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- PDB-9zwe: Soluble ectodomain of Herpes simplex virus 2 (HSV-2) glycoprotein... -

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Basic information

Entry
Database: PDB / ID: 9zwe
TitleSoluble ectodomain of Herpes simplex virus 2 (HSV-2) glycoprotein B (gB) in the prefusion conformation in complex with 2c and D48 Fabs
Components
  • Antibody 2c Heavy Chain
  • Antibody 2c Light Chain
  • Antibody D48 Heavy Chain
  • Antibody D48 Light Chain
  • Envelope glycoprotein B
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / prefusion / ectodomain / viral fusion protein / VIRAL PROTEIN-IMMUNE SYSTEM 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
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 HG52
Homo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsSponholtz, M.R. / Johnson, N.V. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Cell Rep / Year: 2026
Title: Structure-based design of soluble prefusion-stabilized herpes simplex virus type 2 glycoprotein B antigens.
Authors: Madeline R Sponholtz / Daphne Y Ma / Emmanuel Ndashimye / Patrick O Byrne / Yi Shu / Christopher Warren / Nithya Thambi / Ryan S McCool / Matthew D Slein / Nicole V Johnson / William A Rose ...Authors: Madeline R Sponholtz / Daphne Y Ma / Emmanuel Ndashimye / Patrick O Byrne / Yi Shu / Christopher Warren / Nithya Thambi / Ryan S McCool / Matthew D Slein / Nicole V Johnson / William A Rose / Lan Zhang / Eberhard Durr / Dai Wang / Jason S McLellan /
Abstract: Herpes simplex virus type 2 (HSV-2) infection causes recurrent genital herpes throughout life, yet no vaccines have been approved. Glycoprotein B (gB) is a class III fusion protein that mediates HSV- ...Herpes simplex virus type 2 (HSV-2) infection causes recurrent genital herpes throughout life, yet no vaccines have been approved. Glycoprotein B (gB) is a class III fusion protein that mediates HSV-2 entry by transitioning from a metastable prefusion conformation to a stable postfusion conformation. Here, using structure-based design, we stabilize HSV-2 gB in its prefusion conformation. A 2.8 Å resolution cryo-EM structure reveals a closed state of prefusion gB, which differs from recently published open states. Vaccination of mice with protein subunit and mRNA-based vaccines of pre- and postfusion gB variants elicits robust humoral and cellular responses. Although prefusion stabilization of gB does not improve neutralizing antibody titers relative to the postfusion construct, prefusion gB elicits antibodies exhibiting higher FcγR-mediated effector activities. Collectively, these findings reveal insights into prefusion gB conformational dynamics, provide stabilized reagents for studying gB-directed immune responses, and inform HSV-2 vaccine design.
History
DepositionJan 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Sep 30, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Envelope glycoprotein B
H: Antibody D48 Heavy Chain
I: Antibody D48 Light Chain
J: Antibody 2c Heavy Chain
K: Antibody 2c Light Chain
A: Envelope glycoprotein B
C: Antibody D48 Heavy Chain
D: Antibody D48 Light Chain
E: Antibody 2c Heavy Chain
F: Antibody 2c Light Chain
G: Envelope glycoprotein B
L: Antibody D48 Heavy Chain
M: Antibody D48 Light Chain
N: Antibody 2c Heavy Chain
O: Antibody 2c Light Chain


Theoretical massNumber of molelcules
Total (without water)539,11415
Polymers539,11415
Non-polymers00
Water00
1


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

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Components

#1: Protein Envelope glycoprotein B / gB


Mass: 83540.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Fusion protein, homotrimer, ectodomain,Fusion protein, homotrimer, ectodomain
Source: (gene. exp.) Human herpesvirus 2 strain HG52 / Gene: gB, UL27 / Production host: Homo sapiens (human) / References: UniProt: P08666
#2: Antibody Antibody D48 Heavy Chain


Mass: 24402.555 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Antibody D48 Light Chain


Mass: 23476.164 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Antibody 2c Heavy Chain


Mass: 24262.426 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#5: Antibody Antibody 2c Light Chain


Mass: 24022.785 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
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: HSV-2 prefusion gB bound 1:1 with Fabs D48 and 2c / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.555 MDa / Experimental value: NO
Source (natural)Organism: Human herpesvirus 2 (strain HG52)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2PHENIXmodel refinement
13cryoSPARC4.53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227517 / Symmetry type: POINT
RefinementHighest resolution: 2.75 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325128
ELECTRON MICROSCOPYf_angle_d0.62734125
ELECTRON MICROSCOPYf_dihedral_angle_d11.5789111
ELECTRON MICROSCOPYf_chiral_restr0.0453738
ELECTRON MICROSCOPYf_plane_restr0.0134383

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