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- EMDB-10810: In-situ structure of the trimeric HEF from influenza C viral part... -

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Basic information

Entry
Database: EMDB / ID: EMD-10810
TitleIn-situ structure of the trimeric HEF from influenza C viral particles with a matrix layer by cryo-ET
Map dataFiltered map
Sample
  • Virus: Influenza C virus
    • Protein or peptide: Hemagglutinin-esterase-fusion glycoprotein
    • Protein or peptide: Hemagglutinin-esterase-fusion glycoprotein
KeywordsReceptor / esterase / fusion / influenza / VIRAL PROTEIN
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 (strain C/Johannesburg/1/1966) / Influenza C virus
Methodsubtomogram averaging / cryo EM / Resolution: 9.1 Å
AuthorsHalldorsson S / Rosenthal PB
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)FC001143 United Kingdom
Wellcome TrustFC001143 United Kingdom
Cancer Research UKFC001143 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: In situ structure and organization of the influenza C virus surface glycoprotein.
Authors: Steinar Halldorsson / Kasim Sader / Jack Turner / Lesley J Calder / Peter B Rosenthal /
Abstract: The lipid-enveloped influenza C virus contains a single surface glycoprotein, the haemagglutinin-esterase-fusion (HEF) protein, that mediates receptor binding, receptor destruction, and membrane ...The lipid-enveloped influenza C virus contains a single surface glycoprotein, the haemagglutinin-esterase-fusion (HEF) protein, that mediates receptor binding, receptor destruction, and membrane fusion at the low pH of the endosome. Here we apply electron cryotomography and subtomogram averaging to describe the structural basis for hexagonal lattice formation by HEF on the viral surface. The conformation of the glycoprotein in situ is distinct from the structure of the isolated trimeric ectodomain, showing that a splaying of the membrane distal domains is required to mediate contacts that form the lattice. The splaying of these domains is also coupled to changes in the structure of the stem region which is involved in membrane fusion, thereby linking HEF's membrane fusion conformation with its assembly on the virus surface. The glycoprotein lattice can form independent of other virion components but we show a major role for the matrix layer in particle formation.
History
DepositionMar 31, 2020-
Header (metadata) releaseMar 24, 2021-
Map releaseMar 24, 2021-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yi5
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6yi5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10810.png

Downloads & links

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Map

FileDownload / File: emd_10810.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFiltered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 200 pix.
= 440. Å		2.2 Å/pix.
x 200 pix.
= 440. Å		2.2 Å/pix.
x 200 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.41414785 - 0.57119703
Average (Standard dev.)0.00081748265 (±0.028198803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z440.000440.000440.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.4140.5710.001

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Supplemental data

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Mask #1

Fileemd_10810_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unfiltered map

Fileemd_10810_additional_1.map
AnnotationUnfiltered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_10810_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_10810_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Influenza C virus

EntireName: Influenza C virus
Components
  • Virus: Influenza C virus
    • Protein or peptide: Hemagglutinin-esterase-fusion glycoprotein
    • Protein or peptide: Hemagglutinin-esterase-fusion glycoprotein

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Supramolecule #1: Influenza C virus

SupramoleculeName: Influenza C virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified from infected cells. / NCBI-ID: 100673 / Sci species name: Influenza C virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Hemagglutinin-esterase-fusion glycoprotein

MacromoleculeName: Hemagglutinin-esterase-fusion glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: sialate O-acetylesterase
Source (natural)Organism: Influenza C virus (strain C/Johannesburg/1/1966)
Molecular weightTheoretical: 48.230699 KDa
SequenceString: EKIKICLQKQ VNSSFSLHNG FGGNLYATEE KRMFELVKPK AGASVLNQST WIGFGDSRTD KSNSAFPRSA DVSAKTADKF RFLSGGSLM LSMFGPPGKV DYLYQGCGKH KVFYEGVNWS PHAAINCYRK NWTDIKLNFQ KNIYELASQS HCMSLVNALD K TIPLQVTA ...String:
EKIKICLQKQ VNSSFSLHNG FGGNLYATEE KRMFELVKPK AGASVLNQST WIGFGDSRTD KSNSAFPRSA DVSAKTADKF RFLSGGSLM LSMFGPPGKV DYLYQGCGKH KVFYEGVNWS PHAAINCYRK NWTDIKLNFQ KNIYELASQS HCMSLVNALD K TIPLQVTA GTAGNCNNSF LKNPALYTQE VKPSENKCGK ENLAFFTLPT QFGTYECKLH LVASCYFIYD SKEVYNKRGC DN YFQVIYD SFGKVVGGLD NRVSPYTGNS GDTPTMQCDM LQLKPGRYSV RSSPRFLLMP ERSYCFDMKE KGPVTAVQSI WGK GRESDY AVDQACLSTP GCMLIQKQKP YIGEADDHHG DQEMRELLSG LDYEARCISQ SGWVNETSPF TEKYLLPPKF GRCP LAAKE ESIPKIPDGL LIPTSGTDTT VTKPKSR

UniProtKB: Hemagglutinin-esterase-fusion glycoprotein

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Macromolecule #2: Hemagglutinin-esterase-fusion glycoprotein

MacromoleculeName: Hemagglutinin-esterase-fusion glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: sialate O-acetylesterase
Source (natural)Organism: Influenza C virus (strain C/Johannesburg/1/1966)
Molecular weightTheoretical: 18.977541 KDa
SequenceString:
IFGIDDLIIG VLFVAIVETG IGGYLLGSRK ESGGGVTKES AEKGFEKIGN DIQILKSSIN IAIEKLNDRI SHDEQAIRDL TLEIENARS EALLGELGII RALLVGNISI GLQESLWELA SEITNRAGDL AVEVSPGCWI IDNNICDQSC QNFIFKFNET A PVPTIPPL DTKIDLQ

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
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 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 2 / Average exposure time: 1.57 sec. / Average electron dose: 1.57 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: 0.0045000000000000005 µm / Nominal defocus min: 0.0025 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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 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) / Number subtomograms used: 14057
ExtractionNumber tomograms: 41 / Number images used: 31947 / Method: Random seeds / Software - Name: Dynamo (ver. 1.4.01) / Details: A vesicle model with random seeds on the surface.
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1flc


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6yi5:
In-situ structure of the trimeric HEF from influenza C by flexible fitting into a cryo-ET map.

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