› 5t70

X-ray diffraction
2.1Å resolution

KIR3DL1 in complex with HLA-B*57:01 presenting TSNLQEQIGW

Released:
DOI: 10.2210/pdb5t70/pdb
PDB entry 5t70 coloured by chain, front view.
PDB entry 5t70 coloured by chain, side view.
PDB entry 5t70 coloured by chain, top view.
Source organisms:
Primary publication:
MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape.
Pymm P, Illing PT, Ramarathinam SH, O'Connor GM, Hughes VA, Hitchen C, Price DA, Ho BK, McVicar DW, Brooks AG, Purcell AW, Rossjohn J, Vivian JP
Nat Struct Mol Biol 24 387-394 (2017)
PMID: 28218747

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-135135 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
HLA class I histocompatibility antigen, B alpha chain Chain: A
Molecule details ›
Chain: A
Length: 276 amino acids
Theoretical weight: 31.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P01889 (Residues: 25-300; Coverage: 82%)
Gene names: HLA-B, HLAB
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.75 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
Structure domains: Immunoglobulins
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: Homo sapiens
UniProt:
  • Canonical: P43629 (Residues: 22-320; Coverage: 71%)
Gene names: CD158E, KIR3DL1, NKAT3, NKB1
Sequence domains: Immunoglobulin domain
Structure domains: Immunoglobulins
Capsid protein p24 Chain: C
Molecule details ›
Chain: C
Length: 10 amino acids
Theoretical weight: 1.18 KDa
Source organism: synthetic construct
Expression system: Not provided
UniProt:
  • Canonical: P03366 (Residues: 240-249; Coverage: 1%)
Gene name: gag-pol

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: 51.726Å b: 61.209Å c: 65.186Å
α: 96.04° β: 97.46° γ: 108.72°
R-values:
R R work R free
0.177 0.174 0.224
Expression systems:
  • Escherichia coli BL21
  • Homo sapiens
  • Not provided

Quick links

Citations

12 review citations

Predicting Antigen Presentation-What Could We Learn From a Million Peptides?
Gfeller et al. (2018)
11 more

4 mentions without citation

Unconventional Peptide Presentation by Classical MHC Class I and Implications for T and NK Cell Activation.
Zajonc DM. (2020)
3 more