› 6lsa

X-ray diffraction
2.2Å resolution

Complex structure of bovine herpesvirus 1 glycoprotein D and bovine nectin-1 IgV

Released:
DOI: 10.2210/pdb6lsa/pdb
Model geometry
Fit model/data
PDB entry 6lsa coloured by chain, front view.
PDB entry 6lsa coloured by chain, side view.
PDB entry 6lsa coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of bovine herpesvirus 1 glycoprotein D bound to nectin-1 reveals the basis for its low-affinity binding to the receptor.
Yue D, Chen Z, Yang F, Ye F, Lin S, He B, Cheng Y, Wang J, Chen Z, Lin X, Yang J, Chen H, Zhang Z, You Y, Sun H, Wen A, Wang L, Zheng Y, Cao Y, Li Y, Lu G
OpenAccess logo Sci Adv 6 eaba5147 (2020)
PMID: 32426511

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123313 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Nectin-1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 109 amino acids
Theoretical weight: 12.1 KDa
Source organism: Bos taurus
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: F1MQJ3 (Residues: 37-145; Coverage: 24%)
Gene name: NECTIN1
Sequence domains: Immunoglobulin V-set domain
Herpesvirus glycoprotein D/GG/GX domain-containing protein Chains: C, F
Molecule details ›
Chains: C, F
Length: 311 amino acids
Theoretical weight: 34.87 KDa
Source organism: bovine alphaherpesvirus 1
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q76PF1 (Residues: 19-319; Coverage: 72%)
Gene name: US6
Sequence domains: Herpesvirus glycoprotein D/GG/GX domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2
Unit cell:
a: 180.871Å b: 64.234Å c: 102.931Å
α: 90° β: 91.78° γ: 90°
R-values:
R R work R free
0.201 0.2 0.236
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Trichoplusia ni

Quick links

Citations

1 review citation

Current Status and Challenge of Pseudorabies Virus Infection in China.
Tan et al. (2021)
7 other articles

2 mentions without citation

Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling.
Mutz et al. (2023)
1 more