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- EMDB-3287: Evidence for a conformational switch in Influenzavirus M1 and its... -

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Basic information

Entry
Database: EMDB / ID: EMD-3287
TitleEvidence for a conformational switch in Influenzavirus M1 and its role in filamentous virion architecture
Map dataReconstruction of trailing tips from influenza A virions.
Sample
  • Sample: Trailing tips of filamentous influenza A virions, showing M1 and parts of the viral ribonucleoprotein
  • 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: 100.0 Å
AuthorsKiss G / Abdulsattar BO / Phapugrangkul P / Birch K / Jones IM / Neuman BW
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Structural organization of a filamentous influenza A virus.
Authors: Lesley J Calder / Sebastian Wasilewski / John A Berriman / Peter B Rosenthal /
Abstract: Influenza is a lipid-enveloped, pleomorphic virus. We combine electron cryotomography and analysis of images of frozen-hydrated virions to determine the structural organization of filamentous ...Influenza is a lipid-enveloped, pleomorphic virus. We combine electron cryotomography and analysis of images of frozen-hydrated virions to determine the structural organization of filamentous influenza A virus. Influenza A/Udorn/72 virions are capsule-shaped or filamentous particles of highly uniform diameter. We show that the matrix layer adjacent to the membrane is an ordered helix of the M1 protein and its close interaction with the surrounding envelope determines virion morphology. The ribonucleoprotein particles (RNPs) that package the genome segments form a tapered assembly at one end of the virus interior. The neuraminidase, which is present in smaller numbers than the hemagglutinin, clusters in patches and are typically present at the end of the virion opposite to RNP attachment. Incubation of virus at low pH causes a loss of filamentous morphology, during which we observe a structural transition of the matrix layer from its helical, membrane-associated form to a multilayered coil structure inside the virus particle. The polar organization of the virus provides a model for assembly of the virion during budding at the host membrane. Images and tomograms of A/Aichi/68 X-31 virions show the generality of these conclusions to non-filamentous virions.
History
DepositionDec 17, 2015-
Header (metadata) releaseFeb 10, 2016-
Map releaseMay 31, 2017-
UpdateMay 31, 2017-
Current statusMay 31, 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
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  • Surface view colored by radius
  • Surface level: 0.52
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3287.png

Downloads & links

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Map

FileDownload / File: emd_3287.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of trailing tips from influenza A virions.
Voxel sizeX=Y=Z: 10 Å
Density
Contour LevelBy AUTHOR: 0.52 / Movie #1: 0.52
Minimum - Maximum-3.14941382 - 2.12140012
Average (Standard dev.)0.01397126 (±0.27022281)
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-3.1492.1210.014

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Supplemental data

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Sample components

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Entire : Trailing tips of filamentous influenza A virions, showing M1 and ...

EntireName: Trailing tips of filamentous influenza A virions, showing M1 and parts of the viral ribonucleoprotein
Components
  • Sample: Trailing tips of filamentous influenza A virions, showing M1 and parts of the viral ribonucleoprotein
  • Virus: Influenza A virus

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Supramolecule #1000: Trailing tips of filamentous influenza A virions, showing M1 and ...

SupramoleculeName: Trailing tips of filamentous influenza A virions, showing M1 and parts of the viral ribonucleoprotein
type: sample / ID: 1000 / 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 from trailing tips of 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
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateJan 1, 2010
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 50 e/Å2

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Image processing

Final 3D classificationNumber classes: 2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 100.0 Å / Resolution method: OTHER / Software - Name: MRC, IMOD, IVE / Number subtomograms used: 23
DetailsSubtomograms were manually selected. Alignments and cropping of the region of interest was done interactively with EMAN2.
FSC plot (resolution estimation)

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