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- EMDB-10813: In-situ structure of a dimer of the trimeric HEF from influenza C... -

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Basic information

Entry
Database: EMDB / ID: EMD-10813
TitleIn-situ structure of a dimer of the trimeric HEF from influenza C viral particles without a matrix layer by cryo-ET
Map dataPost-processed map. Dimer of trimers from virions without a matrix layer
Sample
  • Virus: Influenza C virus
    • Protein or peptide: Hemagglutinin esterase fusion
Function / homology
Function and homology information


sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase / viral budding from plasma membrane / endocytosis involved in viral entry into host cell / host cell surface receptor binding / 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 / endocytosis involved in viral entry into host cell / host cell surface receptor binding / 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 speciesCanis lupus (gray wolf) / Influenza C virus
Methodsubtomogram averaging / cryo EM / Resolution: 11.3 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-
UpdateApr 7, 2021-
Current statusApr 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10813.png

Downloads & links

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Map

FileDownload / File: emd_10813.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed map. Dimer of trimers from virions without a matrix layer
Voxel sizeX=Y=Z: 2.2 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.15331967 - 0.21219388
Average (Standard dev.)0.00048974244 (±0.015747678)
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-0.1530.2120.000

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Supplemental data

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Mask #1

Fileemd_10813_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_10813_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_10813_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_10813_half_map_2.map
AnnotationHalf map 2
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 C virus

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

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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: 11552 / Sci species name: Influenza C virus / Sci species strain: C/Johannesburg/1/1966 / 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

MacromoleculeName: Hemagglutinin esterase fusion / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: sialate O-acetylesterase
Source (natural)Organism: Canis lupus (gray wolf)
SequenceString: MFFSLLLVLG LTEAEKIKIC LQKQVNSSFS LHNGFGGNLY ATEEKRMFEL VKPKAGASVL NQSTWIGFG DSRTDKSNSA FPRSADVSAK TADKFRFLSG GSLMLSMFGP PGKVDYLYQG C GKHKVFYE GVNWSPHAAI NCYRKNWTDI KLNFQKNIYE LASQSHCMSL ...String:
MFFSLLLVLG LTEAEKIKIC LQKQVNSSFS LHNGFGGNLY ATEEKRMFEL VKPKAGASVL NQSTWIGFG DSRTDKSNSA FPRSADVSAK TADKFRFLSG GSLMLSMFGP PGKVDYLYQG C GKHKVFYE GVNWSPHAAI NCYRKNWTDI KLNFQKNIYE LASQSHCMSL VNALDKTIPL QV TAGTAGN CNNSFLKNPA LYTQEVKPSE NKCGKENLAF FTLPTQFGTY ECKLHLVASC YFI YDSKEV YNKRGCDNYF QVIYDSFGKV VGGLDNRVSP YTGNSGDTPT MQCDMLQLKP GRYS VRSSP RFLLMPERSY CFDMKEKGPV TAVQSIWGKG RESDYAVDQA CLSTPGCMLI QKQKP YIGE ADDHHGDQEM RELLSGLDYE ARCISQSGWV NETSPFTEKY LLPPKFGRCP LAAKEE SIP KIPDGLLIPT SGTDTTVTKP KSRIFGIDDL IIGVLFVAIV ETGIGGYLLG SRKESGG GV TKESAEKGFE KIGNDIQILK SSINIAIEKL NDRISHDEQA IRDLTLEIEN ARSEALLG E LGIIRALLVG NISIGLQESL WELASEITNR AGDLAVEVSP GCWIIDNNIC DQSCQNFIF KFNETAPVPT IPPLDTKIDL QSDPFYWGSS LGLAITATIS LAALVISGIA ICRTK

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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 chloridesodium chloride
10.0 mMCaCl2calcium chloride
GridModel: Quantifoil / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.0045000000000000005 µm / Nominal defocus min: 0.0025 µm / Nominal magnification: 64000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 41 / Number images used: 31947 / Method: Random seeds / Details: A vesicle model with random seeds on the surface.
CTF correctionSoftware: (Name: CTFFIND (ver. 4.1.5), NOVACTF)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 11.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number subtomograms used: 8142
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1flc

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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