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- EMDB-4034: influenza virus membrane fusion -

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Basic information

Entry
Database: EMDB / ID: EMD-4034
Titleinfluenza virus membrane fusion
Map datatomogram containing 3 contact zones
Sample
  • Virus: influenza virus
    • Other: influenza virus
Biological speciesinfluenza virus
Methodelectron tomography / cryo EM
AuthorsCalder LJ / Rosenthal PB
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Cryomicroscopy provides structural snapshots of influenza virus membrane fusion.
Authors: Lesley J Calder / Peter B Rosenthal /
Abstract: The lipid-enveloped influenza virus enters host cells during infection by binding cell-surface receptors and, after receptor-mediated endocytosis, fusing with the membrane of the endosome and ...The lipid-enveloped influenza virus enters host cells during infection by binding cell-surface receptors and, after receptor-mediated endocytosis, fusing with the membrane of the endosome and delivering the viral genome and transcription machinery into the host cell. These events are mediated by the hemagglutinin (HA) surface glycoprotein. At the low pH of the endosome, an irreversible conformational change in the HA, including the exposure of the hydrophobic fusion peptide, activates membrane fusion. Here we used electron cryomicroscopy and cryotomography to image the fusion of influenza virus with target membranes at low pH. We visualized structural intermediates of HA and their interactions with membranes during the course of membrane fusion as well as ultrastructural changes in the virus that accompany membrane fusion. Our observations are relevant to a wide range of protein-mediated membrane-fusion processes and demonstrate how dynamic membrane events may be studied by cryomicroscopy.
History
DepositionJun 21, 2016-
Header (metadata) releaseAug 10, 2016-
Map releaseAug 10, 2016-
UpdateSep 21, 2016-
Current statusSep 21, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Simplified surface model
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4034.png

Downloads & links

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Map

FileDownload / File: emd_4034.map.gz / Format: CCP4 / Size: 283.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtomogram containing 3 contact zones
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.3 Å/pix.
x 249 pix.
= 1070.7 Å		4.3 Å/pix.
x 530 pix.
= 2279. Å		4.3 Å/pix.
x 564 pix.
= 2425.2 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.3 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum0. - 255.
Average (Standard dev.)129.445390000000003 (±34.777549999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin626629
Dimensions530564249
Spacing564530249
CellA: 2425.2002 Å / B: 2279.0 Å / C: 1070.7001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.34.34.3
M x/y/z564530249
origin x/y/z0.0000.0000.000
length x/y/z2425.2002279.0001070.700
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS666229
NC/NR/NS564530249
D min/max/mean0.000255.000129.445

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Supplemental data

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Sample components

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Entire : influenza virus

EntireName: influenza virus
Components
  • Virus: influenza virus
    • Other: influenza virus

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Supramolecule #1: influenza virus

SupramoleculeName: influenza virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11309 / Sci species name: influenza virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: influenza virus

MacromoleculeName: influenza virus / type: other / ID: 1 / Classification: other
SequenceString:
XXX

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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
Details: Sample was incubated at pH5 for 1min and then neutralised
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: British Biocell / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: TVIPS TEMCAM-F224 (2k x 2k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Average electron dose: 2.0 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 Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 40

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