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- EMDB-11077: Structure of the influenza A matrix protein M1 from influenza A/H... -

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Basic information

Entry
Database: EMDB / ID: EMD-11077
TitleStructure of the influenza A matrix protein M1 from influenza A/Hong Kong/1/1968 virions
Map dataStructure of the influenza A matrix protein M1 from influenza A/Hong Kong/1968 virions
Sample
  • Virus: Influenza A virus
    • Complex: Matrix protein 1
Function / homology
Function and homology information


virion assembly / viral budding from plasma membrane / structural constituent of virion / host cell nucleus / virion membrane / RNA binding / membrane
Similarity search - Function
Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Methodsubtomogram averaging / cryo EM / Resolution: 8.0 Å
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
  • Surface view with section colored by density value
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11077.png

Downloads & links

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Map

FileDownload / File: emd_11077.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the influenza A matrix protein M1 from influenza A/Hong Kong/1968 virions
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 120 pix.
= 204. Å		1.7 Å/pix.
x 120 pix.
= 204. Å		1.7 Å/pix.
x 120 pix.
= 204. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17 / Movie #1: 0.17
Minimum - Maximum-0.60524774 - 0.81951
Average (Standard dev.)-0.0008217951 (±0.07080767)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 204.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.71.71.7
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z204.000204.000204.000
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-0.6050.820-0.001

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Supplemental data

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Mask #1

Fileemd_11077_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11077_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11077_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Influenza A virus

EntireName: Influenza A virus
Components
  • Virus: Influenza A virus
    • Complex: Matrix protein 1

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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 / Sci species strain: A/Hong Kong/1/1968 (H3N2) / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Matrix protein 1

SupramoleculeName: Matrix protein 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: The M1 map was generated by subtomogram averaging of the M1 protein density in tomograms of influenza A virions.
Source (natural)Organism: Influenza A virus / Strain: A/Hong Kong/1/1968 (H3N2)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP

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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: COUNTING / Average electron dose: 3.2 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: 4.0 µm / Nominal defocus min: 1.5 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 12128
ExtractionNumber tomograms: 5 / Number images used: 100000
Method: Volumes picked semi-automatically along the particles membrane
Software: (Name: TOM, MATLAB, UCSF Chimera)
Details: Initial positions were generated by simulating the surface of a cylindricated volume around the manually determined central axis of each particle. Initial positions have been 2X oversampled.
CTF correctionSoftware: (Name: CTFFIND, NOVACTF)
Details: CTF determination was performed using CTFFIND4. CTF correction was performed using 3D-CTF correction by CTF multiplication in NovaCTF.
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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