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- EMDB-4006: Structure of wt PFV glycoprotein by cryo-electron tomography -

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Basic information

Entry
Database: EMDB / ID: EMD-4006
TitleStructure of wt PFV glycoprotein by cryo-electron tomography
Map dataNone
Sample
  • Virus: Human spumaretrovirus
Biological speciesHuman spumaretrovirus
Methodsubtomogram averaging / cryo EM / Resolution: 32.0 Å
AuthorsEffantin G
CitationJournal: Plos Pathog. / Year: 2016
Title: Cryo-electron Microscopy Structure of the Native Prototype Foamy Virus Glycoprotein and Virus Architecture.
Authors: Effantin G / Estrozi LF / Aschman N / Renesto P / Stanke N / Lindemann D / Schoehn G / Weissenhorn W
History
DepositionJun 3, 2016-
Header (metadata) releaseJun 22, 2016-
Map releaseJun 22, 2016-
UpdateJul 20, 2016-
Current statusJul 20, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.112
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.112
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_4006.map.gz / Format: CCP4 / Size: 251 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 7.6 Å
Density
Contour LevelBy AUTHOR: 0.112 / Movie #1: 0.112
Minimum - Maximum-1.3012384 - 3.4423227
Average (Standard dev.)0.19545639 (±0.5566395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-20-20-20
Dimensions404040
Spacing404040
CellA=B=C: 304.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.67.67.6
M x/y/z404040
origin x/y/z0.0000.0000.000
length x/y/z304.000304.000304.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS-20-20-20
NC/NR/NS404040
D min/max/mean-1.3013.4420.195

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Supplemental data

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Sample components

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Entire : Human spumaretrovirus

EntireName: Human spumaretrovirus
Components
  • Virus: Human spumaretrovirus

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Supramolecule #1: Human spumaretrovirus

SupramoleculeName: Human spumaretrovirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11963 / Sci species name: Human spumaretrovirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host systemOrganism: Homo sapiens (human) / Recombinant plasmid: pcoPG4, pcoPE, pcoPP
Molecular weightTheoretical: 330 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 2000
ExtractionNumber tomograms: 17 / Number images used: 2785
Final angle assignmentType: PROJECTION MATCHING

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