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- EMDB-11079: Helical reconstruction of influenza A virus M1 in complex with nu... -

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Basic information

Entry
Database: EMDB / ID: EMD-11079
TitleHelical reconstruction of influenza A virus M1 in complex with nucleic acid.
Map datasymmetrised helical reconstruction map
Sample
  • Complex: Helical reconstruction of influenza A virus M1 protein in complex with nucleic acid
    • Protein or peptide: Matrix protein 1
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 (strain A/Puerto Rico/8/1934 H1N1)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsXiong X / Qu K / Briggs JAG
Funding support United Kingdom, Germany, European Union, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
German Research Foundation (DFG)240245660 - SFB1129 Germany
European Research Council (ERC)ERC-CoG-648432European Union
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 LJ / Schraidt O / Kummer S / Freund SMV / Krausslich HG / Briggs JAG
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: 0.0114
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0114
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z5l
  • Surface level: 0.0114
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6z5l
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11079.png

Downloads & links

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Map

FileDownload / File: emd_11079.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsymmetrised helical reconstruction map
Voxel sizeX=Y=Z: 1.128 Å
Density
Contour LevelBy AUTHOR: 0.0114 / Movie #1: 0.0114
Minimum - Maximum-0.01972976 - 0.052892283
Average (Standard dev.)0.0007184917 (±0.0037097456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 564.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z564.000564.000564.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0200.0530.001

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Supplemental data

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Mask #1

Fileemd_11079_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helical reconstruction of influenza A virus M1 protein in complex...

EntireName: Helical reconstruction of influenza A virus M1 protein in complex with nucleic acid
Components
  • Complex: Helical reconstruction of influenza A virus M1 protein in complex with nucleic acid
    • Protein or peptide: Matrix protein 1

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Supramolecule #1: Helical reconstruction of influenza A virus M1 protein in complex...

SupramoleculeName: Helical reconstruction of influenza A virus M1 protein in complex with nucleic acid
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Influenza A M1 in complex with 6.4 Kb DNA plasmid
Source (natural)Organism: Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta 2 / Recombinant plasmid: pET21b
Molecular weightExperimental: 28 KDa

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Macromolecule #1: Matrix protein 1

MacromoleculeName: Matrix protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Molecular weightTheoretical: 28.97143 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSLLTEVETY VLSIIPSGPL KAEIAQRLED VFAGKNTDLE VLMEWLKTRP ILSPLTKGIL GFVFTLTVPS ERGLQRRRFV QNALNGNGD PNNMDKAVKL YRKLKREITF HGAKEISLSY SAGALASCMG LIYNKMGAVT TEVAFGLVCA TCEQIADSQH R SHRQMVTT ...String:
MSLLTEVETY VLSIIPSGPL KAEIAQRLED VFAGKNTDLE VLMEWLKTRP ILSPLTKGIL GFVFTLTVPS ERGLQRRRFV QNALNGNGD PNNMDKAVKL YRKLKREITF HGAKEISLSY SAGALASCMG LIYNKMGAVT TEVAFGLVCA TCEQIADSQH R SHRQMVTT TNPLIRHENR MVLASTTAKA MEQMAGSSEQ AAEAMEVASQ ARQMVQAMRT IGTHPSSSAG LKNDLLENLQ AY QKRMGVQ MQRFKLEHHH HHH

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 10
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
100.0 mMC2H5NO2glycine
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Details: sample was applied 3 times each with 30s adsorption time.
DetailsM1 at 0.1 mg/ml plasmid DNA at 0.25 mg/ml

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2347 / Average electron dose: 47.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 463152 / Software - Name: SPRING (ver. 0.86)
Software - details: Used for selecting segments of similar diameters
Details: Manual picking
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.08)
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 3.08413 Å
Applied symmetry - Helical parameters - Δ&Phi: -11.1081 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 17984

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Atomic model buiding 1

Initial modelPDB ID:

1aa7


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 37.9 / Target criteria: correlation coefficient
Output model

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

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