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- PDB-6yi5: In-situ structure of the trimeric HEF from influenza C by flexibl... -

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Basic information

Entry
Database: PDB / ID: 6yi5
TitleIn-situ structure of the trimeric HEF from influenza C by flexible fitting into a cryo-ET map.
Components(Hemagglutinin-esterase-fusion glycoprotein) x 2
KeywordsVIRAL PROTEIN / Receptor / esterase / fusion / influenza
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
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.1 Å
AuthorsHalldorsson, S. / Rosenthal, P.B.
Funding support United Kingdom, 3items
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, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Hemagglutinin-esterase-fusion glycoprotein
B: Hemagglutinin-esterase-fusion glycoprotein
E: Hemagglutinin-esterase-fusion glycoprotein
F: Hemagglutinin-esterase-fusion glycoprotein
C: Hemagglutinin-esterase-fusion glycoprotein
D: Hemagglutinin-esterase-fusion glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,90415
Polymers201,6256
Non-polymers5,2799
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Cryo electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area31920 Å2
ΔGint-55 kcal/mol
Surface area77140 Å2
MethodPISA

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Components

#1: Protein Hemagglutinin-esterase-fusion glycoprotein / HEF


Mass: 48230.699 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Influenza C virus (strain C/Johannesburg/1/1966)
Cell line: MDCK / References: UniProt: P07975, sialate O-acetylesterase
#2: Protein Hemagglutinin-esterase-fusion glycoprotein / HEF


Mass: 18977.541 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Influenza C virus (strain C/Johannesburg/1/1966)
Cell line: MDCK / References: UniProt: P07975, sialate O-acetylesterase
#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Influenza C virus / Type: VIRUS / Details: Purified from infected cells. / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Influenza C virus
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTRIS1
2150 mMsodium chlorideNaCl1
310 mMcalcium chlorideCaCl21
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Heterogeneous mix of viral particles, viral like particles and cellular vesicles
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 4.5 nm / Nominal defocus min: 2.5 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.57 sec. / Electron dose: 1.57 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 2
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 4

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Processing

EM software
IDNameVersionCategory
1Dynamo1.4.01volume selection
4CTFFIND4.1.5CTF correction
5NOVACTFCTF correction
8MDFF0.5model fitting
10Coot7.5model refinement
12RELION3final Euler assignment
13RELION3classification
14RELION33D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14057 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionMethod: Random seeds / Details: A vesicle model with random seeds on the surface. / Num. of tomograms: 41 / Num. of volumes extracted: 31947
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 1FLC

1flc


Accession code: 1FLC / Source name: PDB / Type: experimental model

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