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- EMDB-11076: Tomogram of influenza A/Hong Kong/1/1968 virus like particles (HA... -

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Basic information

Entry
Database: EMDB / ID: EMD-11076
TitleTomogram of influenza A/Hong Kong/1/1968 virus like particles (HA,NA,M1,M2)
Map dataTomograms showing a influenza A/HK68 virus like particle
Sample
  • Virus: Influenza A virus
Biological speciesInfluenza A virus
Methodelectron tomography / cryo EM
AuthorsPeukes J / Xiong X / Erlendsson S / Qu K / Wan W / Kraeusslich H-G / Briggs JAG
Funding supportEuropean Union, Germany, United Kingdom, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-648432European Union
German Research Foundation (DFG)project number 240245660 - SFB1129 Germany
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
CitationJournal: Nature / Year: 2020
Title: The native structure of the assembled matrix protein 1 of influenza A virus.
Authors: Julia Peukes / Xiaoli Xiong / Simon Erlendsson / Kun Qu / William Wan / Leslie J Calder / Oliver Schraidt / Susann Kummer / Stefan M V Freund / Hans-Georg Kräusslich / John A G Briggs /
Abstract: Influenza A virus causes millions of severe cases of disease during annual epidemics. The most abundant protein in influenza virions is matrix protein 1 (M1), which mediates virus assembly by ...Influenza A virus causes millions of severe cases of disease during annual epidemics. The most abundant protein in influenza virions is matrix protein 1 (M1), which mediates virus assembly by forming an endoskeleton beneath the virus membrane. The structure of full-length M1, and how it oligomerizes to mediate the assembly of virions, is unknown. Here we determine the complete structure of assembled M1 within intact virus particles, as well as the structure of M1 oligomers reconstituted in vitro. We find that the C-terminal domain of M1 is disordered in solution but can fold and bind in trans to the N-terminal domain of another M1 monomer, thus polymerizing M1 into linear strands that coat the interior surface of the membrane of the assembling virion. In the M1 polymer, five histidine residues-contributed by three different monomers of M1-form a cluster that can serve as the pH-sensitive disassembly switch after entry into a target cell. These structures therefore reveal mechanisms of influenza virus assembly and disassembly.
History
DepositionMay 26, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing 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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Movie viewer
Supplemental images

emd_11076.png

Downloads & links

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Map

FileDownload / File: emd_11076.map.gz / Format: CCP4 / Size: 788.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomograms showing a influenza A/HK68 virus like particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.12 Å/pix.
x 240 pix.
= 1708.8 Å		7.12 Å/pix.
x 928 pix.
= 6607.36 Å		7.12 Å/pix.
x 928 pix.
= 6607.36 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: 7.12 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-2355.1042 - 1953.1804
Average (Standard dev.)121.0025 (±219.60457)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928928240
Spacing928928240
CellA: 6607.36 Å / B: 6607.36 Å / C: 1708.7999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.127.127.12
M x/y/z928928240
origin x/y/z0.0000.0000.000
length x/y/z6607.3606607.3601708.800
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS928928240
D min/max/mean-2355.1041953.180121.003

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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
Details: virus like particles were formed by expressing plasmids coding for a subset (HA,NA,M1,M2) of the viral proteins
NCBI-ID: 11320 / Sci species name: Influenza A virus / Sci species strain: A/Hong Kong/1/1968 (H3N2) / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Homo sapiens (human) / Recombinant cell: HEK293-T

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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: 7.5
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: um / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 2.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: eTomo / Number images used: 40

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