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- EMDB-3362: Natively membrane-anchored full-length Herpes simplex virus 1 gly... -

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Basic information

Entry
Database: EMDB / ID: EMD-3362
TitleNatively membrane-anchored full-length Herpes simplex virus 1 glycoprotein B
Map dataSubtomogram average of HSV-1 gB on membrane
Sample
  • Sample: Glycoprotein B of Herpes Simplex Virus 1
  • Protein or peptide: Glycoprotein B
Keywordsmembrane fusion / class III fusogen / pre-fusion
Function / homology
Function and homology information


virion component => GO:0044423 / host cell Golgi membrane / host cell membrane / viral process / host cell endosome membrane / host cell endosome / host cell Golgi apparatus / membrane => GO:0016020 / symbiont entry into host cell / viral envelope ...virion component => GO:0044423 / host cell Golgi membrane / host cell membrane / viral process / host cell endosome membrane / host cell endosome / host cell Golgi apparatus / membrane => GO:0016020 / 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 / 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
Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Methodsubtomogram averaging / cryo EM / Resolution: 23.0 Å
AuthorsZeev-Ben-Mordehai T / Vasishtan D / Duran AH / Vollmer B / White P / Pandurangan AP / Siebert CA / Topf M / Grunewald K
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Two distinct trimeric conformations of natively membrane-anchored full-length herpes simplex virus 1 glycoprotein B.
Authors: Tzviya Zeev-Ben-Mordehai / Daven Vasishtan / Anna Hernández Durán / Benjamin Vollmer / Paul White / Arun Prasad Pandurangan / C Alistair Siebert / Maya Topf / Kay Grünewald /
Abstract: Many viruses are enveloped by a lipid bilayer acquired during assembly, which is typically studded with one or two types of glycoproteins. These viral surface proteins act as the primary interface ...Many viruses are enveloped by a lipid bilayer acquired during assembly, which is typically studded with one or two types of glycoproteins. These viral surface proteins act as the primary interface between the virus and the host. Entry of enveloped viruses relies on specialized fusogen proteins to help merge the virus membrane with the host membrane. In the multicomponent herpesvirus fusion machinery, glycoprotein B (gB) acts as this fusogen. Although the structure of the gB ectodomain postfusion conformation has been determined, any other conformations (e.g., prefusion, intermediate conformations) have so far remained elusive, thus restricting efforts to develop antiviral treatments and prophylactic vaccines. Here, we have characterized the full-length herpes simplex virus 1 gB in a native membrane by displaying it on cell-derived vesicles and using electron cryotomography. Alongside the known postfusion conformation, a novel one was identified. Its structure, in the context of the membrane, was determined by subvolume averaging and found to be trimeric like the postfusion conformation, but appeared more condensed. Hierarchical constrained density-fitting of domains unexpectedly revealed the fusion loops in this conformation to be apart and pointing away from the anchoring membrane. This vital observation is a substantial step forward in understanding the complex herpesvirus fusion mechanism, and opens up new opportunities for more targeted intervention of herpesvirus entry.
History
DepositionMar 4, 2016-
Header (metadata) releaseMar 23, 2016-
Map releaseMar 23, 2016-
UpdateJun 22, 2016-
Current statusJun 22, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.74
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.74
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3362.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of HSV-1 gB on membrane
Voxel sizeX=Y=Z: 4.6 Å
Density
Contour LevelBy AUTHOR: 2.74 / Movie #1: 2.74
Minimum - Maximum-15.234740260000001 - 12.593956950000001
Average (Standard dev.)-0.48875326 (±1.23137927)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.64.64.6
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z368.000368.000368.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-15.23512.594-0.489

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Supplemental data

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Sample components

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Entire : Glycoprotein B of Herpes Simplex Virus 1

EntireName: Glycoprotein B of Herpes Simplex Virus 1
Components
  • Sample: Glycoprotein B of Herpes Simplex Virus 1
  • Protein or peptide: Glycoprotein B

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Supramolecule #1000: Glycoprotein B of Herpes Simplex Virus 1

SupramoleculeName: Glycoprotein B of Herpes Simplex Virus 1 / type: sample / ID: 1000 / Details: Sample bound to extracellular vesicles / Oligomeric state: Trimeric / Number unique components: 1
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Glycoprotein B

MacromoleculeName: Glycoprotein B / type: protein_or_peptide / ID: 1 / Name.synonym: gB / Number of copies: 3 / Oligomeric state: Trimeric / Recombinant expression: Yes
Source (natural)Organism: Human herpesvirus 1 (Herpes simplex virus type 1) / synonym: HSV-1
Molecular weightTheoretical: 300 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster) / Recombinant cell: BHK 21 / Recombinant plasmid: pPEP98
SequenceUniProtKB: Envelope glycoprotein B
GO: viral process, virion attachment to host cell, symbiont entry into host cell, membrane, membrane => GO:0016020, virion component => GO:0044423, viral envelope, host cell plasma membrane, host ...GO: viral process, virion attachment to host cell, symbiont entry into host cell, membrane, membrane => GO:0016020, virion component => GO:0044423, viral envelope, host cell plasma membrane, host cell membrane, host cell endosome, host cell endosome membrane, host cell Golgi apparatus, host cell Golgi membrane, virion membrane
InterPro: Herpesvirus Glycoprotein B

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 25mM HEPES, 130mM NaCl
GridDetails: Holey carbon on top of 200 mesh gold grid.
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 3 sec before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 95000
Specialist opticsEnergy filter - Name: Gatan Quantum 964 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: Polara holder / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -52 ° / Tilt series - Axis1 - Max angle: 53 °
TemperatureMin: 80 K / Max: 100 K / Average: 85 K
Detailscounting mode
DateSep 16, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 20 / Average electron dose: 60 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTF correction of tilt series prior to tomogram reconstruction
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: OTHER / Software - Name: IMOD, PEET / Number subtomograms used: 1909
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

Chain - Chain ID: A
SoftwareName: Chimera, Flex-EM, ADP-EM, GMFit, TEMPy
DetailsIndividual domains of 2GUM were fitted separately, using a hierarchical fitting approach
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: CCC, SCCC, Atom Protrusion Score

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