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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 / 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: To Be Published
Title: Structure-based design of soluble prefusion-stabilized herpes simplex virus type 2 glycoprotein B antigens
Authors: Sponholtz, M.R. / Ma, D. / Byrne, P.O. / Shu, Y. / Warren, C. / Thambi, N. / McCool, R.S. / Slein, M.D. / Johnson, N.V. / Rose, W.A. / Zhang, L. / Durr, E. / Wang, D. / McLellan, J.M.
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
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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