› 5vod

X-ray diffraction
5.9Å resolution

Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6

Released:
DOI: 10.2210/pdb5vod/pdb
PDB entry 5vod coloured by chain, front view.
PDB entry 5vod coloured by chain, side view.
PDB entry 5vod coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for potent antibody-mediated neutralization of human cytomegalovirus.
Chandramouli S, Malito E, Nguyen T, Luisi K, Donnarumma D, Xing Y, Norais N, Yu D, Carfi A
Sci Immunol 2 (2017)
PMID: 28783665

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero heptamer (preferred)
hetero tetradecamer
PDBe Complex ID:
PDB-CPX-123565 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (10 distinct):
Envelope glycoprotein H Chain: A
Molecule details ›
Chain: A
Length: 725 amino acids
Theoretical weight: 82.42 KDa
Source organism: Human herpesvirus 5 strain Merlin
Expression system: Homo sapiens
UniProt:
  • Canonical: Q6SW67 (Residues: 1-715; Coverage: 96%)
Gene names: UL75, gH
Sequence domains:
Envelope glycoprotein L Chain: B
Molecule details ›
Chain: B
Length: 278 amino acids
Theoretical weight: 30.85 KDa
Source organism: Human herpesvirus 5 strain 5508
Expression system: Homo sapiens
UniProt:
  • Canonical: Q68674 (Residues: 1-278; Coverage: 100%)
Gene names: UL115, gL
Sequence domains: Cytomegalovirus glycoprotein L
Envelope glycoprotein UL128 Chain: C
Molecule details ›
Chain: C
Length: 171 amino acids
Theoretical weight: 19.78 KDa
Source organism: Human herpesvirus 5 strain AD169
Expression system: Homo sapiens
UniProt:
  • Canonical: P16837 (Residues: 1-171; Coverage: 100%)
Gene name: UL128
Envelope glycoprotein UL130 Chain: D
Molecule details ›
Chain: D
Length: 252 amino acids
Theoretical weight: 28.66 KDa
Source organism: Human herpesvirus 5 strain Merlin
Expression system: Homo sapiens
UniProt:
  • Canonical: F5HCP3 (Residues: 1-214; Coverage: 100%)
Gene name: UL130
Sequence domains: HCMV glycoprotein pUL130
Protein UL131A Chain: E
Molecule details ›
Chain: E
Length: 129 amino acids
Theoretical weight: 15.01 KDa
Source organism: Human herpesvirus 5 strain Merlin
Expression system: Homo sapiens
UniProt:
  • Canonical: F5HET4 (Residues: 1-129; Coverage: 100%)
Gene name: UL131A
Ig-like domain-containing protein Chain: H
Molecule details ›
Chain: H
Length: 288 amino acids
Theoretical weight: 30.61 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: S6B291 (Residues: 1-116, 117-241; Coverage: 50%)
Sequence domains:
Ig-like domain-containing protein Chain: L
Molecule details ›
Chain: L
Length: 241 amino acids
Theoretical weight: 26.62 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8TCD0 (Residues: 1-121, 122-239; Coverage: 100%)
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: I212121
Unit cell:
a: 148.259Å b: 208.82Å c: 267.979Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.26 0.258 0.299
Expression system: Homo sapiens

Quick links

Citations

7 review citations

The structural basis of herpesvirus entry.
Connolly et al. (2021)
6 more

5 mentions without citation

Antibodies to combat viral infections: development strategies and progress.
Pantaleo et al. (2022)
4 more