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- EMDB-42250: Varicella-zoster virus glycoprotein B; H527P prefusion class I. -

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Basic information

Entry
Database: EMDB / ID: EMD-42250
TitleVaricella-zoster virus glycoprotein B; H527P prefusion class I.
Map dataCryo-ET map of the VZV gB mutant H527P; class I
Sample
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
    • Protein or peptide: Varicella-zoster virus gB[H527P] mutant
KeywordsHerpesvirus / Fusogen / Glycoprotein B / Varicella Zoster-Virus / VIRAL PROTEIN
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
Methodsubtomogram averaging / cryo EM / Resolution: 9.8 Å
AuthorsZhou M / Oliver SL / Muyuan C / Vollmer B
Funding support United States, Germany, European Union, 9 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI102546 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R21-MH125285 United States
German Research Foundation (DFG)EXC 2155 Germany
Marie Sklodowska-Curie Actions, FragNET ITN101065943European Union
German Federal Ministry for Education and Research05K18BHA Germany
German Research Foundation (DFG)INST 152/772-1 Germany
German Research Foundation (DFG)INST 152/774-1 Germany
German Research Foundation (DFG)INST |152/775-1 Germany
German Research Foundation (DFG)INST 152/776-1 Germany
CitationJournal: Nat Commun / Year: 2023
Title: Targeted mutagenesis of the herpesvirus fusogen central helix captures transition states.
Authors: Momei Zhou / Benjamin Vollmer / Emily Machala / Muyuan Chen / Kay Grünewald / Ann M Arvin / Wah Chiu / Stefan L Oliver /
Abstract: Herpesviruses remain a burden for animal and human health, including the medically important varicella-zoster virus (VZV). Membrane fusion mediated by conserved core glycoproteins, the fusogen gB and ...Herpesviruses remain a burden for animal and human health, including the medically important varicella-zoster virus (VZV). Membrane fusion mediated by conserved core glycoproteins, the fusogen gB and the heterodimer gH-gL, enables herpesvirus cell entry. The ectodomain of gB orthologs has five domains and is proposed to transition from a prefusion to postfusion conformation but the functional relevance of the domains for this transition remains poorly defined. Here we describe structure-function studies of the VZV gB DIII central helix targeting residues EHV. Critically, a H527P mutation captures gB in a prefusion conformation as determined by cryo-EM, a loss of membrane fusion in a virus free assay, and failure of recombinant VZV to spread in cell monolayers. Importantly, two predominant cryo-EM structures of gB[H527P] are identified by 3D classification and focused refinement, suggesting they represented gB conformations in transition. These studies reveal gB DIII as a critical element for herpesvirus gB fusion function.
History
DepositionOct 7, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42250.png

Downloads & links

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Map

FileDownload / File: emd_42250.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-ET map of the VZV gB mutant H527P; class I
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.19 Å/pix.
x 168 pix.
= 367.92 Å		2.19 Å/pix.
x 168 pix.
= 367.92 Å		2.19 Å/pix.
x 168 pix.
= 367.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2000.0
Minimum - Maximum1.0 - 4095.0
Average (Standard dev.)1661.868400000000065 (±95.105320000000006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 367.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map even

Fileemd_42250_half_map_1.map
AnnotationHalf map even
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map odd

Fileemd_42250_half_map_2.map
AnnotationHalf map odd
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human alphaherpesvirus 3

EntireName: Human alphaherpesvirus 3 (Varicella-zoster virus)
Components
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
    • Protein or peptide: Varicella-zoster virus gB[H527P] mutant

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Supramolecule #1: Human alphaherpesvirus 3

SupramoleculeName: Human alphaherpesvirus 3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Extracellular vesicles produced by BHK-21 cells transfected with a plasmid expressing VZV glycoprotein B mutant H527P.
NCBI-ID: 10335 / Sci species name: Human alphaherpesvirus 3 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Varicella-zoster virus gB[H527P] mutant

MacromoleculeName: Varicella-zoster virus gB[H527P] mutant / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: MSPCGYYSKW RNRDRPEYRR NLRFRRFFSS IHPNAAAGSG FNGPGVFITS VTGVWLCFLC IFSMFVTAVV SVSPSSFYES LQVEPTQSED ITRSAHLGDG DEIREAIHKS QDAETKPTFY VCPPPTGSTI VRLEPPRTCP DYHLGKNFTE GIAVVYKENI AAYKFKATVY ...String:
MSPCGYYSKW RNRDRPEYRR NLRFRRFFSS IHPNAAAGSG FNGPGVFITS VTGVWLCFLC IFSMFVTAVV SVSPSSFYES LQVEPTQSED ITRSAHLGDG DEIREAIHKS QDAETKPTFY VCPPPTGSTI VRLEPPRTCP DYHLGKNFTE GIAVVYKENI AAYKFKATVY YKDVIVSTAW AGSSYTQITN RYADRVPIPV SEITDTIDKF GKCSSKATYV RNNHKVEAFN EDKNPQDMPL IASKYNSVGS KAWHTTNDTY MVAGTPGTYR TGTSVNCIIE EVEARSIFPY DSFGLSTGDI IYMSPFFGLR DGAYREHSNY AMDRFHQFEG YRQRDLDTRA LLEPAARNFL VTPHLTVGWN WKPKRTEVCS LVKWREVEDV VRDEYAHNFR FTMKTLSTTF ISETNEFNLN QIHLSQCVKE EARAIINRIY TTRYNSSHVR TGDIQTYLAR GGFVVVFQPL LSNSLARLYL QELVRENTNH SPQKHPTRNT RSRRSVPVEL RANRTITTTS SVEFAMLQFT YDHIQEPVNE MLARISSSWC QLQNRERALW SGLFPINPSA LASTILDQRV KARILGDVIS VSNCPELGSD TRIILQNSMR VSGSTTRCYS RPLISIVSLN GSGTVEGQLG TDNELIMSRD LLEPCVANHK RYFLFGHHYV YYEDYRYVRE IAVHDVGMIS TYVDLNLTLL KDREFMPLRV YTRDELRDTG LLDYSEIQRR NQMHSLRFYD IDKVVQYDSG TAIMQGMAQF FQGLGTAGQA VGHVVLGATG ALLSTVHGFT TFLSNPFGAL AVGLLVLAGL VAAFFAYRYV LKLKTSPMKA LYPLTTKGLK QLPEGMDPFA EKPNATDTPI EEIGDSQNTE PSVNSGFDPD KFREAQEMIK YMTLVSAAER QESKARKKNK TSALLTSRLT GLALRNRRGY SRVRTENVTG V

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.3 sec. / Average electron dose: 3.22 e/Å2 / Details: A total of 43 tilt series.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.002 µm / Nominal defocus min: 0.002 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 43
ExtractionNumber tomograms: 1 / Number images used: 2074

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