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- EMDB-52965: HSV-1 prefusion glycoprotein B bound by Nb1_gbHSV -

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Basic information

Entry
Database: EMDB / ID: EMD-52965
TitleHSV-1 prefusion glycoprotein B bound by Nb1_gbHSV
Map data
Sample
  • Complex: Glycoprotein B bound by Nb1_gbHSV
    • Complex: Nb1_gbHSV
      • Protein or peptide: Nb1_gbHSV
    • Complex: Glycoprotein B
      • Protein or peptide: Glycoprotein B
KeywordsGlycoprotein B / viral membrane fusion protein / Herpes simplex virus 1 / nanobody / 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 / 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 alphaherpesvirus 1 strain 17 / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsVollmer B / Mulvaney T / Ebel H / Nentwig J / Gruenewald K
Funding support Germany, United Kingdom, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 152/772-1, 152/774-1, 152/776-1 Germany
German Federal Ministry for Education and ResearchASPIRE project Germany
German Research Foundation (DFG)Research training groups 2771 & 2887 Germany
Wellcome Trust209250/Z/17/Z United Kingdom
CitationJournal: Nature / Year: 2025
Title: A nanobody specific to prefusion glycoprotein B neutralizes HSV-1 and HSV-2.
Authors: Benjamin Vollmer / Henriette Ebel / Renate Rees / Julia Nentwig / Thomas Mulvaney / Jürgen Schünemann / Jens Krull / Maya Topf / Dirk Görlich / Kay Grünewald /
Abstract: The nine human herpesviruses, including herpes simplex virus 1 and 2, human cytomegalovirus and Epstein-Barr virus, present a significant burden to global public health. Their envelopes contain at ...The nine human herpesviruses, including herpes simplex virus 1 and 2, human cytomegalovirus and Epstein-Barr virus, present a significant burden to global public health. Their envelopes contain at least ten different glycoproteins, which are necessary for host cell tropism, attachment and entry. The best conserved among them, glycoprotein B (gB), is essential as it performs membrane fusion by undergoing extensive rearrangements from a prefusion to postfusion conformation. At present, there are no antiviral drugs targeting gB or neutralizing antibodies directed against its prefusion form, because of the difficulty in structurally determining and using this metastable conformation. Here we show the isolation of prefusion-specific nanobodies, one of which exhibits strong neutralizing and cross-species activity. By mutational stabilization we solved the herpes simplex virus 1 gB full-length prefusion structure, which allowed the bound epitope to be determined. Our analyses show the membrane-embedded regions of gB and previously unresolved structural features, including a new fusion loop arrangement, providing insights into the initial conformational changes required for membrane fusion. Binding an epitope spanning three domains, proximal only in the prefusion state, the nanobody keeps wild-type HSV-2 gB in this conformation and enabled its native prefusion structure to be determined. This also indicates the mode of neutralization and an attractive avenue for antiviral interventions.
History
DepositionFeb 26, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52965.png

Downloads & links

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Map

FileDownload / File: emd_52965.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.2064079 - 0.5164912
Average (Standard dev.)-0.00041922063 (±0.012103049)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map

Fileemd_52965_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52965_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52965_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Glycoprotein B bound by Nb1_gbHSV

EntireName: Glycoprotein B bound by Nb1_gbHSV
Components
  • Complex: Glycoprotein B bound by Nb1_gbHSV
    • Complex: Nb1_gbHSV
      • Protein or peptide: Nb1_gbHSV
    • Complex: Glycoprotein B
      • Protein or peptide: Glycoprotein B

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Supramolecule #1: Glycoprotein B bound by Nb1_gbHSV

SupramoleculeName: Glycoprotein B bound by Nb1_gbHSV / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human alphaherpesvirus 1 strain 17

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Supramolecule #2: Nb1_gbHSV

SupramoleculeName: Nb1_gbHSV / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Vicugna pacos (alpaca)

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Supramolecule #3: Glycoprotein B

SupramoleculeName: Glycoprotein B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human alphaherpesvirus 1 strain 17

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Macromolecule #1: Glycoprotein B

MacromoleculeName: Glycoprotein B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 105.128523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 SSDAICTTFT TNLT EYPLS RVDLGDCIGK DARDAMDRIF ARRYNATHIK VGQPQYYLAN GGFLIAYQPL LSNTLAELYV REHLREQSRK PPNPT PPPP GASANASVER IKTTSSIEFA RLQFTYNHIQ RPVNDMLGRV AIAWCELCNH ELTLWNEARK LNPNAIASVT VGRRVS ARM LGDVMAVSTC VPVAADNVIV QNSMRISSRP GACYSRPLVS FRYEDQGPLV EGQLGENNEL RLTRDAIEPC TVGHRRY FT FGGGYVYFEE YAYSHQLSRA DITTVSTFID LNITMLEDHE FVPLEVYTRH EIKDSGLLDY TEVQRRVQLH DLRFADID T VIHADANAAM FAGLGAFFEG MGDLGRAVGK VVMGIVGGVV SAVSGVSSFM SNPFGALAVG LLVLAGLAAA FFAFRYVMR LQSNPMKALY PLTTKELKNP TNPDASGEGE EGGDFDEAKL AEAREMIRYM ALVSAMERTE HKAKKKGTSA LLSAKVTDMV MRKRRNTNA TQVPNKDGDA DEDDLQLGSG SGTLEVLFQG PGGSGSAWSH PQFEKGGGSG GGSGGSAWSH PQFEK

UniProtKB: Glycoprotein B

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Macromolecule #2: Nb1_gbHSV

MacromoleculeName: Nb1_gbHSV / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 12.821279 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVESGGG SVQPGGSLRL SCAASASGRL SMSGALGWYR QVQGKSRELV ATITDRSSTN YADSVKGRFT ISIDDAENTM YLQMNSLKP EDTGVYYCNA RWRGMNVWGK GTRVTVSSTS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHepes
300.0 mMNaClSodium Chloride
5.0 mMH2NCOCH2CH2CH(NH2)CO2HL-Glutamin
5.0 mMC6H14N4O2HClL-Arginine, hydrochloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Details: Grid was overlayed with 2 nm carbon
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 80 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 3066 / Average exposure time: 2.13 sec. / Average electron dose: 45.83 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
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

Particle selectionNumber selected: 956386
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.0) / Number images used: 394394
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 59.59
Output model

PDB-9ih8:
HSV-2 postfusion glycoprotein B

PDB-9q9n:
HSV-1 prefusion glycoprotein B bound by Nb1_gbHSV

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