8yj2

N17.1.2 recognition of NRAS neoantigens

Method: X-RAY DIFFRACTION Dmax: 130.8 Å Quality: GOOD

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

human leukocyte antigen

Homo sapiens

UniProt F6IQR9

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) ILE-LEU-ASP-THR-ALA-GLY-ARG-GLU-GLU-TYR × 1 tcr beta × 1 tcr alpha × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;10mg/ml, 0.2 M NH4 citrate tribasic, 16% PEG3350, pH 7.4 Resolution 2.26 Å R-free 0.229

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F6IQR9_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 human leukocyte antigen × 1 (F6IQR9) ILE-LEU-ASP-THR-ALA-GLY-ARG-GLU-GLU-TYR × 1 tcr beta × 1 tcr alpha × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;10mg/ml, 0.2 M NH4 citrate tribasic, 16% PEG3350, pH 7.4 Resolution 2.26 Å R-free 0.229

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 8yj2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8yj2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8yj2
Deposition date deposition_date2024-02-29
最后修订 last_revision2024-12-04
Structure title titleN17.1.2 recognition of NRAS neoantigens
Keywords keywordsT cell receptor, p-MHC, 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_guinier37.23
Radius of gyration Rg (electron density) rg_electron37.39
Forward intensity I(0) i0146624000.00
Molecular weight molecular_weight94753.0 kDa
Excluded volume excluded_volume117270 ų
Envelope volume envelope_volume157970 ų
Hydration-shell volume shell_volume38410 ų
Envelope diameter envelope_diameter139.3
Shell Rg shell_rg39.29
Envelope Rg envelope_rg37.84
Shape Rg shape_rg37.40
Total Rg total_rg37.48
Total atoms total_atoms6680
Residues n_residues832
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 dmax130.8
Rg (real space) rg_real37.82
Rg uncertainty (real space) rg_real_error1.32
I(0) (real space) i0_real1.4660e+08
I(0) uncertainty (real space) i0_real_error2.6970e+06
Rg (reciprocal space) rg_reciprocal37.46
I(0) (reciprocal space) i0_reciprocal146600000.0000
Solution quality estimate total_estimate0.7816
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary
Skewness Skewness skewness0.661
Kurtosis Kurtosis kurtosis-0.170
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19510000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.627; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.713; Smooth: 0.565

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)