130) ZN ZINC ION × 4 NA SODIUM ION × 3 CL CHLORIDE ION × 1 K POTASSIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;18% PEG 3350, 0.2 M KI Resolution 1.97 Å R-free 0.246

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 1–278; UniProt 25–302 Author chain C; PDBConstruct 1–278; UniProt 25–302

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 peptide N75-83 × 1 (P15130) ZN ZINC ION × 7 NA SODIUM ION × 1 CL CHLORIDE ION × 8 K POTASSIUM ION × 8 BR BROMIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;18% PEG 3350, 0.2 M KI Resolution 1.97 Å R-free 0.246
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 peptide N75-83 × 1 (P15130) ZN ZINC ION × 4 NA SODIUM ION × 3 CL CHLORIDE ION × 1 K POTASSIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;18% PEG 3350, 0.2 M KI Resolution 1.97 Å R-free 0.246

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 peptide N75-83

OrganismNot specified

UniProt P15130

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 F; UniProt 75–83 Not recorded HLA class I histocompatibility antigen, B alpha chain × 1 (P01889) Beta-2-microglobulin × 1 (P61769) ZN ZINC ION × 7 NA SODIUM ION × 1 CL CHLORIDE ION × 8 K POTASSIUM ION × 8 BR BROMIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;18% PEG 3350, 0.2 M KI Resolution 1.97 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 75–83 Not recorded HLA class I histocompatibility antigen, B alpha chain × 1 (P01889) Beta-2-microglobulin × 1 (P61769) ZN ZINC ION × 4 NA SODIUM ION × 3 CL CHLORIDE ION × 1 K POTASSIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;18% PEG 3350, 0.2 M KI Resolution 1.97 Å R-free 0.246

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_CVH22
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–9; UniProt 75–83 Author chain F; PDBConstruct 1–9; UniProt 75–83

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 7lgt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7lgt
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7lgt
Deposition date deposition_date2021-01-21
Structure title titleHLA-B*07:02 in complex with 229E-derived coronavirus nucleocapsid peptide N75-83
Keywords keywordsHLA-B7, 229E coronavirus, SARS-CoV-2, T cell, recognition, cross-recognition, COVID-19, 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_guinier32.79
Radius of gyration Rg (electron density) rg_electron32.05
Forward intensity I(0) i0141775000.00
Molecular weight molecular_weight91318.0 kDa
Excluded volume excluded_volume112250 ų
Envelope volume envelope_volume144890 ų
Hydration-shell volume shell_volume37971 ų
Envelope diameter envelope_diameter112.9
Shell Rg shell_rg38.37
Envelope Rg envelope_rg31.94
Shape Rg shape_rg32.04
Total Rg total_rg32.59
Total atoms total_atoms6378
Residues n_residues767
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 dmax107.5
Rg (real space) rg_real32.75
Rg uncertainty (real space) rg_real_error0.92
I(0) (real space) i0_real1.4180e+08
I(0) uncertainty (real space) i0_real_error2.1950e+06
Rg (reciprocal space) rg_reciprocal32.77
I(0) (reciprocal space) i0_reciprocal141800000.0000
Solution quality estimate total_estimate0.8959
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.1
Skewness Skewness skewness0.273
Kurtosis Kurtosis kurtosis-0.455
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15020000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.906

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

8. Citations (1)

9. Files and Curves (10)