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- EMDB-3286: Evidence for a conformational switch in Influenzavirus M1 and its... -

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Basic information

Entry
Database: EMDB / ID: EMD-3286
TitleEvidence for a conformational switch in Influenzavirus M1 and its role in filamentous virion architecture
Map dataReconstruction of inner membrane leaflet, M1 and attached densities at leading virion tips
Sample
  • Sample: Leading tip of filamentous Influenza A virions including inner leaflet, M1 and internal crown
  • Virus: Influenza A virus
KeywordsInfluenza A virus / FLUAV / polymerase / M1 / crown / leading tip / trailing tip / filamentous
Biological speciesInfluenza A virus
Methodsubtomogram averaging / cryo EM / Resolution: 76.0 Å
AuthorsKiss G / Abdulsattar BO / Phapugrangkul P / Birch K / Jones IM / Neuman BW
CitationJournal: To Be Published
Title: Evidence for a conformational switch in Influenzavirus M1 and its role in filamentous virion architecture
Authors: Kiss G / Abdulsattar BO / Phapugrangkul P / Birch K / Jones IM / Neuman BW
History
DepositionDec 17, 2015-
Header (metadata) releaseOct 12, 2016-
Map releaseAug 2, 2017-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.52
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.52
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3286.png

Downloads & links

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Map

FileDownload / File: emd_3286.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of inner membrane leaflet, M1 and attached densities at leading virion tips
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10 Å/pix.
x 64 pix.
= 640. Å		10 Å/pix.
x 64 pix.
= 640. Å		10 Å/pix.
x 64 pix.
= 640. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.52 / Movie #1: 0.52
Minimum - Maximum-3.09326649 - 3.06961107
Average (Standard dev.)0.00004166 (±0.28897005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 640.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z101010
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z640.000640.000640.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-3.0933.0700.000

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Supplemental data

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Sample components

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Entire : Leading tip of filamentous Influenza A virions including inner le...

EntireName: Leading tip of filamentous Influenza A virions including inner leaflet, M1 and internal crown
Components
  • Sample: Leading tip of filamentous Influenza A virions including inner leaflet, M1 and internal crown
  • Virus: Influenza A virus

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Supramolecule #1000: Leading tip of filamentous Influenza A virions including inner le...

SupramoleculeName: Leading tip of filamentous Influenza A virions including inner leaflet, M1 and internal crown
type: sample / ID: 1000
Details: Compare to matched image of the opposite virion tip
Number unique components: 1

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Supramolecule #1: Influenza A virus

SupramoleculeName: Influenza A virus / type: virus / ID: 1 / Name.synonym: Influenza virus
Details: Reconstruction of the inner layer of the viral envelope and attached densities likely representing polymerase molecules from native virions of mixed A/Aichi/X31 and A/Udorn strains. Map is ...Details: Reconstruction of the inner layer of the viral envelope and attached densities likely representing polymerase molecules from native virions of mixed A/Aichi/X31 and A/Udorn strains. Map is Gaussian filtered to 7.6 nm the 0.5 FSC. Reconstructed in EMAN2.
NCBI-ID: 11320 / Sci species name: Influenza A virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No / Syn species name: Influenza virus
Host (natural)Organism: Homo sapiens (human) / Strain: Combined A/Aichi/2/68 and A/Udorn/307/72 / synonym: VERTEBRATES
Host systemOrganism: Homo sapiens (human) / Recombinant cell: MDCK
Virus shellShell ID: 1 / Name: M1

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK III
Details: Details for EM and reconstruction published in Calder et al., Proc Natl Acad Sci U S A. 2010 Jun 8; 107(23): 10685 to 10690.
Method: Blotted 4s before plunging

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Electron microscopy

MicroscopeOTHER
DateJan 1, 2010
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 50 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsSubtomograms were manually selected. Alignments and cropping of the region of interest was done interactively with EMAN2.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 76.0 Å / Resolution method: OTHER / Software - Name: MRC, IMOD, IVE / Number subtomograms used: 23
Final 3D classificationNumber classes: 2
FSC plot (resolution estimation)

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