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- PDB-9uy9: Macacine gammaherpesvirus 4 glycoprotein B in complex with Fab5 -

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Basic information

Entry
Database: PDB / ID: 9uy9
TitleMacacine gammaherpesvirus 4 glycoprotein B in complex with Fab5
Components
  • Fab5 H chain
  • Fab5 L chain
  • Macacine gammaherpesvirus 4 glycoprotein B
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / rhLCV / gB / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMacacine gammaherpesvirus 4 (Rhesus lymphocryptovirus)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCheng, B.Z. / Liu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: To Be Published
Title: Macacine gammaherpesvirus 4 glycoprotein B in complex with Fab5
Authors: Cheng, B.Z. / Fang, X.Y. / Sun, C. / Xie, C. / Liu, Z. / Zeng, M.S.
History
DepositionMay 15, 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
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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: Macacine gammaherpesvirus 4 glycoprotein B
B: Macacine gammaherpesvirus 4 glycoprotein B
C: Macacine gammaherpesvirus 4 glycoprotein B
H: Fab5 H chain
I: Fab5 H chain
J: Fab5 H chain
L: Fab5 L chain
M: Fab5 L chain
N: Fab5 L chain


Theoretical massNumber of molelcules
Total (without water)376,5439
Polymers376,5439
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 Macacine gammaherpesvirus 4 glycoprotein B


Mass: 78052.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macacine gammaherpesvirus 4 (Rhesus lymphocryptovirus)
Production host: Homo sapiens (human)
#2: Antibody Fab5 H chain


Mass: 24199.873 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)
#3: Antibody Fab5 L chain


Mass: 23261.846 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: Structure of rhLCV glycoprotein B in complex with Fab5
Type: COMPLEX / Entity ID: #2-#3, #1 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Macacine gammaherpesvirus 4 (Rhesus lymphocryptovirus)45455
31Mus musculus (house mouse)10090
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 magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 5533

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.3.0particle selection
2PHENIXmodel refinement
5cryoSPARCv4.3.0CTF correction
10cryoSPARCv4.3.0initial Euler assignment
11cryoSPARCv4.3.0final Euler assignment
12cryoSPARCv4.3.0classification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 292826
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91810 / Num. of class averages: 32 / Symmetry type: POINT

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