› 5kd4

X-ray diffraction
3.05Å resolution

Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PVI10) of HIV gp120 MN Isolate (IGPGRAFYVI)

Released:
DOI: 10.2210/pdb5kd4/pdb
PDB entry 5kd4 coloured by chain, front view.
PDB entry 5kd4 coloured by chain, side view.
PDB entry 5kd4 coloured by chain, top view.
Source organisms:
Primary publication:
Effects of Cross-Presentation, Antigen Processing, and Peptide Binding in HIV Evasion of T Cell Immunity.
Frey BF, Jiang J, Sui Y, Boyd LF, Yu B, Tatsuno G, Billeskov R, Solaymani-Mohammadi S, Berman PW, Margulies DH, Berzofsky JA
J Immunol 200 1853-1864 (2018)
PMID: 29374075

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-135031 (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: 277 amino acids
Theoretical weight: 32.27 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01900 (Residues: 26-301; Coverage: 81%)
Gene name: H2-D1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, D
Molecule details ›
Chains: B, D
Length: 100 amino acids
Theoretical weight: 11.79 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
Structure domains: Immunoglobulins
Surface protein gp120 Chains: P, Q
Molecule details ›
Chains: P, Q
Length: 10 amino acids
Theoretical weight: 1.09 KDa
Source organism: Human immunodeficiency virus 1
Expression system: synthetic construct
UniProt:
  • Canonical: P05877 (Residues: 314-321; 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 22-ID
Spacegroup: P21
Unit cell:
a: 47.13Å b: 90.3Å c: 120.07Å
α: 90° β: 113.19° γ: 90°
R-values:
R R work R free
0.186 0.184 0.224
Expression systems:
  • Escherichia coli BL21(DE3)
  • synthetic construct

Quick links

Citations

2 review citations

Strategies for developing and optimizing cancer vaccines.
Maeng et al. (2019)
1 more

1 mention without citation

Effects of Cross-Presentation, Antigen Processing, and Peptide Binding in HIV Evasion of T Cell Immunity.
Frey et al. (2018)