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- EMDB-11078: The structure of the matrix protein M1 from influenza A/Hong Kong... -

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Basic information

Entry
Database: EMDB / ID: EMD-11078
TitleThe structure of the matrix protein M1 from influenza A/Hong Kong/1/1968 VLPs (HA,NA,M1,M2)
Map dataStructure of the influenza A matrix protein M1 from influenza A/Hong Kong/1/1968 VLPs (HA,NA,M1,M2)
Sample
  • Virus: Influenza A virus
    • Complex: Matrix protein 1
      • Protein or peptide: Matrix protein 1
  • Ligand: water
KeywordsViral matrix protein / Membrane binding / pH Sensor / Polymer / VIRAL PROTEIN
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 / Influenza A virus (A/Puerto Rico/8-9NMC3/1934(H1N1))
Methodsubtomogram averaging / cryo EM / Resolution: 8.0 Å
AuthorsPeukes J / Xiong X
Funding supportEuropean Union, United Kingdom, Germany, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-648432European Union
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
German Research Foundation (DFG)project number 240245660 - SFB1129 Germany
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-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z5j
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6z5j
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11078.png

Downloads & links

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Map

FileDownload / File: emd_11078.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/1/1968 VLPs (HA,NA,M1,M2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.78 Å/pix.
x 120 pix.
= 213.6 Å		1.78 Å/pix.
x 120 pix.
= 213.6 Å		1.78 Å/pix.
x 120 pix.
= 213.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.6
Minimum - Maximum-2.1210978 - 2.724315
Average (Standard dev.)0.00067154894 (±0.28326413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 213.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z213.600213.600213.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-2.1212.7240.001

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Supplemental data

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Mask #1

Fileemd_11078_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11078_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11078_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

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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
      • Protein or peptide: Matrix protein 1
  • Ligand: water

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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)

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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 (HK68) virus like particles (VLPs) that were generated by expression of the viral protein HA,NA,M1,M2
Source (natural)Organism: Influenza A virus / Strain: A/Hong Kong/1/1968 (H3N2)

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Macromolecule #1: Matrix protein 1

MacromoleculeName: Matrix protein 1 / type: protein_or_peptide / ID: 1
Details: The PDB model was generated by rigid body fitting of the M1 NTD crystal structure (PBD: 1ea3, from PR8 influenza virus) into the EM density map obtained for HK68 VLPs.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Puerto Rico/8-9NMC3/1934(H1N1))
Strain: A/Puerto Rico/8-9NMC3/1934(H1N1)
Molecular weightTheoretical: 27.928301 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLLTEVETY VLSIIPSGPL KAEIAQRLED VFAGKNTDLE VLMEWLKTRP ILSPLTKGIL GFVFTLTVPS ERGLQRRRFV QNALNGNGD PNNMDKAVKL YRKLKREITF HGAKEISLSY SAGALASCMG LIYNRMGAVT TEVAFGLVCA TCEQIADSQH R SHRQMVTT ...String:
MSLLTEVETY VLSIIPSGPL KAEIAQRLED VFAGKNTDLE VLMEWLKTRP ILSPLTKGIL GFVFTLTVPS ERGLQRRRFV QNALNGNGD PNNMDKAVKL YRKLKREITF HGAKEISLSY SAGALASCMG LIYNRMGAVT TEVAFGLVCA TCEQIADSQH R SHRQMVTT TNPLIRHENR MVLASTTAKA MEQMAGSSEQ AAEAMEVASQ ARQMVQAMRT IGTHPSSSAG LKNDLLENLQ AY QKRMGVQ MQRFK

UniProtKB: Matrix protein 1

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 258 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 / Pretreatment - Type: GLOW DISCHARGE
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: 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: 4.0 µm / Nominal defocus min: 2.0 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) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: NOVACTF / Number subtomograms used: 14767
ExtractionNumber tomograms: 4 / Number images used: 120000
Method: Volumes picked semi-automatically along the particles membrane
Software: (Name: TOM, MATLAB, UCSF Chimera)
Details: Initial positions were generated along the surface of a cylinder simulated around the manually determined central axis of each particle. Initial positions were at least 2X oversampled.
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1ea3


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsMultiple copies of the M1 NTD crystal structure (PDB:1ea3) were fitted as rigid bodies into the EM map to understand the relative arrangement of M1 monomers in the context of the matrix layer inside the virus
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6z5j:
Arrangement of the matrix protein M1 in influenza A/Hong Kong/1/1968 VLPs (HA,NA,M1,M2)

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