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- PDB-6z9m: Pseudoatomic model of the pre-fusion conformation of glycoprotein... -

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Basic information

Entry
Database: PDB / ID: 6z9m
TitlePseudoatomic model of the pre-fusion conformation of glycoprotein B of Herpes simplex virus 1
ComponentsEnvelope glycoprotein B
KeywordsVIRAL PROTEIN / Membrane fusion protein / glycoprotein / gB / UL27 / viral entry protein / class III fusion protein / transmembrane protein / pre-fusion conformation
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily
Similarity search - Domain/homology
Glycoprotein B / Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.1 Å
AuthorsVollmer, B. / Prazak, V. / Vasishtan, D. / Jefferys, E.E. / Hernandez-Duran, A. / Vallbracht, M. / Klupp, B. / Mettenleiter, T.C. / Backovic, M. / Rey, F.A. ...Vollmer, B. / Prazak, V. / Vasishtan, D. / Jefferys, E.E. / Hernandez-Duran, A. / Vallbracht, M. / Klupp, B. / Mettenleiter, T.C. / Backovic, M. / Rey, F.A. / Topf, M. / Gruenewald, K.
Funding support Germany, United Kingdom, European Union, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 152/772-1, 774-1, 775-1, 776-1 FUGG Germany
Wellcome Trust209250/Z/17/Z, 107806/Z/15/Z, 203815/Z/16/A, 203141/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/M019292/1, MR/R017875/1 United Kingdom
Marie Sklodowska-Curie Actions, FragNET ITNKGBVIFEFEuropean Union
CitationJournal: Sci Adv / Year: 2020
Title: The prefusion structure of herpes simplex virus glycoprotein B.
Authors: B Vollmer / V Pražák / D Vasishtan / E E Jefferys / A Hernandez-Duran / M Vallbracht / B G Klupp / T C Mettenleiter / M Backovic / F A Rey / M Topf / K Grünewald /
Abstract: Cell entry of enveloped viruses requires specialized viral proteins that mediate fusion with the host membrane by substantial structural rearrangements from a metastable pre- to a stable postfusion ...Cell entry of enveloped viruses requires specialized viral proteins that mediate fusion with the host membrane by substantial structural rearrangements from a metastable pre- to a stable postfusion conformation. This metastability renders the herpes simplex virus 1 (HSV-1) fusion glycoprotein B (gB) highly unstable such that it readily converts into the postfusion form, thereby precluding structural elucidation of the pharmacologically relevant prefusion conformation. By identification of conserved sequence signatures and molecular dynamics simulations, we devised a mutation that stabilized this form. Functionally locking gB allowed the structural determination of its membrane-embedded prefusion conformation at sub-nanometer resolution and enabled the unambiguous fit of all ectodomains. The resulting pseudo-atomic model reveals a notable conservation of conformational domain rearrangements during fusion between HSV-1 gB and the vesicular stomatitis virus glycoprotein G, despite their very distant phylogeny. In combination with our comparative sequence-structure analysis, these findings suggest common fusogenic domain rearrangements in all class III viral fusion proteins.
History
DepositionJun 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: Envelope glycoprotein B
B: Envelope glycoprotein B
C: Envelope glycoprotein B


Theoretical massNumber of molelcules
Total (without water)301,1503
Polymers301,1503
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area19170 Å2
ΔGint-73 kcal/mol
Surface area82740 Å2
MethodPISA

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Components

#1: Protein Envelope glycoprotein B / gB


Mass: 100383.305 Da / Num. of mol.: 3 / Mutation: H516P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Gene: UL27, gB, HHV1gp041 / Details (production host): derived from pEP98 / Cell (production host): Fibroblast / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: A1Z0P7, UniProt: P06437*PLUS

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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: Human alphaherpesvirus 1 / Type: VIRUS
Details: Protein recombinantly expressed in membrane protein enriched extracellular vesicles (MPEEVs)
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)Organism: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Source (recombinant)Organism: Mesocricetus auratus (golden hamster) / Cell: Fibroblast
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHepesC8H18N2O4S1
2150 mMSodium ChlorideNaClSodium chloride1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Protein recombinantly expressed in membrane protein enriched extracellular vesicles (MPEEVs)
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Details: Additional Dataset collected using Titan Krios (FEI Thermo) at 300 kV with a 70 um C2 aperture and post-column QUANTUM energy filter operated in Zero-Loss mode using 20 eV energy slit and K2 ...Details: Additional Dataset collected using Titan Krios (FEI Thermo) at 300 kV with a 70 um C2 aperture and post-column QUANTUM energy filter operated in Zero-Loss mode using 20 eV energy slit and K2 Summit direct electron detector in counting mode (Gatan). Defocus range: 2300 - 4900 nm.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated defocus min: 1600 nm / Calibrated defocus max: 3500 nm / Cs: 2 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingElectron dose: 2.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 3836 / Height: 3710

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Processing

EM software
IDNameCategory
13dmodvolume selection
2SerialEMimage acquisition
4NOVACTFCTF correction
5CTFPHASEFLIPCTF correction
8UCSF Chimeramodel fitting
11PEETfinal Euler assignment
13PEET3D reconstruction
14MDFFmodel refinement
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: 46067 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionMethod: Manual / Num. of tomograms: 99 / Num. of volumes extracted: 56176
Atomic model buildingB value: 300 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross correlation coefficient
Atomic model buildingPDB-ID: 5V2S

5v2s


Pdb chain-ID: A / Pdb chain residue range: 104-723

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