PDBe 2po6

X-ray diffraction
3.2Å resolution

Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Antigen-presenting glycoprotein CD1d Chains: A, E
Molecule details ›
Chains: A, E
Length: 278 amino acids
Theoretical weight: 31.76 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: NEW P15813 (Residues: 24-295; Coverage: 86%)
Gene name: CD1D
Sequence domains: Immunoglobulin C1-set domain
Structure domains:
Beta-2-microglobulin Chains: B, F
Molecule details ›
Chains: B, F
Length: 99 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: NEW P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
T cell receptor alpha constant Chains: C, G
Molecule details ›
Chains: C, G
Length: 204 amino acids
Theoretical weight: 22.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: NEW P01848 (Residues: 1-90; Coverage: 64%)
Gene names: TCRA, TRAC
Structure domains: Immunoglobulins
NKT15 beta-chain Chains: D, H
Molecule details ›
Chains: D, H
Length: 244 amino acids
Theoretical weight: 27.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: C2
Unit cell:
a: 204.012Å b: 155.636Å c: 85.981Å
α: 90° β: 94.78° γ: 90°
R-values:
R R work R free
0.229 0.226 0.293
Expression systems:
  • Trichoplusia ni
  • Escherichia coli