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- EMDB-17001: In-situ structure of the hexameric HEF trimers from influenza C v... -

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Basic information

Entry
Database: EMDB / ID: EMD-17001
TitleIn-situ structure of the hexameric HEF trimers from influenza C viral particles
Map data
Sample
  • Virus: Influenza C virus (C/Johannesburg/1/66)
    • Protein or peptide: Haemagglutinin-esterase-fusion 1 glycoprotein
    • Protein or peptide: Haemagglutinin-esterase-fusion 2 glycoprotein
KeywordsClass 1 fusion protein / membrane fusion / viral assembly / hexameric / VIRUS
Function / homology
Function and homology information


sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase / viral budding from plasma membrane / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase / viral budding from plasma membrane / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin stalk, influenza C / Influenza C hemagglutinin stalk / Haemagglutinin-esterase glycoprotein, haemagglutinin domain / Haemagglutinin-esterase glycoprotein, core / Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein / Hemagglutinin esterase / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin-esterase-fusion glycoprotein
Similarity search - Component
Biological speciesInfluenza C virus (C/Johannesburg/1/66)
Methodsubtomogram averaging / cryo EM / Resolution: 9.1 Å
AuthorsLiu ZB / Rosenthal PB
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: To Be Published
Title: Topological defects in the spherical virus crystal
Authors: Liu ZB / Rosenthal PB
History
DepositionApr 4, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17001.png

Downloads & links

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Map

FileDownload / File: emd_17001.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 256 pix.
= 353.28 Å		1.38 Å/pix.
x 256 pix.
= 353.28 Å		1.38 Å/pix.
x 256 pix.
= 353.28 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.12809622 - 0.12090022
Average (Standard dev.)0.0004280312 (±0.016545486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17001_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17001_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17001_half_map_2.map
Projections & Slices
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Sample components

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Entire : Influenza C virus (C/Johannesburg/1/66)

EntireName: Influenza C virus (C/Johannesburg/1/66)
Components
  • Virus: Influenza C virus (C/Johannesburg/1/66)
    • Protein or peptide: Haemagglutinin-esterase-fusion 1 glycoprotein
    • Protein or peptide: Haemagglutinin-esterase-fusion 2 glycoprotein

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Supramolecule #1: Influenza C virus (C/Johannesburg/1/66)

SupramoleculeName: Influenza C virus (C/Johannesburg/1/66) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified viruses / NCBI-ID: 100673 / Sci species name: Influenza C virus (C/Johannesburg/1/66) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Molecular weightTheoretical: 1.24 MDa

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Macromolecule #1: Haemagglutinin-esterase-fusion 1 glycoprotein

MacromoleculeName: Haemagglutinin-esterase-fusion 1 glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: sialate O-acetylesterase
Source (natural)Organism: Influenza C virus (C/Johannesburg/1/66)
SequenceString: EKIKICLQKQ VNSSFSLHNG FGGNLYATEE KRMFELVKPK AGASVLNQST WIGFGDSRTD KSNSAFPRSA DVSAKTADKF RFLSGGSLML SMFGPPGKVD YLYQGCGKHK VFYEGVNWSP HAAINCYRKN WTDIKLNFQK NIYELASQSH CMSLVNALDK TIPLQVTAGT ...String:
EKIKICLQKQ VNSSFSLHNG FGGNLYATEE KRMFELVKPK AGASVLNQST WIGFGDSRTD KSNSAFPRSA DVSAKTADKF RFLSGGSLML SMFGPPGKVD YLYQGCGKHK VFYEGVNWSP HAAINCYRKN WTDIKLNFQK NIYELASQSH CMSLVNALDK TIPLQVTAGT AGNCNNSFLK NPALYTQEVK PSENKCGKEN LAFFTLPTQF GTYECKLHLV ASCYFIYDSK EVYNKRGCDN YFQVIYDSFG KVVGGLDNRV SPYTGNSGDT PTMQCDMLQL KPGRYSVRSS PRFLLMPERS YCFDMKEKGP VTAVQSIWGK GRESDYAVDQ ACLSTPGCML IQKQKPYIGE ADDHHGDQEM RELLSGLDYE ARCISQSGWV NETSPFTEKY LLPPKFGRCP LAAKEESIPK IPDGLLIPTS GTDTTVTKPK SR

UniProtKB: Hemagglutinin-esterase-fusion glycoprotein

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Macromolecule #2: Haemagglutinin-esterase-fusion 2 glycoprotein

MacromoleculeName: Haemagglutinin-esterase-fusion 2 glycoprotein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: sialate O-acetylesterase
Source (natural)Organism: Influenza C virus (C/Johannesburg/1/66)
SequenceString:
IFGIDDLIIG VLFVAIVETG IGGYLLGSRK ESGGGVTKES AEKGFEKIGN DIQILKSSIN IAIEKLNDRI SHDEQAIRDL TLEIENARSE ALLGELGIIR ALLVGNISIG LQESLWELAS EITNRAGDLA VEVSPGCWII DNNICDQSCQ NFIFKFNETA PVPTIPPLDT KIDLQ

UniProtKB: Hemagglutinin-esterase-fusion glycoprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTRISTris
150.0 mMNaClSodium chloride
10.0 mMCaCl2Calcium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AMYLAMINE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III
DetailsHeterogeneous mix of viral particles, viral like particles and cellular vesicles

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number real images: 1 / Average exposure time: 1.1 sec. / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 64000
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 reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number subtomograms used: 35001
ExtractionNumber tomograms: 83 / Number images used: 83 / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6yi5


Chain - Source name: PDB / Chain - Initial model type: experimental model

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