› 4no0

X-ray diffraction
2.7Å resolution

Crystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to HLA-A2 in complex with LILRB1

Released:
DOI: 10.2210/pdb4no0/pdb
PDB entry 4no0 coloured by chain, front view.
PDB entry 4no0 coloured by chain, side view.
PDB entry 4no0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status.
Mohammed F, Stones DH, Zarling AL, Willcox CR, Shabanowitz J, Cummings KL, Hunt DF, Cobbold M, Engelhard VH, Willcox BE
Oncotarget 8 54160-54172 (2017)
PMID: 28903331

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-137684 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
HLA class I histocompatibility antigen, A alpha chain Chain: A
Molecule details ›
Chain: A
Length: 276 amino acids
Theoretical weight: 31.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04439 (Residues: 25-299; Coverage: 81%)
Gene names: HLA-A, HLAA
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(DE3)
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Lymphocyte-specific protein 1 Chain: C
Molecule details ›
Chain: C
Length: 12 amino acids
Theoretical weight: 1.3 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P33241 (Residues: 249-260; Coverage: 4%)
Gene names: LSP1, WP34
Leukocyte immunoglobulin-like receptor subfamily B member 1 Chain: D
Molecule details ›
Chain: D
Length: 195 amino acids
Theoretical weight: 21.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8NHL6 (Residues: 27-221; Coverage: 31%)
Gene names: ILT2, LILRB1, LIR1, MIR7
Sequence domains: Immunoglobulin domain
Structure domains: Immunoglobulins

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P3121
Unit cell:
a: 117.3Å b: 117.3Å c: 96.1Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.271 0.269 0.309
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

11 review citations

Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes.
Antunes et al. (2018)
10 more

3 mentions without citation

The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status.
Mohammed et al. (2017)
2 more