› 3ecb

X-ray diffraction
1.7Å resolution

Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human immunodeficiency virus envelope glycoprotein 120

Released:
DOI: 10.2210/pdb3ecb/pdb
PDB entry 3ecb coloured by chain, front view.
PDB entry 3ecb coloured by chain, side view.
PDB entry 3ecb coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of the CD8 alpha beta/MHC class I interaction: focused recognition orients CD8 beta to a T cell proximal position.
Wang R, Natarajan K, Margulies DH
J Immunol 183 2554-64 (2009)
PMID: 19625641

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-135033 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, D-D alpha chain Chain: A
Molecule details ›
Chain: A
Length: 277 amino acids
Theoretical weight: 32.27 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01900 (Residues: 26-301; Coverage: 81%)
Gene name: H2-D1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 100 amino acids
Theoretical weight: 11.79 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Surface protein gp120 Chain: P
Molecule details ›
Chain: P
Length: 10 amino acids
Theoretical weight: 1.08 KDa
Source organism: Human immunodeficiency virus type 1 (MFA ISOLATE)
Expression system: Not provided
UniProt:
  • Canonical: P19551 (Residues: 309-318; Coverage: 1%)
Gene name: env

Ligands and Environments

2 bound ligands:
Ligand EDO 6 x EDO
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 46.727Å b: 89.452Å c: 109.705Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.227
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

The structural basis of αβ T-lineage immune recognition: TCR docking topologies, mechanotransduction, and co-receptor function.
Wang et al. (2012)
11 more

11 mentions without citation

The Role of Molecular Flexibility in Antigen Presentation and T Cell Receptor-Mediated Signaling.
Natarajan et al. (2018)
10 more