6miy

X-ray diffraction
2.75Å resolution

Crystal structure of the mCD1d/xxa (JJ239)/iNKTCR ternary complex

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-100911 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 distinct):
Ig-like domain-containing protein Chains: C, G
Molecule details ›
Chains: C, G
Length: 209 amino acids
Theoretical weight: 23.06 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: K7N5M3 (Residues: 3-3, 96-114, 116-210; Coverage: 52%)
  • Canonical: A0A0B4J1J9 (Residues: 22-114; Coverage: 100%)
Gene names: B2M, HDCMA22P, Trav11, Trav11d
Sequence domains:
Structure domains: Immunoglobulins
Ig-like domain-containing protein; T cell receptor beta constant 2 Chains: D, H
Molecule details ›
Chains: D, H
Length: 241 amino acids
Theoretical weight: 27.03 KDa
Source organisms: Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A2NTY6 (Residues: 29-123, 132-144; Coverage: 81%)
  • Canonical: A0N8J3 (Residues: 109-126; Coverage: 6%)
  • Canonical: A0A5B9 (Residues: 19-128; Coverage: 62%)
Gene names: TCRBC2, TRBC2
Sequence domains:
Structure domains: Immunoglobulins
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: Spodoptera frugiperda
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer : NEW Components: NAG, FUC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: C2
Unit cell:
a: 78.865Å b: 192.477Å c: 150.418Å
α: 90° β: 90.79° γ: 90°
R-values:
R R work R free
0.194 0.192 0.247
Expression systems:
  • Escherichia coli BL21(DE3)
  • Spodoptera frugiperda