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- PDB-6j7v: Structure of HRPV6 VP5 fitted in the cryoEM density of the spike -

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Basic information

Entry
Database: PDB / ID: 6j7v
TitleStructure of HRPV6 VP5 fitted in the cryoEM density of the spike
ComponentsVP5
KeywordsVIRAL PROTEIN / HRPV6 / spike / envelope protein / fusion protein / archaea / haloarchaea
Function / homologyTwin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / membrane / VP5
Function and homology information
Biological speciesHalorubrum pleomorphic virus 6
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 16 Å
AuthorsEl Omari, K. / Li, S. / Huiskonen, J.T. / Stuart, D.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council649053 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: The structure of a prokaryotic viral envelope protein expands the landscape of membrane fusion proteins.
Authors: Kamel El Omari / Sai Li / Abhay Kotecha / Thomas S Walter / Eduardo A Bignon / Karl Harlos / Pentti Somerharju / Felix De Haas / Daniel K Clare / Mika Molin / Felipe Hurtado / Mengqiu Li / ...Authors: Kamel El Omari / Sai Li / Abhay Kotecha / Thomas S Walter / Eduardo A Bignon / Karl Harlos / Pentti Somerharju / Felix De Haas / Daniel K Clare / Mika Molin / Felipe Hurtado / Mengqiu Li / Jonathan M Grimes / Dennis H Bamford / Nicole D Tischler / Juha T Huiskonen / David I Stuart / Elina Roine /
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, ...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.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Data collection / Category: em_imaging_optics / Item: _em_imaging_optics.phase_plate
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
A: VP5


Theoretical massNumber of molelcules
Total (without water)57,3341
Polymers57,3341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein VP5


Mass: 57333.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorubrum pleomorphic virus 6 / References: UniProt: H9ABP6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Halorubrum / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.057 MDa / Experimental value: NO
Source (natural)Organism: Halorubrum (archaea)
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Halorubrum
Virus shellName: Envelope
Buffer solutionpH: 7.2
Buffer componentConc.: 1.6 M / Name: sodium chloride / Formula: NaClSodium chloride
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 1.6 sec. / Electron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
10Dynamofinal Euler assignment
12Dynamo3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6057 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 10 / Num. of volumes extracted: 8953
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: cross correlation
Atomic model buildingPDB-ID: 6QGL

6qgl


Pdb chain-ID: A / Accession code: 6QGL / Source name: PDB / Type: experimental model

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