› 8tq8

X-ray diffraction
2.69Å resolution

Crystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd)

Released:
DOI: 10.2210/pdb8tq8/pdb
Model geometry
Fit model/data
PDB entry 8tq8 coloured by chain, front view.
PDB entry 8tq8 coloured by chain, side view.
PDB entry 8tq8 coloured by chain, top view.
Source organisms:
Primary publication:
Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction.
Boyd LF, Jiang J, Ahmad J, Natarajan K, Margulies DH
J Immunol (2024)
PMID: 38456672

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-279440 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
H-2 class I histocompatibility antigen, D-D alpha chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 273 amino acids
Theoretical weight: 31.82 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01900 (Residues: 26-298; Coverage: 80%)
Gene name: H2-D1
Sequence domains:
Beta-2-microglobulin Chains: B, D
Molecule details ›
Chains: B, D
Length: 99 amino acids
Theoretical weight: 11.7 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Surface protein gp120 Chains: E, P
Fab.34.5.8 Heavy chain Chains: F, H
Fab.34.5.8 Light chain Chains: G, L

Ligands and Environments

2 bound ligands:
Ligand GOL 5 x GOL
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P2
Unit cell:
a: 87.087Å b: 50.892Å c: 224.825Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.201 0.242
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided
  • Mus musculus

Quick links

Citations

2 mentions without citation

Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction.
Boyd et al. (2024)
1 more