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- EMDB-9779: Reconstruction of HRPV6 VP5 spike -

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Basic information

Database: EMDB / ID: 9779
TitleReconstruction of HRPV6 VP5 spike
Map data
virus / VP5
Function / homologyTwin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / integral component of membrane / VP5
Function and homology information
SourceHalorubrum (archaea) / Halorubrum pleomorphic virus 6
Methodsubtomogram averaging / cryo EM / 16 Å resolution
AuthorsLi S / Huiskonen JT
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 ReportPDB-ID: 6j7v

SummaryFull reportAbout validation report
DateDeposition: Jan 18, 2019 / Header (metadata) release: Mar 6, 2019 / Map release: Mar 6, 2019 / Last update: Mar 6, 2019

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.32
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.32
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6j7v
  • Surface level: 0.32
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6j7v
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_9779.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.24 Å/pix.
= 286.72 Å
128 pix
2.24 Å/pix.
= 286.72 Å
128 pix
2.24 Å/pix.
= 286.72 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.24 Å
Contour Level:0.32 (by author), 0.32 (movie #1):
Minimum - Maximum-1.6049082 - 2.0089715
Average (Standard dev.)0.005550784 (0.39763904)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 286.72 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.242.242.24
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z286.720286.720286.720
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-1.6052.0090.006

Supplemental data

Mask #1

Projections & Slices
Slices (1/2)
Density Histograms

Sample components

Entire Halorubrum

EntireName: Halorubrum / Number of components: 2

Component #1: virus, Halorubrum

VirusName: Halorubrum / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: SPECIES
MassTheoretical: 57 kDa
SpeciesSpecies: Halorubrum (archaea)
Source (natural)Host Species: Halorubrum (archaea)
Shell #1Name of element: Envelope

Component #2: protein, VP5

ProteinName: VP5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.333914 kDa
SourceSpecies: Halorubrum pleomorphic virus 6

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.2
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 6057
3D reconstructionSoftware: Dynamo / Resolution: 16 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Sub-volume alignment
FSC plot
(resolution estimation)

Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: cross correlation
Input PDB model: 6QGL
Chain ID: A
Output model

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