› 7umt

Electron Microscopy
3.4Å resolution

Structure of the VP5*/VP8* assembly from the human rotavirus strain CDC-9 - Reversed conformation

Released:
DOI: 10.2210/pdb7umt/pdb
PDB entry 7umt coloured by chain, front view.
PDB entry 7umt coloured by chain, side view.
PDB entry 7umt coloured by chain, top view.
Source organism: Rotavirus
Primary publication:
Rotavirus VP4 Epitope of a Broadly Neutralizing Human Antibody Defined by Its Structure Bound with an Attenuated-Strain Virion.
Jenni S, Li Z, Wang Y, Bessey T, Salgado EN, Schmidt AG, Greenberg HB, Jiang B, Harrison SC
J Virol e0062722 (2022)
PMID: 35924923
Related structures: EMD-26609

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 39-mer (preferred)
PDBe Complex ID:
PDB-CPX-103961 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Outer capsid protein VP5* Chains: 1, 2, 3
Molecule details ›
Chains: 1, 2, 3
Length: 529 amino acids
Theoretical weight: 59.61 KDa
Source organism: Rotavirus
Expression system: Chlorocebus aethiops
UniProt:
  • Canonical: X4YMN0 (Residues: 247-775; Coverage: 68%)
Gene names: VP4, W907_45309gpVP4, W907_45314gpVP4, W907_45315gpVP4, W907_45321gpVP4, W907_45328gpVP4, W907_45346gpVP4
Sequence domains:
Intermediate capsid protein VP6 Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
Length: 397 amino acids
Theoretical weight: 44.99 KDa
Source organism: Rotavirus
Expression system: Chlorocebus aethiops
UniProt:
  • Canonical: A0A223GHC7 (Residues: 1-397; Coverage: 100%)
Gene name: VP6
Sequence domains: Rotavirus major capsid protein VP6
Outer capsid glycoprotein VP7 Chains: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r
Molecule details ›
Chains: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r
Length: 326 amino acids
Theoretical weight: 37.44 KDa
Source organism: Rotavirus
Expression system: Chlorocebus aethiops
UniProt:
  • Canonical: B1NP55 (Residues: 1-326; Coverage: 100%)
Gene names: NC78_51708gpVP7, NC78_52349gpVP7, NC78_52352gpVP7, NC78_52353gpVP7, NC78_52354gpVP7, NC78_52356gpVP7, NC78_52357gpVP7b, VP7, W907_45360gpVP7, W907_45361gpVP7, W907_45368gpVP7
Sequence domains: Glycoprotein VP7

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Ligand NAG 2 x NAG
Ligand BMA 1 x BMA
2 bound ligands:
Ligand NAG 35 x NAG
Ligand CA 72 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-26609
Expression system: Chlorocebus aethiops

Quick links

Citations

2 citation in other articles

14th International dsRNA Virus Symposium, Banff, Alberta, Canada, 10-14 October 2022.
Desselberger U. (2023)
1 more

1 mention without citation

Rotavirus VP4 Epitope of a Broadly Neutralizing Human Antibody Defined by Its Structure Bound with an Attenuated-Strain Virion.
Jenni et al. (2022)