› 4zfz

X-ray diffraction
1.76Å resolution

Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein

Released:
DOI: 10.2210/pdb4zfz/pdb
PDB entry 4zfz coloured by chain, front view.
PDB entry 4zfz coloured by chain, side view.
PDB entry 4zfz coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of the N-myristoylated lipopeptide-bound MHC class I complex.
Morita D, Yamamoto Y, Mizutani T, Ishikawa T, Suzuki J, Igarashi T, Mori N, Shiina T, Inoko H, Fujita H, Iwai K, Tanaka Y, Mikami B, Sugita M
OpenAccess logo Nat Commun 7 10356 (2016)
PMID: 26758274

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-125554 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 277 amino acids
Theoretical weight: 31.69 KDa
Source organism: Macaca mulatta
Expression system: Escherichia coli
UniProt:
  • Canonical: K4MU32 (Residues: 24-300; Coverage: 82%)
Gene names: B, Mamu-B
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 100 amino acids
Theoretical weight: 11.73 KDa
Source organism: Macaca mulatta
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6V7J5 (Residues: 20-119; Coverage: 100%)
Gene name: B2M
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Protein Nef Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 5 amino acids
Theoretical weight: 403 Da
Source organism: Simian immunodeficiency virus (F236/SMH4 ISOLATE) (SOOTY MANGABEY)
Expression system: Not provided
UniProt:
  • Canonical: P12482 (Residues: 2-6; Coverage: 2%)
Gene name: nef

Ligands and Environments

5 bound ligands:
Ligand ZN 18 x ZN
Ligand EDO 65 x EDO
Ligand TRS 2 x TRS
Ligand CL 3 x CL
Ligand MYR 4 x MYR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P1
Unit cell:
a: 46.402Å b: 85.179Å c: 127.99Å
α: 89.2° β: 79.57° γ: 90.02°
R-values:
R R work R free
0.196 0.194 0.228
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Comparative genomics of the human, macaque and mouse major histocompatibility complex.
Shiina et al. (2017)
3 more

4 mentions without citation

Structural aspects of chemical modifications in the MHC-restricted immunopeptidome; Implications for immune recognition.
Sandalova et al. (2022)
3 more