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- EMDB-22384: Full-length three-dimensional structure of the influenza A virus ... -

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Basic information

Entry
Database: EMDB / ID: EMD-22384
TitleFull-length three-dimensional structure of the influenza A virus M1 protein and its organization into a matrix layer
Map data
Sample
  • Complex: M1-V97K oligomer
    • Protein or peptide: Matrix protein 1
Keywordsinfluenza A / virus / matrix layer / M1 protein / VIRAL 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 (A/Puerto Rico/8/1934(H1N1)) / Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSu Z / Pintilie G
Funding support United States, 3 items
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, 2020-
Header (metadata) releaseAug 12, 2020-
Map releaseAug 12, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jm3
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7jm3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22384.png

Downloads & links

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Map

FileDownload / File: emd_22384.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.024308806 - 0.049378447
Average (Standard dev.)0.00031036927 (±0.002329324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 393.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0240.0490.000

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Supplemental data

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Additional map: Segmented M1 protein

Fileemd_22384_additional.map
AnnotationSegmented M1 protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Segmented M1 protein

Fileemd_22384_additional_1.map
AnnotationSegmented M1 protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : M1-V97K oligomer

EntireName: M1-V97K oligomer
Components
  • Complex: M1-V97K oligomer
    • Protein or peptide: Matrix protein 1

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Supramolecule #1: M1-V97K oligomer

SupramoleculeName: M1-V97K oligomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Molecular weightTheoretical: 143 kDa/nm

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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)
Strain: A/Puerto Rico/8/1934 H1N1
Molecular weightTheoretical: 27.827152 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SLLTEVETYV LSIIPSGPLK AEIAQRLEDV FAGKNTDLEV LMEWLKTRPI LSPLTKGILG FVFTLTVPSE RGLQRRRFVQ NALNGNGDP NNMDKAKKLY RKLKREITFH GAKEISLSYS AGALASCMGL IYNRMGAVTT EVAFGLVCAT CEQIADSQHR S HRQMVTTT ...String:
SLLTEVETYV LSIIPSGPLK AEIAQRLEDV FAGKNTDLEV LMEWLKTRPI LSPLTKGILG FVFTLTVPSE RGLQRRRFVQ NALNGNGDP NNMDKAKKLY RKLKREITFH GAKEISLSYS AGALASCMGL IYNRMGAVTT EVAFGLVCAT CEQIADSQHR S HRQMVTTT NPLIRHENRM VLASTTAKAM EQMAGSSEQA AEAMEVASQA RQMVQAMRTI GTHPSSSAGL KNDLLENLQA YQ KRMGVQM QRFK

UniProtKB: Matrix protein 1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration5 mg/mL
BufferpH: 7
Component:
ConcentrationNameFormula
50.0 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
2.0 Msodium chlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 3 seconds once before plunging..
DetailsInfluenza A virus matrix protein with V97K mutation assembled in vitro

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.0 K / Max: 78.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-20 / Number grids imaged: 2 / Number real images: 440 / Average exposure time: 4.0 sec. / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 4.3 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000
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 reconstructionNumber classes used: 200
Applied symmetry - Helical parameters - Δz: 1.96 Å
Applied symmetry - Helical parameters - Δ&Phi: 17.1 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 56602
Segment selectionNumber selected: 2268 / Software - Name: EMAN2 (ver. 2.23)
Startup modelType of model: INSILICO MODEL / In silico model: EMAN2.23
Details: Created a cylindrical density map in EMAN2 and used it as an initial model.
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0.6)

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Atomic model buiding 1

Initial modelPDB ID:

1ea3


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Correlation coefficient
Output model

PDB-7jm3:
Full-length three-dimensional structure of the influenza A virus M1 protein and its organization into a matrix layer

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