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- EMDB-52966: HSV-2 prefusion glycoprotein B bound by Nb1_gbHSV -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52966
TitleHSV-2 prefusion glycoprotein B bound by Nb1_gbHSV
Map data
Sample
  • Complex: Herpes Simplex Virus 2 Glycoprotein B in complex with Nb1_gbHSV
    • Complex: Glycoprotein B
      • Complex: Nb1_gbHSV
        • Protein or peptide: Nb1_gbHSV
      • Protein or peptide: Envelope glycoprotein B
Keywordsviral membrane fusion protein / glycoprotein B / Herpes simplex virus 2 / nanobody complex / VIRAL PROTEIN
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / 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
Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman herpesvirus 2 strain 333 / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsVollmer B / Mulvaney T / Ebel H / Nentwig J / Gruenewald K
Funding support Germany, United Kingdom, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)2771, 2887 Germany
German Research Foundation (DFG)INST 152/772-1|152/774-1|152/776-1 FUGG Germany
German Federal Ministry for Education and ResearchASPIRE 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-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52966.png

Downloads & links

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Map

FileDownload / File: emd_52966.map.gz / Format: CCP4 / Size: 282.6 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 420 pix.
= 348.6 Å		0.83 Å/pix.
x 420 pix.
= 348.6 Å		0.83 Å/pix.
x 420 pix.
= 348.6 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: 0.104
Minimum - Maximum-0.3322687 - 0.7068631
Average (Standard dev.)-0.00048547905 (±0.013224374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 348.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_52966_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52966_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_52966_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Herpes Simplex Virus 2 Glycoprotein B in complex with Nb1_gbHSV

EntireName: Herpes Simplex Virus 2 Glycoprotein B in complex with Nb1_gbHSV
Components
  • Complex: Herpes Simplex Virus 2 Glycoprotein B in complex with Nb1_gbHSV
    • Complex: Glycoprotein B
      • Complex: Nb1_gbHSV
        • Protein or peptide: Nb1_gbHSV
      • Protein or peptide: Envelope glycoprotein B

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Supramolecule #1: Herpes Simplex Virus 2 Glycoprotein B in complex with Nb1_gbHSV

SupramoleculeName: Herpes Simplex Virus 2 Glycoprotein B in complex with Nb1_gbHSV
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human herpesvirus 2 strain 333

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Supramolecule #2: Glycoprotein B

SupramoleculeName: Glycoprotein B / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 / Details: prefusion conformation
Source (natural)Organism: Human herpesvirus 2 strain 333

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Supramolecule #3: Nb1_gbHSV

SupramoleculeName: Nb1_gbHSV / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #1 / Details: one nanobody bound per glycoprotein B protomer
Source (natural)Organism: Vicugna pacos (alpaca)

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Macromolecule #1: Nb1_gbHSV

MacromoleculeName: Nb1_gbHSV / type: protein_or_peptide / ID: 1 / 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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Macromolecule #2: Envelope glycoprotein B

MacromoleculeName: Envelope glycoprotein B / type: protein_or_peptide / ID: 2 / Details: C-terminal HRV 3C + Strep Tag II / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 2 strain 333
Molecular weightTheoretical: 104.648422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRGGGLICAL VVGALVAAVA SAAPAAPAAP RASGGVAATV AANGGPASRP PPVPSPATTK ARKRKTKKPP KRPEATPPPD ANATVAAGH ATLRAHLREI KVENADAQFY VCPPPTGATV VQFEQPRRCP TRPEGQNYTE GIAVVFKENI APYKFKATMY Y KDVTVSQV ...String:
MRGGGLICAL VVGALVAAVA SAAPAAPAAP RASGGVAATV AANGGPASRP PPVPSPATTK ARKRKTKKPP KRPEATPPPD ANATVAAGH ATLRAHLREI KVENADAQFY VCPPPTGATV VQFEQPRRCP TRPEGQNYTE GIAVVFKENI APYKFKATMY Y KDVTVSQV WFGHRYSQFM GIFEDRAPVP FEEVIDKINA KGVCRSTAKY VRNNMETTAF HRDDHETDME LKPAKVATRT SR GWHTTDL KYNPSRVEAF HRYGTTVNCI VEEVDARSVY PYDEFVLATG DFVYMSPFYG YREGSHTEHT SYAADRFKQV DGF YARDLT TKARATSPTT RNLLTTPKFT VAWDWVPKRP AVCTMTKWQE VDEMLRAEYG GSFRFSSDAI STTFTTNLTQ YSLS RVDLG DCIGRDAREA IDRMFARKYN ATHIKVGQPQ YYLATGGFLI AYQPLLSNTL AELYVREYMR EQDRKPRNAT PAPLR EAPS ANASVERIKT TSSIEFARLQ FTYNHIQRHV NDMLGRIAVA WCELQNHELT LWNEARKLNP NAIASATVGR RVSARM LGD VMAVSTCVPV APDNVIVQNS MRVSSRPGTC YSRPLVSFRY EDQGPLIEGQ LGENNELRLT RDALEPCTVG HRRYFIF GG GYVYFEEYAY SHQLSRADVT TVSTFIDLNI TMLEDHEFVP LEVYTRHEIK DSGLLDYTEV QRRNQLHDLR FADIDTVI R ADANAAMFAG LCAFFEGMGD LGRAVGKVVM GVVGGVVSAV SGVSSFMSNP FGALAVGLLV LAGLVAAFFA FRYVLQLQR NPMKALYPLT TKELKTSDPG GVGGEGEEGA EGGGFDEAKL AEAREMIRYM ALVSAMERTE HKARKKGTSA LLSSKVTNMV LRKRNKARY SPLHNEDEAG DEDELGTLEV LFQGPGGSGS AWSHPQFEKG GGSGGGSGGS AWSHPQFEK

UniProtKB: Envelope glycoprotein B

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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 mMC6H14N4O2HClL-Arginine hydrochloride
5.0 mMH2NCOCH2CH2CH(NH2)CO2HL-Glutamine
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
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: 14886 / Average exposure time: 2.2 sec. / Average electron dose: 43.84 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
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: 3901343
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-Initio Reconstruction
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.0) / Number images used: 158509
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: experimental model / Details: ModelAngelo
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 44.04
Output model

PDB-9ih8:
HSV-2 postfusion glycoprotein B

PDB-9q9s:
HSV-2 prefusion glycoprotein B bound by Nb1_gbHSV

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