› 7lfl

X-ray diffraction
1.6Å resolution

MODEL OF MHC CLASS Ib H2-M3 WITH MOUSE ND1 N-TERMINAL HEPTAPEPTIDE, VAL MUTANT, MONOCLINIC CELL, REFINED AT 1.60 ANGSTROMS RESOLUTION

Released:
DOI: 10.2210/pdb7lfl/pdb
PDB entry 7lfl coloured by chain, front view.
PDB entry 7lfl coloured by chain, side view.
PDB entry 7lfl coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structure and dynamics of major histocompatibility class Ib molecule H2-M3 complexed with mitochondrial-derived peptides.
Strand A, Shen ST, Tomchick DR, Wang J, Wang CR, Deisenhofer J
J Biomol Struct Dyn 1-13 (2021)
PMID: 34176438

Function and Biology Details

Reaction catalysed: 
NADH + ubiquinone + 5 H(+)(Side 1) = NAD(+) + ubiquinol + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135070 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 282 amino acids
Theoretical weight: 32.65 KDa
Source organism: Mus musculus
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: Q31093 (Residues: 25-305; Coverage: 88%)
Gene names: H-2M3, H2-M3
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.7 KDa
Source organism: Mus musculus
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
NADH-ubiquinone oxidoreductase chain 1 Chain: C
Molecule details ›
Chain: C
Length: 7 amino acids
Theoretical weight: 911 Da
Source organism: Mus musculus
Expression system: Not provided
UniProt:
  • Canonical: P03888 (Residues: 1-7; Coverage: 2%)
Gene names: Mtnd1, Nd1, mt-Nd1

Ligands and Environments

1 bound ligand:
Ligand NAG 1 x NAG
1 modified residue:
Ligand FME 1 x FME

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: C2
Unit cell:
a: 116.376Å b: 66.009Å c: 55.216Å
α: 90° β: 113.334° γ: 90°
R-values:
R R work R free
0.201 0.2 0.239
Expression systems:
  • Drosophila melanogaster
  • Not provided

Quick links

Citations

1 citations in other articles

Discovery of Potent and Selective CB2 Agonists Utilizing a Function-Based Computational Screening Protocol.
Ge et al. (2023)

1 mention without citation

Structure and dynamics of major histocompatibility class Ib molecule H2-M3 complexed with mitochondrial-derived peptides.
Strand et al. (2022)