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- PDB-9uvc: Structure of MHV68 glycoprotein B -

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Basic information

Entry
Database: PDB / ID: 9uvc
TitleStructure of MHV68 glycoprotein B
ComponentsMurid herpesvirus 68 glycoprotein B
KeywordsVIRAL PROTEIN / MHV68 / gB
Biological speciesMurid gammaherpesvirus 4 (Murine herpesvirus 68)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsCheng, B.Z. / Fang, X.Y. / Xie, C. / Sun, C. / Liu, Z. / Zeng, M.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: To Be Published
Title: Structure of MHV68 glycoprotein B
Authors: Cheng, B.Z. / Xie, C. / Sun, C. / Zeng, M.S. / Liu, Z. / Fang, X.Y.
History
DepositionMay 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 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
A: Murid herpesvirus 68 glycoprotein B
B: Murid herpesvirus 68 glycoprotein B
C: Murid herpesvirus 68 glycoprotein B


Theoretical massNumber of molelcules
Total (without water)224,7593
Polymers224,7593
Non-polymers00
Water00
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 Murid herpesvirus 68 glycoprotein B


Mass: 74919.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid gammaherpesvirus 4 (Murine herpesvirus 68)
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: Murid herpesvirus 68 glycoprotein B / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Murid gammaherpesvirus 4 (Murine herpesvirus 68)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109332 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00111362
ELECTRON MICROSCOPYf_angle_d0.40615538
ELECTRON MICROSCOPYf_dihedral_angle_d2.0391693
ELECTRON MICROSCOPYf_chiral_restr0.0411793
ELECTRON MICROSCOPYf_plane_restr0.0022048

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