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- EMDB-4065: Influenza virus membrane fusion -

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Basic information

Entry
Database: EMDB / ID: EMD-4065
TitleInfluenza virus membrane fusion
Map data
Sample
  • Virus: unidentified influenza virus
    • Other: Influenza virus
Biological speciesunidentified influenza virus
Methodelectron tomography / cryo EM
AuthorsRosenthal PB / Calder LJ
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
DepositionJul 21, 2016-
Header (metadata) releaseAug 10, 2016-
Map releaseAug 10, 2016-
UpdateSep 20, 2017-
Current statusSep 20, 2017Processing 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_4065.png

Downloads & links

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Map

FileDownload / File: emd_4065.map.gz / Format: CCP4 / Size: 2.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.3 Å/pix.
x 296 pix.
= 1272.8 Å		4.3 Å/pix.
x 1494 pix.
= 6424.2 Å		4.3 Å/pix.
x 1299 pix.
= 5585.7 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.)129.204219999999992 (±33.72007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin17415134
Dimensions14941299296
Spacing12991494296
CellA: 5585.7 Å / B: 6424.2 Å / C: 1272.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.34.34.3
M x/y/z12991494296
origin x/y/z0.0000.0000.000
length x/y/z5585.7006424.2001272.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS15117434
NC/NR/NS12991494296
D min/max/mean0.000255.000129.204

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Supplemental data

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Sample components

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Entire : unidentified influenza virus

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

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Supramolecule #1: unidentified influenza virus

SupramoleculeName: unidentified influenza virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11309 / Sci species name: unidentified influenza virus / Sci species strain: A/Udorn/72 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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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 30min 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) / 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 reconstructionSoftware - Name: IMOD / Number images used: 40

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