› 3tvm

X-ray diffraction
2.8Å resolution

Structure of the mouse CD1d-SMC124-iNKT TCR complex

Released:
DOI: 10.2210/pdb3tvm/pdb
PDB entry 3tvm coloured by chain, front view.
PDB entry 3tvm coloured by chain, side view.
PDB entry 3tvm coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Glycolipids that elicit IFN-γ-biased responses from natural killer T cells.
Tyznik AJ, Farber E, Girardi E, Birkholz A, Li Y, Chitale S, So R, Arora P, Khurana A, Wang J, Porcelli SA, Zajonc DM, Kronenberg M, Howell AR
Chem Biol 18 1620-30 (2011)
PMID: 22195564

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-105336 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 distinct):
Antigen-presenting glycoprotein CD1d1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 285 amino acids
Theoretical weight: 32.63 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P11609 (Residues: 19-297; Coverage: 88%)
Gene names: Cd1.1, Cd1d1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, F
Molecule details ›
Chains: B, F
Length: 99 amino acids
Theoretical weight: 11.66 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
T cell receptor alpha chain constant Chains: C, G
Molecule details ›
Chains: C, G
Length: 209 amino acids
Theoretical weight: 23.06 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
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 2 Chains: D, H
Molecule details ›
Chains: D, H
Length: 241 amino acids
Theoretical weight: 27.03 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A5B9 (Residues: 1-128; Coverage: 72%)
Gene names: TCRBC2, TRBC2
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
4 bound ligands:
Ligand NAG 2 x NAG
Ligand 07P 2 x 07P
Ligand CL 1 x CL
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P21
Unit cell:
a: 78.97Å b: 150.57Å c: 101.96Å
α: 90° β: 96.35° γ: 90°
R-values:
R R work R free
0.226 0.224 0.273
Expression systems:
  • Spodoptera frugiperda
  • Trichoplusia ni
  • Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

T cell antigen receptor recognition of antigen-presenting molecules.
Rossjohn et al. (2015)
7 more

3 mentions without citation

Recognition of CD1d-restricted antigens by natural killer T cells.
Rossjohn et al. (2012)
2 more