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

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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 / integral component of membrane / VP5
Function and homology information
Specimen sourceHalorubrum pleomorphic virus 6
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / 16 Å resolution
AuthorsEl Omari, K. / Li, S. / Huiskonen, J.T. / Stuart, D.I.
Funding supportUnited Kingdom , 1 items
OrganizationGrant numberCountry
European Research Council649053United 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 / Jonathan M Grimes / Dennis H Bamford / Nicole D Tischler / Juha T Huiskonen / David I Stuart / Elina Roine
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 18, 2019 / Release: Mar 6, 2019

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Assembly

Deposited unit
A: VP5


Theoretical massNumber of molelcules
Total (without water)57,3341
Polyers57,3341
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide VP5


Mass: 57333.914 Da / Num. of mol.: 1 / 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 / Reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Halorubrum / Type: VIRUS / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 0.057 MDa / Experimental value: NO
Source (natural)Organism: Halorubrum (archaea)
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Halorubrum
Virus shellName: Envelope
Buffer solutionpH: 7.2
Buffer componentConc.: 1.6 M / Name: sodium chloride / Formula: NaCl
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
MicroscopyMicroscope model: 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
3D reconstructionResolution: 16 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 6057 / Symmetry type: POINT
EM volume selectionNumber of tomograms: 10 / Number of volumes extracted: 8953
Atomic model buildingRef protocol: RIGID BODY FIT / Target criteria: cross correlation
Atomic model buildingPDB-ID: 6QGL
Pdb chain ID: A

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