› 6npr

X-ray diffraction
2.37Å resolution

Crystal structure of H-2Dd with C84-C139 disulfide in complex with gp120 derived peptide P18-I10

Released:
DOI: 10.2210/pdb6npr/pdb
PDB entry 6npr coloured by chain, front view.
PDB entry 6npr coloured by chain, side view.
PDB entry 6npr coloured by chain, top view.
Source organisms:
Primary publication:
Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection.
McShan AC, Devlin CA, Overall SA, Park J, Toor JS, Moschidi D, Flores-Solis D, Choi H, Tripathi S, Procko E, Sgourakis NG
OpenAccess logo Proc Natl Acad Sci U S A 116 25602-25613 (2019)
PMID: 31796585

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135292 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, D-D alpha chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 276 amino acids
Theoretical weight: 32.09 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01900 (Residues: 26-301; Coverage: 81%)
Gene name: H2-D1
Sequence domains:
Beta-2-microglobulin Chains: B, D
Molecule details ›
Chains: B, D
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Surface protein gp120 Chains: P, R
Molecule details ›
Chains: P, R
Length: 10 amino acids
Theoretical weight: 1.08 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P04578 (Residues: 311-320; Coverage: 1%)
Gene name: env

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Unit cell:
a: 66.99Å b: 105.33Å c: 117.27Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.178 0.251
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

Dynamics of MHC-I molecules in the antigen processing and presentation pathway.
Truong et al. (2021)
8 more

1 mention without citation

Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection.
McShan et al. (2019)