Crystal structure of VP5 from Haloarchaeal pleomorphic virus 6

Experimental Data Snapshot

  • Resolution: 2.69 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


The structure of a prokaryotic viral envelope protein expands the landscape of membrane fusion proteins.

El Omari, K.Li, S.Kotecha, A.Walter, T.S.Bignon, E.A.Harlos, K.Somerharju, P.De Haas, F.Clare, D.K.Molin, M.Hurtado, F.Li, M.Grimes, J.M.Bamford, D.H.Tischler, N.D.Huiskonen, J.T.Stuart, D.I.Roine, E.

(2019) Nat Commun 10: 846-846

  • DOI: https://doi.org/10.1038/s41467-019-08728-7
  • Primary Citation of Related Structures:  
    6J7V, 6QGI, 6QGL

  • PubMed Abstract: 

    Lipid membrane fusion is an essential function in many biological processes. Detailed mechanisms of membrane fusion and the protein structures involved have been mainly studied in eukaryotic systems, whereas very little is known about membrane fusion in prokaryotes. Haloarchaeal pleomorphic viruses (HRPVs) have a membrane envelope decorated with spikes that are presumed to be responsible for host attachment and membrane fusion. Here we determine atomic structures of the ectodomains of the 57-kDa spike protein VP5 from two related HRPVs revealing a previously unreported V-shaped fold. By Volta phase plate cryo-electron tomography we show that VP5 is monomeric on the viral surface, and we establish the orientation of the molecules with respect to the viral membrane. We also show that the viral membrane fuses with the host cytoplasmic membrane in a process mediated by VP5. This sheds light on protein structures involved in prokaryotic membrane fusion.

  • Organizational Affiliation

    Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
512Halorubrum pleomorphic virus 6Mutation(s): 0 
Find proteins for H9ABP6 (Halorubrum pleomorphic virus 6)
Explore H9ABP6 
Go to UniProtKB:  H9ABP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH9ABP6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BR

Download Ideal Coordinates CCD File 
AA [auth B]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
AA [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.69 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.3α = 90
b = 114.3β = 90
c = 445.22γ = 120
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomG1000099
Medical Research Council (United Kingdom)United KingdomMR/N00065X/1
Wellcome TrustUnited Kingdom090532/Z/09/Z
European Research CouncilUnited Kingdom649053
Academy of FinlandFinland283072
Academy of FinlandFinland255342

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references