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

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Basic information

Entry
Database: PDB / ID: 9q9s
TitleHSV-2 prefusion glycoprotein B bound by Nb1_gbHSV
Components
  • Envelope glycoprotein B
  • Nb1_gbHSV
KeywordsVIRAL PROTEIN / viral membrane fusion protein / glycoprotein B / Herpes simplex virus 2 / nanobody complex
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 speciesVicugna pacos (alpaca)
Human herpesvirus 2 strain 333
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsVollmer, B. / Mulvaney, T. / Ebel, H. / Nentwig, J. / Gruenewald, K.
Funding support Germany, United Kingdom, 4items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
d: Nb1_gbHSV
e: Nb1_gbHSV
f: Nb1_gbHSV
A: Envelope glycoprotein B
B: Envelope glycoprotein B
C: Envelope glycoprotein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,50218
Polymers352,4096
Non-polymers5,09312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody Nb1_gbHSV


Mass: 12821.279 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pQE80 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): C3029 / Variant (production host): SHuffle
#2: Protein Envelope glycoprotein B / gB


Mass: 104648.422 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: C-terminal HRV 3C + Strep Tag II / Source: (gene. exp.) Human herpesvirus 2 strain 333 / Gene: gB, UL27 / Plasmid: pHR-CAG / Details (production host): lentiviral transduction / Cell line (production host): HEK-293T / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: P06763
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Herpes Simplex Virus 2 Glycoprotein B in complex with Nb1_gbHSVCOMPLEX#1-#20RECOMBINANT
2Glycoprotein BCOMPLEX#21RECOMBINANTprefusion conformation
3Nb1_gbHSVCOMPLEX#12RECOMBINANTone nanobody bound per glycoprotein B protomer
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Human herpesvirus 2 strain 33310313
32Human herpesvirus 2 strain 33310313
43Vicugna pacos (alpaca)30538
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCellPlasmid
21Homo sapiens (human)9606HEK-293TpHR-CAG
32Homo sapiens (human)9606HEK-293TpHR-CAG
43Escherichia coli (E. coli)562C3029pQE80 derivative
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2300 mMSodium ChlorideNaCl1
35 mML-Arginine hydrochlorideC6H14N4O2HCl1
45 mML-GlutamineH2NCOCH2CH2CH(NH2)CO2H1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: grid was overlayed with 2 nm carbon / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 80 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.2 sec. / Electron dose: 43.84 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14886
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategoryDetails
1Warp1.09particle selection
2SerialEM4.1.0betaimage acquisition
4cryoSPARC4.2.0CTF correction
71model fittingModelAngelo
8ISOLDE1.8model fitting
10cryoSPARC4.2.0initial Euler assignment
11cryoSPARC4.2.0final Euler assignment
124.2.0classification
13cryoSPARC4.2.03D reconstruction
14PHENIX1.20.1model refinement
151.2model refinementTEMPy-ReFF
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3901343
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158509 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 44.04 / Protocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: experimental model

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