› 4jfe

X-ray diffraction
2.7Å resolution

Preservation of peptide specificity during TCR-MHC contact dominated affinity enhancement of a melanoma-specific TCR

Released:
DOI: 10.2210/pdb4jfe/pdb
PDB entry 4jfe coloured by chain, front view.
PDB entry 4jfe coloured by chain, side view.
PDB entry 4jfe coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
T-cell receptor specificity maintained by altered thermodynamics.
Madura F, Rizkallah PJ, Miles KM, Holland CJ, Bulek AM, Fuller A, Schauenburg AJ, Miles JJ, Liddy N, Sami M, Li Y, Hossain M, Baker BM, Jakobsen BK, Sewell AK, Cole DK
OpenAccess logo J Biol Chem 288 18766-75 (2013)
PMID: 23698002

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-134733 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
HLA class I histocompatibility antigen, A alpha chain Chain: A
Molecule details ›
Chain: A
Length: 276 amino acids
Theoretical weight: 31.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04439 (Residues: 25-299; Coverage: 81%)
Gene names: HLA-A, HLAA
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Melanoma peptide L7A Chain: C
Molecule details ›
Chain: C
Length: 10 amino acids
Theoretical weight: 943 Da
T cell receptor alpha chain constant Chain: D
Molecule details ›
Chain: D
Length: 197 amino acids
Theoretical weight: 21.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01848 (Residues: 1-87; Coverage: 62%)
Gene names: TCRA, TRAC
Sequence domains: Domain of unknown function (DUF1968)
Structure domains: Immunoglobulins
T cell receptor beta constant 1 Chain: E
Molecule details ›
Chain: E
Length: 245 amino acids
Theoretical weight: 27.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01850 (Residues: 1-129; Coverage: 73%)
Gene name: TRBC1
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

2 bound ligands:
Ligand SO4 4 x SO4
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P43
Unit cell:
a: 121.61Å b: 121.61Å c: 82.25Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.202 0.25
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes.
Singh et al. (2017)
4 more

3 mentions without citation

T-cell receptor specificity maintained by altered thermodynamics.
Madura et al. (2013)
2 more