› 7zqi

X-ray diffraction
2.15Å resolution

MHC class I from a wild bird in complex with a nonameric peptide P2

Released:
DOI: 10.2210/pdb7zqi/pdb
PDB entry 7zqi coloured by chain, front view.
PDB entry 7zqi coloured by chain, side view.
PDB entry 7zqi coloured by chain, top view.
Source organisms:
Primary publication:
The structure of songbird MHC class I reveals antigen binding that is flexible at the N-terminus and static at the C-terminus.
Eltschkner S, Mellinger S, Buus S, Nielsen M, Paulsson KM, Lindkvist-Petersson K, Westerdahl H
Front Immunol 14 1209059 (2023)
PMID: 37483599

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-215273 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 275 amino acids
Theoretical weight: 31.63 KDa
Source organism: Acrocephalus arundinaceus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O98187 (Residues: 26-299; Coverage: 81%)
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 122 amino acids
Theoretical weight: 14.21 KDa
Source organism: Acrocephalus arundinaceus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A076JEK1 (Residues: 14-112; Coverage: 88%)
Gene name: B2M
Sequence domains: Immunoglobulin C1-set domain
CBS domain-containing protein Chain: F
Molecule details ›
Chain: F
Length: 9 amino acids
Theoretical weight: 1.07 KDa
Source organism: Vibrio sp.
Expression system: Not provided
UniProt:
  • Canonical: Q9KT74 (Residues: 17-25; Coverage: 6%)
Gene name: VC_1031

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand CL 1 x CL
Ligand MPD 1 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: P212121
Unit cell:
a: 39.202Å b: 48.78Å c: 202.135Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.18 0.229
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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