› 1qo3

X-ray diffraction
2.3Å resolution

Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd

Released:
DOI: 10.2210/pdb1qo3/pdb
PDB entry 1qo3 coloured by chain, front view.
PDB entry 1qo3 coloured by chain, side view.
PDB entry 1qo3 coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of a lectin-like natural killer cell receptor bound to its MHC class I ligand.
Tormo J, Natarajan K, Margulies DH, Mariuzza RA
Nature 402 623-31 (1999)
PMID: 10604468

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-219169 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
H-2 class I histocompatibility antigen, D-D alpha chain Chain: A
Molecule details ›
Chain: A
Length: 277 amino acids
Theoretical weight: 32.27 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01900 (Residues: 26-301; Coverage: 81%)
Gene name: H2-D1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 100 amino acids
Theoretical weight: 11.79 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
T-cell surface glycoprotein YE1/48 Chains: C, D
Molecule details ›
Chains: C, D
Length: 137 amino acids
Theoretical weight: 15.92 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P20937 (Residues: 126-262; Coverage: 52%)
Gene names: Klra1, Ly-49, Ly-49a, Ly49, Ly49A
Sequence domains: Lectin C-type domain
Structure domains: Mannose-Binding Protein A, subunit A
Surface protein gp120 Chain: P
Molecule details ›
Chain: P
Length: 10 amino acids
Theoretical weight: 1.08 KDa
Source organism: Human immunodeficiency virus
Expression system: Not provided
UniProt:
  • Canonical: P04582 (Residues: 311-320; Coverage: 1%)
Gene name: env

Ligands and Environments

1 bound ligand:
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-ID-B
Spacegroup: P212121
Unit cell:
a: 78.963Å b: 96.957Å c: 99.318Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.198 0.238
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

40 review citations

NK cell recognition.
Lanier LL. (2005)
39 more

15 mentions without citation

Cis interactions of immunoreceptors with MHC and non-MHC ligands.
Held et al. (2008)
14 more