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- PDB-6z5l: Helical reconstruction of influenza A virus M1 in complex with nu... -

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Basic information

Entry
Database: PDB / ID: 6z5l
TitleHelical reconstruction of influenza A virus M1 in complex with nucleic acid.
ComponentsMatrix protein 1
KeywordsVIRAL PROTEIN / M1 / Matrix protein / Influenza virus / Assembly / ribonucleoprotein complex
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
Biological speciesInfluenza A virus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsXiong, X. / Qu, K. / Briggs, J.A.G.
Funding support United Kingdom, European Union, Germany, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
European Research Council (ERC)ERC-CoG-648432European Union
German Research Foundation (DFG)240245660 - SFB1129 Germany
Citation
Journal: 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.
#1: Journal: Biorxiv / Year: 2020
Title: The native structure of the full-length, assembled influenza A virus matrix protein, M1.
Authors: Peukes, J. / Xiong, X. / Erlendsson, S. / Qu, K. / Wan, W. / Calder, L.J. / Schraidt, O. / Kummer, S. / Freund, S.M.V. / Krausslich, H.G. / Briggs, J.A.G.
History
DepositionMay 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Dec 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

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Assembly

Deposited unit
A: Matrix protein 1


Theoretical massNumber of molelcules
Total (without water)28,9711
Polymers28,9711
Non-polymers00
Water0
1
A: Matrix protein 1
x 80


Theoretical massNumber of molelcules
Total (without water)2,317,71480
Polymers2,317,71480
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation79

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Components

#1: Protein Matrix protein 1 / M1


Mass: 28971.430 Da / Num. of mol.: 1 / Mutation: R134K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Variant: R134K / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: P03485

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Helical reconstruction of influenza A virus M1 protein in complex with nucleic acid
Type: COMPLEX / Details: Influenza A M1 in complex with 6.4 Kb DNA plasmid / Entity ID: all / Source: RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.028 MDaYES
213.978 MDaYES
310.028 MDaYES
Source (natural)Organism: Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: Rosetta 2 / Plasmid: pET21b
Buffer solutionpH: 10
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaClSodium chloride1
2100 mMglycineC2H5NO21
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: M1 at 0.1 mg/ml plasmid DNA at 0.25 mg/ml
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K
Details: sample was applied 3 times each with 30s adsorption time

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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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 47.1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2347
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2SPRING0.86particle selectionUsed for selecting segments of similar diameters
3SerialEM3.7image acquisition
5CTFFIND4CTF correction
8Coot0.9model fitting
10PHENIX1.18.2model refinement
11RELION3.08initial Euler assignment
12RELION3.08final Euler assignment
13RELION3.08classification
14RELION3.083D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -11.1081 ° / Axial rise/subunit: 3.08413 Å / Axial symmetry: D1
Particle selectionNum. of particles selected: 463152 / Details: Manual picking
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17984 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingB value: 37.9 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: correlation coefficient
Atomic model buildingPDB-ID: 1AA7

1aa7


Pdb chain-ID: A
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00431392
ELECTRON MICROSCOPYf_angle_d0.45342272
ELECTRON MICROSCOPYf_dihedral_angle_d24.7584336
ELECTRON MICROSCOPYf_chiral_restr0.0354896
ELECTRON MICROSCOPYf_plane_restr0.0035456

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