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- PDB-9lld: Post-fusion ectodomain of KSHV gB in complex with 2C4 Fab -

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Basic information

Entry
Database: PDB / ID: 9lld
TitlePost-fusion ectodomain of KSHV gB in complex with 2C4 Fab
Components
  • 2C4 Fab H chain
  • 2C4 Fab L chain
  • Core gene UL27 family protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / KSHV / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endosome / host cell Golgi apparatus / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma 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
Core gene UL27 family protein
Similarity search - Component
Biological speciesHuman gammaherpesvirus 8
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFang, X.Y. / Sun, C. / Xie, C. / Zeng, M.S. / Liu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: To Be Published
Title: Post-fusion ectodomain of KSHV gB in complex with 2C4 Fab
Authors: Fang, X.Y. / Sun, C. / Xie, C. / Zeng, M.S. / Liu, Z.
History
DepositionJan 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Core gene UL27 family protein
H: 2C4 Fab H chain
L: 2C4 Fab L chain
A: Core gene UL27 family protein
D: 2C4 Fab H chain
F: 2C4 Fab L chain
B: Core gene UL27 family protein
E: 2C4 Fab H chain
G: 2C4 Fab L chain


Theoretical massNumber of molelcules
Total (without water)374,5369
Polymers374,5369
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 Core gene UL27 family protein / KSHV gB / Envelope glycoprotein gB / Glycoprotein B / ORF8


Mass: 73137.594 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 8 / Gene: ORF8 / Production host: Human gammaherpesvirus 8 / References: UniProt: Q77UU3
#2: Antibody 2C4 Fab H chain


Mass: 26851.230 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 2C4 Fab L chain


Mass: 24856.516 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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: Complex of KSHV post-fusion gB with 2C4 Fab / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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 / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 339379 / Symmetry type: POINT

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