6uk4

Complex of T cell Receptor with HHAT Neoantigen Peptide KQWLVWLFL Presented by HLA-A206

Method: X-RAY DIFFRACTION Dmax: 111.6 Å Quality: EXCELLENT

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

MHC class I antigen

Homo sapiens

UniProt U5YJP1

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 25–299 Fragment:UNP residues 25-299 Beta-2-microglobulin × 1 (P61769) Protein-cysteine N-palmitoyltransferase HHAT × 1 (Q5VTY9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.3;277 K;0.1 M sodium citrate, pH 6.3, 7.5% PEG6000, 0.2 M lithium nitrate Resolution 2.70 Å R-free 0.252

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.

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name U5YJP1_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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 21–119 Fragment:UNP residues 21-119 MHC class I antigen × 1 (U5YJP1) Protein-cysteine N-palmitoyltransferase HHAT × 1 (Q5VTY9) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.3;277 K;0.1 M sodium citrate, pH 6.3, 7.5% PEG6000, 0.2 M lithium nitrate Resolution 2.70 Å R-free 0.252

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

Protein-cysteine N-palmitoyltransferase HHAT

OrganismNot specified

UniProt Q5VTY9

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 C; UniProt 68–76 Fragment:Neoantigen peptide (UNP residues 68-76) Mutation:L75F MHC class I antigen × 1 (U5YJP1) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.3;277 K;0.1 M sodium citrate, pH 6.3, 7.5% PEG6000, 0.2 M lithium nitrate Resolution 2.70 Å R-free 0.252

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.

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HHAT_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 68–76

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 6uk4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6uk4
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id6uk4
Deposition date deposition_date2019-10-04
Structure title titleComplex of T cell Receptor with HHAT Neoantigen Peptide KQWLVWLFL Presented by HLA-A206
Keywords keywordsNeoantigen, Peptide/MHC, IMMUNE SYSTEM, T cell receptor; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.33
Radius of gyration Rg (electron density) rg_electron35.50
Forward intensity I(0) i0150007000.00
Molecular weight molecular_weight95424.0 kDa
Excluded volume excluded_volume117990 ų
Envelope volume envelope_volume169970 ų
Hydration-shell volume shell_volume39409 ų
Envelope diameter envelope_diameter112.4
Shell Rg shell_rg43.17
Envelope Rg envelope_rg33.76
Shape Rg shape_rg35.51
Total Rg total_rg36.02
Total atoms total_atoms6728
Residues n_residues830
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 dmax111.6
Rg (real space) rg_real36.19
Rg uncertainty (real space) rg_real_error0.93
I(0) (real space) i0_real1.5000e+08
I(0) uncertainty (real space) i0_real_error2.3650e+06
Rg (reciprocal space) rg_reciprocal36.28
I(0) (reciprocal space) i0_reciprocal150000000.0000
Solution quality estimate total_estimate0.9052
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary55.8
Skewness Skewness skewness0.026
Kurtosis Kurtosis kurtosis-0.829
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14010000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.931

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)