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- EMDB-11123: Pre-fusion conformation of glycoprotein B of Herpes simplex virus 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-11123
TitlePre-fusion conformation of glycoprotein B of Herpes simplex virus 1
Map dataPre-fusion structure of glycoprotein B of Herpes simplex virus 1
Sample
  • Virus: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
    • Protein or peptide: Envelope glycoprotein B
KeywordsMembrane fusion protein / glycoprotein / gB / UL27 / viral entry protein / class III fusion protein / transmembrane protein / pre-fusion conformation / VIRAL PROTEIN
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / host cell endosome / host cell Golgi apparatus / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
: / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain
Similarity search - Domain/homology
Glycoprotein B / Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1) / Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Methodsubtomogram averaging / cryo EM / Resolution: 9.1 Å
AuthorsVollmer B / Prazak V
Funding support Germany, United Kingdom, European Union, 4 items
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, 2020-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.056
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.056
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z9m
  • Surface level: 0.056
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11123.png

Downloads & links

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Map

FileDownload / File: emd_11123.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPre-fusion structure of glycoprotein B of Herpes simplex virus 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.6 Å/pix.
x 100 pix.
= 160. Å		1.6 Å/pix.
x 100 pix.
= 160. Å		1.6 Å/pix.
x 100 pix.
= 160. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.056 / Movie #1: 0.056
Minimum - Maximum-0.33630377 - 0.3112999
Average (Standard dev.)0.0000015608573 (±0.0327678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 160.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.61.61.6
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z160.000160.000160.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.3360.3110.000

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Supplemental data

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Sample components

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Entire : Human alphaherpesvirus 1

EntireName: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Components
  • Virus: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
    • Protein or peptide: Envelope glycoprotein B

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Supramolecule #1: Human alphaherpesvirus 1

SupramoleculeName: Human alphaherpesvirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Protein recombinantly expressed in membrane protein enriched extracellular vesicles (MPEEVs)
NCBI-ID: 10298 / Sci species name: Human alphaherpesvirus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Envelope glycoprotein B

MacromoleculeName: Envelope glycoprotein B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 100.383305 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: MHQGAPSWGR RWFVVWALLG LTLGVLVASA APSSPGTPGV AAATQAANGG PATPAPPALG AAPTGDPKPK KNKKPKNPTP PRPAGDNAT VAAGHATLRE HLRDIKAENT DANFYVCPPP TGATVVQFEQ PRRCPTRPEG QNYTEGIAVV FKENIAPYKF K ATMYYKDV ...String:
MHQGAPSWGR RWFVVWALLG LTLGVLVASA APSSPGTPGV AAATQAANGG PATPAPPALG AAPTGDPKPK KNKKPKNPTP PRPAGDNAT VAAGHATLRE HLRDIKAENT DANFYVCPPP TGATVVQFEQ PRRCPTRPEG QNYTEGIAVV FKENIAPYKF K ATMYYKDV TVSQVWFGHR YSQFMGIFED RAPVPFEEVI DKINAKGVCR STAKYVRNNL ETTAFHRDDH ETDMELKPAN AA TRTSRGW HTTDLKYNPS RVEAFHRYGT TVNCIVEEVD ARSVYPYDEF VLATGDFVYM SPFYGYREGS HTEHTSYAAD RFK QVDGFY ARDLTTKARA TAPTTRNLLT TPKFTVAWDW VPKRPSVCTM TKWQEVDEML RSEYGGSFRF SSDAISTTFT TNLT EYPLS RVDLGDCIGK DARDAMDRIF ARRYNATHIK VGQPQYYLAN GGFLIAYQPL LSNTLAELYV REHLREQSRK PPNPT PPPP GASANASVER IKTTSSIEFA RLQFTYNHIQ RPVNDMLGRV AIAWCELQNH ELTLWNEARK LNPNAIASVT VGRRVS ARM LGDVMAVSTC VPVAADNVIV QNSMRISSRP GACYSRPLVS FRYEDQGPLV EGQLGENNEL RLTRDAIEPC TVGHRRY FT FGGGYVYFEE YAYSHQLSRA DITTVSTFID LNITMLEDHE FVPLEVYTRH EIKDSGLLDY TEVQRRNQLH DLRFADID T VIHADANAAM FAGLGAFFEG MGDLGRAVGK VVMGIVGGVV SAVSGVSSFM SNPFGALAVG LLVLAGLAAA FFAFRYVMR LQSNPMKALY PLTTKELKNP TNPDASGEGE EGGDFDEAKL AEAREMIRYM ALVSAMERTE HKAKKKGTSA LLSAKVTDMV MRKRRNTNY TQVPNKDGDA DEDDL

UniProtKB: 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: 7.8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHepes
150.0 mMNaClSodium Chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
DetailsProtein recombinantly expressed in membrane protein enriched extracellular vesicles (MPEEVs)

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
DetailsAdditional 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.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3836 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 2.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 1.6 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / 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: PEET / Number subtomograms used: 46067
ExtractionNumber tomograms: 99 / Number images used: 56176 / Method: Manual / Software - Name: 3dmod
Final angle assignmentType: OTHER / Software - Name: PEET
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5v2s


Chain - Chain ID: A / Chain - Residue range: 104-723 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 300 / Target criteria: Cross correlation coefficient
Output model

PDB-6z9m:
Pseudoatomic model of the pre-fusion conformation of glycoprotein B of Herpes simplex virus 1

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