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- EMDB-24303: In situ cryoET map of influenza A hemagglutinin -

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Basic information

Entry
Database: EMDB / ID: EMD-24303
TitleIn situ cryoET map of influenza A hemagglutinin
Map data
Sample
  • Virus: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
    • Protein or peptide: Influenza A H1 hemagglutinin
Biological speciesInfluenza A virus (A/Puerto Rico/8/1934(H1N1))
Methodsubtomogram averaging / cryo EM / Resolution: 12.9 Å
AuthorsHuang QY / Song K / Schiffer CA / Somasundaran M
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-14-PR United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135919 United States
CitationJournal: Structure / Year: 2022
Title: Quantitative structural analysis of influenza virus by cryo-electron tomography and convolutional neural networks.
Authors: Qiuyu J Huang / Kangkang Song / Chen Xu / Daniel N A Bolon / Jennifer P Wang / Robert W Finberg / Celia A Schiffer / Mohan Somasundaran /
Abstract: Influenza viruses pose severe public health threats globally. Influenza viruses are extensively pleomorphic, in shape, size, and organization of viral proteins. Analysis of influenza morphology and ...Influenza viruses pose severe public health threats globally. Influenza viruses are extensively pleomorphic, in shape, size, and organization of viral proteins. Analysis of influenza morphology and ultrastructure can help elucidate viral structure-function relationships and aid in therapeutics and vaccine development. While cryo-electron tomography (cryoET) can depict the 3D organization of pleomorphic influenza, the low signal-to-noise ratio inherent to cryoET and viral heterogeneity have precluded detailed characterization of influenza viruses. In this report, we leveraged convolutional neural networks and cryoET to characterize the morphological architecture of the A/Puerto Rico/8/34 (H1N1) influenza strain. Our pipeline improved the throughput of cryoET analysis and accurately identified viral components within tomograms. Using this approach, we successfully characterized influenza morphology, glycoprotein density, and conducted subtomogram averaging of influenza glycoproteins. Application of this processing pipeline can aid in the structural characterization of not only influenza viruses, but other pleomorphic viruses and infected cells.
History
DepositionJun 25, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateMay 18, 2022-
Current statusMay 18, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.002
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.002
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24303.png

Downloads & links

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Map

FileDownload / File: emd_24303.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.087 Å
Density
Contour LevelBy AUTHOR: 0.002 / Movie #1: 0.002
Minimum - Maximum-0.004592979 - 0.008658736
Average (Standard dev.)4.1595384e-05 (±0.00043742885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 400.70398 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.0872.0872.087
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z400.704400.704400.704
α/β/γ90.00090.00090.000
start NX/NY/NZ149141182
NX/NY/NZ215231150
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-0.0050.0090.000

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Supplemental data

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Half map: #2

Fileemd_24303_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_24303_half_map_2.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 : Influenza A virus (A/Puerto Rico/8/1934(H1N1))

EntireName: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Components
  • Virus: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
    • Protein or peptide: Influenza A H1 hemagglutinin

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Supramolecule #1: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

SupramoleculeName: Influenza A virus (A/Puerto Rico/8/1934(H1N1)) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purchased from Charles River Laboratories. / NCBI-ID: 211044
Sci species name: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 198 KDa

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Macromolecule #1: Influenza A H1 hemagglutinin

MacromoleculeName: Influenza A H1 hemagglutinin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
SequenceString: MKANLLVLLC ALAAADADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDSHNGKLCR LKGIAPLQLG KCNIAGWLLG NPECDPLLPV RSWSYIVETP NSENGICYPG DFIDYEELRE QLSSVSSFER FEIFPKESSW PNHNTTKGVT AACSHAGKSS FYRNLLWLTE ...String:
MKANLLVLLC ALAAADADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDSHNGKLCR LKGIAPLQLG KCNIAGWLLG NPECDPLLPV RSWSYIVETP NSENGICYPG DFIDYEELRE QLSSVSSFER FEIFPKESSW PNHNTTKGVT AACSHAGKSS FYRNLLWLTE KEGSYPKLKN SYVNKKGKEV LVLWGIHHPS NSKDQQNIYQ NENAYVSVVT SNYNRRFTPE IAERPKVRDQ AGRMNYYWTL LKPGDTIIFE ANGNLIAPRY AFALSRGFGS GIITSNASMH ECNTKCQTPL GAINSSLPFQ NIHPVTIGEC PKYVRSAKLR MVTGLRNIPS IQSRGLFGAI AGFIEGGWTG MIDGWYGYHH QNEQGSGYAA DQKSTQNAIN GITNKVNSVI EKMNIQFTAV GKEFNKLEKR MENLNKKVDD GFLDIWTYNA ELLVLLENER TLDFHDSNVK NLYEKVKSQL KNNAKEIGNG CFEFYHKCDN ECMESVRNGT YDYPKYSEES KLNREKVDGV KLESMGIYQI LAIYSTVASS LVLLVSLGAI SFWMCSNGSL QCRICI

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: EMS-002 RAPID IMMERSION FREEZER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.91) / Number subtomograms used: 76519
ExtractionNumber tomograms: 12 / Number images used: 85021 / Method: Convolutional neural network picker
Final angle assignmentType: NOT APPLICABLE
Crystal parametersUnit cell - A: 400.70398 Å / Unit cell - B: 400.70398 Å / Unit cell - C: 400.70398 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: 1
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1ruz

RefinementProtocol: FLEXIBLE FIT

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