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- PDB-7jm3: Full-length three-dimensional structure of the influenza A virus ... -

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Basic information

Entry
Database: PDB / ID: 7jm3
TitleFull-length three-dimensional structure of the influenza A virus M1 protein and its organization into a matrix layer
ComponentsMatrix protein 1
KeywordsVIRAL PROTEIN / influenza A / virus / matrix layer / M1 protein
Function / homology
Function and homology information


Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery ...Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral mRNA Translation / viral budding from plasma membrane / structural constituent of virion / host cell nucleus / virion membrane / RNA binding / extracellular region / plasma 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
Matrix protein 1 / Matrix protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSu, Z. / Pintilie, G. / Selzer, L. / Chiu, W. / Kirkegaard, K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)P41GM103832 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)S10OD021600 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)P30 CA124435 United States
Citation
Journal: PLoS Biol / Year: 2020
Title: Full-length three-dimensional structure of the influenza A virus M1 protein and its organization into a matrix layer.
Authors: Lisa Selzer / Zhaoming Su / Grigore D Pintilie / Wah Chiu / Karla Kirkegaard /
Abstract: Matrix proteins are encoded by many enveloped viruses, including influenza viruses, herpes viruses, and coronaviruses. Underneath the viral envelope of influenza virus, matrix protein 1 (M1) forms an ...Matrix proteins are encoded by many enveloped viruses, including influenza viruses, herpes viruses, and coronaviruses. Underneath the viral envelope of influenza virus, matrix protein 1 (M1) forms an oligomeric layer critical for particle stability and pH-dependent RNA genome release. However, high-resolution structures of full-length monomeric M1 and the matrix layer have not been available, impeding antiviral targeting and understanding of the pH-dependent transitions involved in cell entry. Here, purification and extensive mutagenesis revealed protein-protein interfaces required for the formation of multilayered helical M1 oligomers similar to those observed in virions exposed to the low pH of cell entry. However, single-layered helical oligomers with biochemical and ultrastructural similarity to those found in infectious virions before cell entry were observed upon mutation of a single amino acid. The highly ordered structure of the single-layered oligomers and their likeness to the matrix layer of intact virions prompted structural analysis by cryo-electron microscopy (cryo-EM). The resulting 3.4-Å-resolution structure revealed the molecular details of M1 folding and its organization within the single-shelled matrix. The solution of the full-length M1 structure, the identification of critical assembly interfaces, and the development of M1 assembly assays with purified proteins are crucial advances for antiviral targeting of influenza viruses.
#1: Journal: Plos Biol. / Year: 2020
Title: Full-length three-dimensional structure of the influenza A virus M1 protein and its organization into a matrix layer
Authors: Selzer, L. / Su, Z. / Pintilie, G. / Chiu, W. / Kirkegaard, K.
History
DepositionJul 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-22384
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
C: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)27,8271
Polymers27,8271
Non-polymers00
Water00
1
C: Matrix protein 1
x 60


Theoretical massNumber of molelcules
Total (without water)1,669,62960
Polymers1,669,62960
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation59
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 60 / Rise per n subunits: 1.96 Å / Rotation per n subunits: 17.1 °)

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Components

#1: Protein Matrix protein 1 / M1


Mass: 27827.152 Da / Num. of mol.: 1 / Mutation: V97K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: M1, M / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2KIU5, UniProt: P03485*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: M1-V97K oligomer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 143 kDa/nm / Experimental value: NO
Source (natural)Organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid1
22 Msodium chlorideNaCl1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Influenza A virus matrix protein with V97K mutation assembled in vitro
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blot for 3 seconds once before plunging.

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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: 165000 X / Calibrated defocus min: 300 nm / Calibrated defocus max: 4300 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 78 K / Temperature (min): 78 K
Image recordingAverage exposure time: 4 sec. / Electron dose: 36 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 440
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 20 / Used frames/image: 1-20

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN22.23particle selection
2SerialEMimage acquisitionManual
4CTFFIND4.1.18CTF correction
7Coot0.8model fitting
9PHENIX1.17model refinement
10RELION3.0.6initial Euler assignment
11RELION3.0.6final Euler assignment
12RELION3.0.6classification
13RELION3.0.63D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 17.1 ° / Axial rise/subunit: 1.96 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 2268
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56602 / Algorithm: FOURIER SPACE / Num. of class averages: 200 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 1EA3

1ea3


Accession code: 1EA3 / Source name: PDB / Type: experimental model

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