› 6v3j

X-ray diffraction
1.98Å resolution

KIR3DL1 in complex with HLA-B*57:03 presenting the peptide LSSPVTKSF

Released:
DOI: 10.2210/pdb6v3j/pdb
PDB entry 6v3j coloured by chain, front view.
PDB entry 6v3j coloured by chain, side view.
PDB entry 6v3j coloured by chain, top view.
Source organisms:
Primary publication:
The molecular basis of how buried human leukocyte antigen polymorphism modulates natural killer cell function.
Saunders PM, MacLachlan BJ, Pymm P, Illing PT, Deng Y, Wong SC, Oates CVL, Purcell AW, Rossjohn J, Vivian JP, Brooks AG
Proc Natl Acad Sci U S A 117 11636-11647 (2020)
PMID: 32404419

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-125111 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 275 amino acids
Theoretical weight: 31.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: I3ZN84 (Residues: 25-299; Coverage: 81%)
Gene names: HLA-B, HLA-B*5703GB
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Peptide Leu-Ser-Ser-Pro-Val-Thr-Lys-Ser-Phe Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 966 Da
Source organism: synthetic construct
Expression system: Not provided
Killer cell immunoglobulin-like receptor 3DL1 Chain: G
Molecule details ›
Chain: G
Length: 299 amino acids
Theoretical weight: 33.08 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P43629 (Residues: 22-320; Coverage: 71%)
Gene names: CD158E, KIR3DL1, NKAT3, NKB1
Sequence domains: Immunoglobulin domain

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P1
Unit cell:
a: 51.759Å b: 60.771Å c: 65.36Å
α: 96.65° β: 97.39° γ: 109.18°
R-values:
R R work R free
0.193 0.19 0.236
Expression systems:
  • Escherichia coli BL21
  • Not provided
  • Trichoplusia ni

Quick links

Citations

10 citation in other articles

Killer Cell Immunoglobulin-like Receptor Variants Are Associated with Protection from Symptoms Associated with More Severe Course in Parkinson Disease.
Anderson et al. (2020)
9 more

2 mentions without citation

The molecular basis of how buried human leukocyte antigen polymorphism modulates natural killer cell function.
Saunders et al. (2020)
1 more