7um2

SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by HLA-A*02:01

Method: X-RAY DIFFRACTION Dmax: 76.0 Å Quality: EXCELLENT

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

HLA class I antigen

Homo sapiens

UniProt Q53Z42

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 1–365 Not recorded Beta-2-microglobulin × 1 (P61769) SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) × 1 ZN ZINC ION × 1 CD CADMIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;14% P3350; 0.1M NaFlu; 2% EG; 1 mM CdCl2 Resolution 1.63 Å R-free 0.195

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.

14 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q53Z42_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–365; UniProt 1–365

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 HLA class I antigen × 1 (Q53Z42) SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) × 1 ZN ZINC ION × 1 CD CADMIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;14% P3350; 0.1M NaFlu; 2% EG; 1 mM CdCl2 Resolution 1.63 Å R-free 0.195

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

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 7um2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7um2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7um2
Deposition date deposition_date2022-04-06
Structure title titleSARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by HLA-A*02:01
Keywords keywordshuman leukocyte antigen, major histocompatibility complex, HLA-A2, HLA-A*02:01, SARS-CoV-2, Spike, 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_guinier24.32
Radius of gyration Rg (electron density) rg_electron23.07
Forward intensity I(0) i037029400.00
Molecular weight molecular_weight45043.0 kDa
Excluded volume excluded_volume55446 ų
Envelope volume envelope_volume68007 ų
Hydration-shell volume shell_volume24667 ų
Envelope diameter envelope_diameter79.0
Shell Rg shell_rg29.82
Envelope Rg envelope_rg23.13
Shape Rg shape_rg23.00
Total Rg total_rg24.07
Total atoms total_atoms3171
Residues n_residues385
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 dmax76.0
Rg (real space) rg_real24.26
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real3.7030e+07
I(0) uncertainty (real space) i0_real_error4.9820e+05
Rg (reciprocal space) rg_reciprocal24.28
I(0) (reciprocal space) i0_reciprocal37030000.0000
Solution quality estimate total_estimate0.9106
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.2
Skewness Skewness skewness0.255
Kurtosis Kurtosis kurtosis-0.461
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8606000.0000
Real-space data points n_real_points64
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: 0.996; Smooth: 0.993

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)