6J7V | pdb_00006j7v

Structure of HRPV6 VP5 fitted in the cryoEM density of the spike

• PDB DOI: https://doi.org/10.2210/pdb6J7V/pdb
• EM Map EMD-9779: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Halorubrum pleomorphic virus 6
• Mutation(s): No 


• Deposited: 2019-01-18 Released: 2019-03-06 
• Deposition Author(s): El Omari, K., Li, S., Huiskonen, J.T., Stuart, D.I.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 16.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Model: experimental

Literature

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

• PubMed: 30783086 
• DOI: https://doi.org/10.1038/s41467-019-08728-7
• Primary Citation 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.

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Organizational Affiliation: 
• Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
School of Life Sciences, Tsinghua University, 100084, Beijing, China.
Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile.
Department of Biochemistry and Developmental Biology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland.
Thermo Fisher Scientific, Achtseweg Noorg 5, 5651 GG, Eindhoven, The Netherlands.
Helsinki Institute of Life Science HiLIFE, Institute of Biotechnology, University of Helsinki, Viikinkaari 5, 00014, Helsinki, Finland.
Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland.
Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile. [e-mail].
Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. [e-mail].
Helsinki Institute of Life Science HiLIFE and Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland. [e-mail].
Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. [e-mail].
Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK. [e-mail].
Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.33 kDa 
• Atom Count: 3,709 
• Modeled Residue Count: 490 
• Deposited Residue Count: 537 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP5	A	537	Halorubrum pleomorphic virus 6	Mutation(s): 0
UniProt
Find proteins for H9ABP6 (Halorubrum pleomorphic virus 6) Explore H9ABP6  Go to UniProtKB:  H9ABP6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 16.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	Dynamo

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-06 
Deposition Author(s): El Omari, K., Li, S., Huiskonen, J.T., Stuart, D.I.

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	649053

Revision History  

• Version 1.0: 2019-03-06
  Type: Initial release
  
• Version 1.1: 2020-08-05
  Changes: Data collection
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Refinement description