› 5efi

X-ray diffraction
1.8Å resolution

Crystal structure of mouse CD1d in complex with the p99p lipopeptide

Released:
DOI: 10.2210/pdb5efi/pdb
PDB entry 5efi coloured by chain, front view.
PDB entry 5efi coloured by chain, side view.
PDB entry 5efi coloured by chain, top view.
Source organisms:
Primary publication:
Structure of an α-Helical Peptide and Lipopeptide Bound to the Nonclassical Major Histocompatibility Complex (MHC) Class I Molecule CD1d.
Girardi E, Wang J, Zajonc DM
J Biol Chem 291 10677-83 (2016)
PMID: 27006394

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135078 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
Antigen-presenting glycoprotein CD1d1 Chain: A
Molecule details ›
Chain: A
Length: 285 amino acids
Theoretical weight: 32.61 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 Chain: B
Molecule details ›
Chain: B
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
p99p Chain: C
Molecule details ›
Chain: C
Length: 22 amino acids
Theoretical weight: 2.82 KDa
Source organism: Mus
Expression system: Not provided

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN, FUC
Carbohydrate polymer
5 bound ligands:
Ligand NAG 1 x NAG
Ligand CIT 1 x CIT
Ligand NA 1 x NA
Ligand PLM 1 x PLM
Ligand OCA 1 x OCA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P212121
Unit cell:
a: 42.19Å b: 107.85Å c: 110.34Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.219 0.244
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

3 review citations

Mechanisms and Consequences of Antigen Presentation by CD1.
Van Kaer et al. (2016)
2 more

1 mention without citation

Structure of an α-Helical Peptide and Lipopeptide Bound to the Nonclassical Major Histocompatibility Complex (MHC) Class I Molecule CD1d.
Girardi et al. (2016)