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- PDB-9mvu: C6 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycop... -

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Basic information

Entry
Database: PDB / ID: 9mvu
TitleC6 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycoprotein gB
Components
  • C6 Neutralizing Nanobody
  • Envelope glycoprotein B
KeywordsANTIVIRAL PROTEIN / Neutralizing Antibody
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 1 (Herpes simplex virus type 1)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsViadiu, H. / Abernathy, E. / Lee, C.V. / Hung, M. / Yu, Y. / Xing, W. / Yu, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2025
Title: Identification and engineering of potent bispecific antibodies that protect against herpes simplex virus recurrent disease.
Authors: Chingwei V Lee / Hector Viadiu / Apurva Kalamkar / David I Bernstein / Andrew Pae / Xinchao Yu / Sylvia Wong / Fernando J Bravo / Sheng Ding / Elbert Seto / Magdeleine Hung / Yu Yu / Weimei ...Authors: Chingwei V Lee / Hector Viadiu / Apurva Kalamkar / David I Bernstein / Andrew Pae / Xinchao Yu / Sylvia Wong / Fernando J Bravo / Sheng Ding / Elbert Seto / Magdeleine Hung / Yu Yu / Weimei Xing / Giuseppe A Papalia / Wei Kan / Brian Carr / Majlinda Thomas / Leah Tong / Priyanka Desai / Nadine Jarrousse / Alexandre Mercier / Meghan M Holdorf / Simon P Fletcher / Emma Abernathy /
Abstract: Herpes simplex virus (HSV) causes lifelong infections, including oral and genital herpes. There is no vaccine, and current antivirals are only partially effective at reducing symptoms and ...Herpes simplex virus (HSV) causes lifelong infections, including oral and genital herpes. There is no vaccine, and current antivirals are only partially effective at reducing symptoms and transmission. Therapeutic antibodies offer a potentially long-acting treatment option, although efforts to pursue this have been limited. We performed an alpaca immunization campaign and discovered high-affinity antibodies that both neutralized and completely blocked cell-to-cell spread (CCS), a key mechanism by which HSV evades neutralizing antibodies. Unexpectedly, we found that engineering antibodies into a bispecific format targeting two viral glycoproteins dramatically increased antiviral potency. Solving the structures of three antibodies using cryo-electron microscopy (cryo-EM) revealed a mechanistic understanding of how the bispecific format could enhance potency. Lastly, these bispecific antibodies significantly reduced lesion development in the guinea pig model of genital herpes, demonstrating that delayed dosing after latency establishment can reduce disease and confirming their potential as a transformative treatment option.
History
DepositionJan 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein B
B: Envelope glycoprotein B
C: Envelope glycoprotein B
D: C6 Neutralizing Nanobody
E: C6 Neutralizing Nanobody
F: C6 Neutralizing Nanobody


Theoretical massNumber of molelcules
Total (without water)289,1346
Polymers289,1346
Non-polymers00
Water78,5814362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Envelope glycoprotein B / gB


Mass: 82038.016 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (strain 17) / Strain: 17 / Gene: gB, UL27 / Production host: Homo sapiens (human) / References: UniProt: P10211
#2: Antibody C6 Neutralizing Nanobody


Mass: 14339.837 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4362 / Source method: isolated from a natural source / Formula: H2O
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

ComponentName: One C6 Neutralizing Nanobody bound to each monomer of the HSV Glycoprotein B Trimer
Type: COMPLEX
Details: There are 6 molecules in the complex. A trimer of HSV Glycoprotein B and one C6 Neutralizing Nanobody bound to each Glycoprotein B monomer.
Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 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: 165000 X / Calibrated magnification: 165000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 600 nm / Calibrated defocus max: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 83 K / Temperature (min): 83 K
Image recordingElectron dose: 52 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149170 / Algorithm: FOURIER SPACE / Num. of class averages: 21 / Symmetry type: POINT
RefinementHighest resolution: 2.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317256
ELECTRON MICROSCOPYf_angle_d0.61123434
ELECTRON MICROSCOPYf_dihedral_angle_d5.3292376
ELECTRON MICROSCOPYf_chiral_restr0.0442528
ELECTRON MICROSCOPYf_plane_restr0.0053072

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