7pb2

Crystal structure of JDI TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide (VVVGADGVGK)

Method: X-RAY DIFFRACTION Dmax: 144.5 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt A0A583ZB34

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) KRAS G12D peptide (VVVGADGVGK) × 1 (P01111) TCR alpha × 1 TCR beta × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 20 % PEG 8000 Resolution 3.41 Å R-free 0.254
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 25–299 Not recorded Beta-2-microglobulin × 1 (P61769) KRAS G12D peptide (VVVGADGVGK) × 1 (P01111) TCR alpha × 1 TCR beta × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 20 % PEG 8000 Resolution 3.41 Å R-free 0.254

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.

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

View Construct and Data Evidence
UniProt name A0A583ZB34_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–275; UniProt 25–299 Author chain F; PDBConstruct 1–275; 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 (A0A583ZB34) KRAS G12D peptide (VVVGADGVGK) × 1 (P01111) TCR alpha × 1 TCR beta × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 20 % PEG 8000 Resolution 3.41 Å R-free 0.254
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 21–119 Not recorded MHC class I antigen × 1 (A0A583ZB34) KRAS G12D peptide (VVVGADGVGK) × 1 (P01111) TCR alpha × 1 TCR beta × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 20 % PEG 8000 Resolution 3.41 Å R-free 0.254

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 G; PDBConstruct 2–100; UniProt 21–119

KRAS G12D peptide (VVVGADGVGK)

OrganismNot specified

UniProt P01111

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 7–16 Not recorded MHC class I antigen × 1 (A0A583ZB34) Beta-2-microglobulin × 1 (P61769) TCR alpha × 1 TCR beta × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 20 % PEG 8000 Resolution 3.41 Å R-free 0.254
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain H; UniProt 7–16 Not recorded MHC class I antigen × 1 (A0A583ZB34) Beta-2-microglobulin × 1 (P61769) TCR alpha × 1 TCR beta × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M ammonium sulfate, 0.1 M Tris pH 8.5, 20 % PEG 8000 Resolution 3.41 Å R-free 0.254

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.

33 other PDB entries and 61 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RASN_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–10; UniProt 7–16 Author chain H; PDBConstruct 1–10; UniProt 7–16

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 7pb2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7pb2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7pb2
Deposition date deposition_date2021-07-30
Structure title titleCrystal structure of JDI TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide (VVVGADGVGK)
Keywords keywordsHLA, T cell receptor, KRAS, 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_guinier42.62
Radius of gyration Rg (electron density) rg_electron42.26
Forward intensity I(0) i0523458000.00
Molecular weight molecular_weight181310.0 kDa
Excluded volume excluded_volume224100 ų
Envelope volume envelope_volume318920 ų
Hydration-shell volume shell_volume64214 ų
Envelope diameter envelope_diameter154.1
Shell Rg shell_rg46.19
Envelope Rg envelope_rg42.04
Shape Rg shape_rg42.26
Total Rg total_rg42.47
Total atoms total_atoms12801
Residues n_residues1593
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 dmax144.5
Rg (real space) rg_real42.66
Rg uncertainty (real space) rg_real_error1.33
I(0) (real space) i0_real5.2350e+08
I(0) uncertainty (real space) i0_real_error1.0810e+07
Rg (reciprocal space) rg_reciprocal42.62
I(0) (reciprocal space) i0_reciprocal523400000.0000
Solution quality estimate total_estimate0.8713
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.8
Skewness Skewness skewness0.405
Kurtosis Kurtosis kurtosis-0.185
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha37500000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.808

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id7pb2A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id7pb2A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7pb2D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7pb2F01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id7pb2F02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7pb2I01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)