7rk7

The complex between TIL 1383i TCR and human Class I MHC HLA-A2 with the bound Tyrosinase(369-377)(N371D) nonameric peptide

Method: X-RAY DIFFRACTION Dmax: 129.7 Å Quality: GOOD

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

HLA class I histocompatibility antigen, A alpha chain

Homo sapiens

UniProt P04439

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 Fragment:UNP residues 25-299 Beta-2-microglobulin × 1 (P61769) Tyrosinase peptide × 1 (P14679) TIL1383i (h3T) T cell receptor alpha chain × 1 TIL1383i (h3T) T cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;16% PEG 3350, 2% tacsimate, 100mM Tris (pH 8.5) Resolution 2.54 Å R-free 0.255

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.

53 other PDB entries and 78 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HLAA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; 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 Fragment:UNP residues 21-119 HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Tyrosinase peptide × 1 (P14679) TIL1383i (h3T) T cell receptor alpha chain × 1 TIL1383i (h3T) T cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;16% PEG 3350, 2% tacsimate, 100mM Tris (pH 8.5) Resolution 2.54 Å R-free 0.255

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

Tyrosinase peptide

OrganismNot specified

UniProt P14679

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 369–377 Fragment:UNP residues 369-377 Mutation:N371D HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) Beta-2-microglobulin × 1 (P61769) TIL1383i (h3T) T cell receptor alpha chain × 1 TIL1383i (h3T) T cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;16% PEG 3350, 2% tacsimate, 100mM Tris (pH 8.5) Resolution 2.54 Å R-free 0.255

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 TYRO_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 369–377

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 7rk7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7rk7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7rk7
Deposition date deposition_date2021-07-22
Structure title titleThe complex between TIL 1383i TCR and human Class I MHC HLA-A2 with the bound Tyrosinase(369-377)(N371D) nonameric peptide
Keywords keywordsTCR, Class I Major Histocompatibility Complex, HLA-A*02, 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_guinier36.03
Radius of gyration Rg (electron density) rg_electron36.16
Forward intensity I(0) i0127117000.00
Molecular weight molecular_weight88073.0 kDa
Excluded volume excluded_volume109020 ų
Envelope volume envelope_volume151520 ų
Hydration-shell volume shell_volume37170 ų
Envelope diameter envelope_diameter136.0
Shell Rg shell_rg39.31
Envelope Rg envelope_rg37.09
Shape Rg shape_rg36.14
Total Rg total_rg36.46
Total atoms total_atoms6213
Residues n_residues773
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 dmax129.7
Rg (real space) rg_real36.51
Rg uncertainty (real space) rg_real_error1.65
I(0) (real space) i0_real1.2710e+08
I(0) uncertainty (real space) i0_real_error2.4060e+06
Rg (reciprocal space) rg_reciprocal36.22
I(0) (reciprocal space) i0_reciprocal127100000.0000
Solution quality estimate total_estimate0.7794
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.4
Skewness Skewness skewness0.644
Kurtosis Kurtosis kurtosis-0.157
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17770000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.581; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.561; Smooth: 0.824

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7rk7A01
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_id7rk7D01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)