› 3d3v

X-ray diffraction
2.8Å resolution

The complex between TCR A6 and human Class I MHC HLA-A2 with the modified HTLV-1 TAX (Y5(3,4-difluoroPhenylalanine)) peptide

Released:
DOI: 10.2210/pdb3d3v/pdb
PDB entry 3d3v coloured by chain, front view.
PDB entry 3d3v coloured by chain, side view.
PDB entry 3d3v coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Fluorine substitutions in an antigenic peptide selectively modulate T-cell receptor binding in a minimally perturbing manner.
Piepenbrink KH, Borbulevych OY, Sommese RF, Clemens J, Armstrong KM, Desmond C, Do P, Baker BM
Biochem J 423 353-61 (2009)
PMID: 19698083

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-208604 (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: 275 amino acids
Theoretical weight: 31.85 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
Modified HTLV-1 TAX (Y5(3,4-difluoro)F) peptide Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.09 KDa
A6 TCR alpha chain Chain: D
Molecule details ›
Chain: D
Length: 200 amino acids
Theoretical weight: 22.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
T cell receptor beta constant 1 Chain: E
Molecule details ›
Chain: E
Length: 245 amino acids
Theoretical weight: 27.36 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

1 bound ligand:
Ligand GOL 6 x GOL
1 modified residue:
Ligand F2F 1 x F2F

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: C2
Unit cell:
a: 224.45Å b: 48.537Å c: 93.794Å
α: 90° β: 90.61° γ: 90°
R-values:
R R work R free
0.224 0.22 0.278
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Fluorinated amino acids: compatibility with native protein structures and effects on protein-protein interactions.
Salwiczek et al. (2012)
4 more

4 mentions without citation

Fluorine substitutions in an antigenic peptide selectively modulate T-cell receptor binding in a minimally perturbing manner.
Piepenbrink et al. (2009)
3 more