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- EMDB-8088: G1S VLP_noVPP -

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Basic information

Entry
Database: EMDB / ID: EMD-8088
TitleG1S VLP_noVPP
Map dataG1S VLP_noVPP
Sample
  • Virus: Influenza A virus
Biological speciesInfluenza A virus
Methodelectron tomography / cryo EM
AuthorsChlanda P / Zimmerberg J
CitationJournal: Nat Microbiol / Year: 2016
Title: The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes.
Authors: Petr Chlanda / Elena Mekhedov / Hang Waters / Cindi L Schwartz / Elizabeth R Fischer / Rolf J Ryham / Fredric S Cohen / Paul S Blank / Joshua Zimmerberg /
Abstract: Influenza A virus haemagglutinin conformational change drives the membrane fusion of viral and endosomal membranes at low pH. Membrane fusion proceeds through an intermediate called hemifusion(1,2). ...Influenza A virus haemagglutinin conformational change drives the membrane fusion of viral and endosomal membranes at low pH. Membrane fusion proceeds through an intermediate called hemifusion(1,2). For viral fusion, the hemifusion structures are not determined(3). Here, influenza virus-like particles(4) carrying wild-type haemagglutinin or haemagglutinin hemifusion mutant G1S(5) and liposome mixtures were studied at low pH by Volta phase plate cryo-electron tomography, which improves the signal-to-noise ratio close to focus. We determined two distinct hemifusion structures: a hemifusion diaphragm and a novel structure termed a 'lipidic junction'. Liposomes with lipidic junctions were ruptured with membrane edges stabilized by haemagglutinin. The rupture frequency and hemifusion diaphragm diameter were not affected by G1S mutation, but decreased when the cholesterol level in the liposomes was close to physiological concentrations. We propose that haemagglutinin induces a merger between the viral and target membranes by one of two independent pathways: a rupture-insertion pathway leading to the lipidic junction and a hemifusion-stalk pathway leading to a fusion pore. The latter is relevant under the conditions of influenza virus infection of cells. Cholesterol concentration functions as a pathway switch because of its negative spontaneous curvature in the target bilayer, as determined by continuum analysis.
History
DepositionFeb 22, 2016-
Header (metadata) releaseMar 23, 2016-
Map releaseJun 8, 2016-
UpdateOct 12, 2016-
Current statusOct 12, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
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  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

FileDownload / File: emd_8088.map.gz / Format: CCP4 / Size: 36.7 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationG1S VLP_noVPP
Voxel sizeX=Y=Z: 7.36 Å
Density
Minimum - Maximum-128. - 127.
Average (Standard dev.)48.204357000000002 (±13.228106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions466574144
Spacing574466144
CellA: 4224.64 Å / B: 3429.76 Å / C: 1059.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z7.367.367.36
M x/y/z574466144
origin x/y/z0.0000.0000.000
length x/y/z4224.6403429.7601059.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-25-77-48
NX/NY/NZ899896
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS574466144
D min/max/mean-128.000127.00048.204

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Supplemental data

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Sample components

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Entire : Influenza A virus

EntireName: Influenza A virus
Components
  • Virus: Influenza A virus

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Supramolecule #1: Influenza A virus

SupramoleculeName: Influenza A virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 11320 / Sci species name: Influenza A virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes
Host systemOrganism: Homo sapiens (human) / Recombinant cell: HEK 293T / Recombinant plasmid: pCAGGS

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 %
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: EMS / Diameter: 100 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 1.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 60

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