› 4y2d

X-ray diffraction
3.05Å resolution

Crystal structure of the mCD1d/7DW8-5/iNKTCR ternary complex

Released:
DOI: 10.2210/pdb4y2d/pdb
PDB entry 4y2d coloured by chain, front view.
PDB entry 4y2d coloured by chain, side view.
PDB entry 4y2d coloured by chain, top view.
Source organisms:
Entry authors: Zajonc DM, Yu ED

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-100913 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 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: Spodoptera frugiperda
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Ig-like domain-containing protein; T cell receptor alpha chain constant 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: A0A0B4J1J9 (Residues: 22-114; Coverage: 100%)
  • Canonical: P01848 (Residues: 1-93; Coverage: 66%)
Gene names: TCRA, TRAC, 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: 29-144; Coverage: 97%)
  • Canonical: A0A5B9 (Residues: 1-128; Coverage: 72%)
Gene names: TCRBC2, TRBC2
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
3 bound ligands:
Ligand NAG 5 x NAG
Ligand 7DW 2 x 7DW
Ligand FUC 1 x FUC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P21
Unit cell:
a: 79.422Å b: 150.264Å c: 100.8Å
α: 90° β: 96.24° γ: 90°
R-values:
R R work R free
0.218 0.217 0.257
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)

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