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- PDB-9my8: D7 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycop... -

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Basic information

Entry
Database: PDB / ID: 9my8
TitleD7 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycoprotein gD
Components
  • Anti-Nb Fab Heavy chain
  • D7 Neutralizing Nanobody against HSV Glycoprotein D
  • Glycoprotein D
  • Ig-like domain-containing protein
KeywordsANTIVIRAL PROTEIN / Neutralizing Antibody
Function / homology
Function and homology information


viral envelope / virion membrane / extracellular region / membrane
Similarity search - Function
Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin ...Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Glycoprotein D / Ig-like domain-containing protein
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
Human herpesvirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 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 21, 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
H: Anti-Nb Fab Heavy chain
L: Ig-like domain-containing protein
A: D7 Neutralizing Nanobody against HSV Glycoprotein D
B: Glycoprotein D


Theoretical massNumber of molelcules
Total (without water)99,6654
Polymers99,6654
Non-polymers00
Water26,8241489
1


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

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Components

#1: Antibody Anti-Nb Fab Heavy chain


Mass: 26328.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Ig-like domain-containing protein


Mass: 23171.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q7Z3Y4
#3: Antibody D7 Neutralizing Nanobody against HSV Glycoprotein D


Mass: 13588.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293 / Production host: Homo sapiens (human)
#4: Protein Glycoprotein D


Mass: 36577.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 2 / Gene: US6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q5ICU7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1489 / 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: D7 Neutralizing Nanobody bound to the HSV Glycoprotein D
Type: COMPLEX
Details: There are 4 molecules in the complex. A HSV Glycoprotein D monomer neutrilized by the D7 Nanobody and one tool Fab to enable CryoEM studies (light and heavy chains).
Entity ID: #1-#4 / Source: RECOMBINANT
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 mesh size: 300 divisions/in. / 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
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4900000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228770 / Algorithm: FOURIER SPACE / Num. of class averages: 128 / Symmetry type: POINT
RefinementHighest resolution: 2.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036063
ELECTRON MICROSCOPYf_angle_d0.748263
ELECTRON MICROSCOPYf_dihedral_angle_d6.03844
ELECTRON MICROSCOPYf_chiral_restr0.047925
ELECTRON MICROSCOPYf_plane_restr0.0051051

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