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- PDB-6z5j: Arrangement of the matrix protein M1 in influenza A/Hong Kong/1/1... -

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Basic information

Entry
Database: PDB / ID: 6z5j
TitleArrangement of the matrix protein M1 in influenza A/Hong Kong/1/1968 VLPs (HA,NA,M1,M2)
ComponentsMatrix protein 1
KeywordsVIRAL PROTEIN / Viral matrix protein / Membrane binding / pH Sensor / Polymer
Function / homology
Function and homology information


viral budding from plasma membrane / structural constituent of virion / host cell nucleus / virion membrane / RNA binding
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
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8 Å
AuthorsPeukes, J. / Xiong, X. / Erlendsson, S. / Qu, K. / Wan, W. / Kraeusslich, H.-G. / Briggs, J.A.G.
Funding supportEuropean Union, United Kingdom, Germany, 3items
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, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
E: Matrix protein 1
F: Matrix protein 1
D: Matrix protein 1
C: Matrix protein 1
B: Matrix protein 1
A: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)167,5706
Polymers167,5706
Non-polymers00
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, The assembly has been determined by tomography and subtomogram averaging
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Matrix protein 1 / M1


Mass: 27928.301 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8-9NMC3/1934(H1N1))
Strain: A/Puerto Rico/8-9NMC3/1934(H1N1) / Gene: M1, M / Cell line (production host): HEK293-T / Production host: Homo sapiens (human) / References: UniProt: F0TTD6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Influenza A virusVIRUSvirus like particles were formed by expressing plasmids coding for a subset (HA,NA,M1,M2) of the viral proteins#10RECOMBINANT
2Matrix protein 1COMPLEXThe 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#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Influenza A virus11320A/Hong Kong/1/1968 (H3N2)
32Influenza A virus11320A/Hong Kong/1/1968 (H3N2)
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606HEK293-T
32Homo sapiens (human)9606HEK293-T
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11YESYESOTHERVIRUS-LIKE PARTICLE
22
Natural host
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens9606
12
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.9 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20

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Processing

EM software
IDNameCategory
1TOMvolume selection
2MATLABvolume selection
3UCSF Chimeravolume selection
4SerialEMimage acquisition
6CTFFINDCTF correction
7NOVACTFCTF correction
10UCSF Chimeramodel fitting
16NOVACTF3D reconstruction
CTF correctionDetails: CTF determination was performed using CTFFIND4. CTF correction was performed by 3D-CTF correction by CTF multiplication in NovaCTF.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14767 / Algorithm: BACK PROJECTION / Symmetry type: POINT
EM volume selectionMethod: Volumes picked semi-automatically along the particles membrane
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.
Num. of tomograms: 4 / Num. of volumes extracted: 120000
Atomic model buildingProtocol: RIGID BODY FIT
Details: Multiple 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
Atomic model buildingPDB-ID: 1EA3

1ea3


Pdb chain-ID: A / Accession code: 1EA3 / Source name: PDB / Type: experimental model

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