› 4x6d

X-ray diffraction
2.98Å resolution

CD1a ternary complex with endogenous lipids and BK6 TCR

Released:
DOI: 10.2210/pdb4x6d/pdb
PDB entry 4x6d coloured by chain, front view.
PDB entry 4x6d coloured by chain, side view.
PDB entry 4x6d coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
αβ T cell antigen receptor recognition of CD1a presenting self lipid ligands.
Birkinshaw RW, Pellicci DG, Cheng TY, Keller AN, Sandoval-Romero M, Gras S, de Jong A, Uldrich AP, Moody DB, Godfrey DI, Rossjohn J
Nat Immunol 16 258-66 (2015)
PMID: 25642819

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-134736 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
T-cell surface glycoprotein CD1a Chains: A, C
Molecule details ›
Chains: A, C
Length: 275 amino acids
Theoretical weight: 31.57 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P06126 (Residues: 21-295; Coverage: 88%)
Gene name: CD1A
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, D
Molecule details ›
Chains: B, D
Length: 99 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
T cell receptor alpha chain constant Chains: E, G
Molecule details ›
Chains: E, G
Length: 207 amino acids
Theoretical weight: 23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01848 (Residues: 1-93; Coverage: 66%)
Gene names: TCRA, TRAC
Sequence domains: Domain of unknown function (DUF1968)
Structure domains: Immunoglobulins
T cell receptor beta constant 1 Chains: F, H
Molecule details ›
Chains: F, H
Length: 245 amino acids
Theoretical weight: 27.6 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

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
2 bound ligands:
Ligand OLA 1 x OLA
Ligand PAM 1 x PAM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P212121
Unit cell:
a: 90.133Å b: 126.322Å c: 226.852Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.177 0.229
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli

Quick links

Citations

36 review citations

The burgeoning family of unconventional T cells.
Godfrey et al. (2015)
35 more

5 mentions without citation

Novel Molecular Insights into Human Lipid-Mediated T Cell Immunity.
Shahine et al. (2021)
4 more