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- PDB-8xh7: Structure of EBV LMP1 oligomer -

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Basic information

Entry
Database: PDB / ID: 8xh7
TitleStructure of EBV LMP1 oligomer
ComponentsLatent membrane protein 1
KeywordsVIRAL PROTEIN / EBV latent membrane protein 1
Function / homologyHerpesvirus latent membrane 1 / Herpesvirus latent membrane protein 1 (LMP1) / transformation of host cell by virus / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / host cell plasma membrane / membrane / Latent membrane protein 1
Function and homology information
Biological specieshuman gammaherpesvirus 4 (Epstein-Barr virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsGao, P. / Huang, J.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2024
Title: Assembly and activation of EBV latent membrane protein 1.
Authors: Jiafeng Huang / Xiaolin Zhang / Xiaohua Nie / Xuyuan Zhang / Yong Wang / Linlong Huang / Xiaohan Geng / Dong Li / Liguo Zhang / Guangxia Gao / Pu Gao /
Abstract: Latent membrane protein 1 (LMP1) is the primary oncoprotein of Epstein-Barr virus (EBV) and plays versatile roles in the EBV life cycle and pathogenesis. Despite decades of extensive research, the ...Latent membrane protein 1 (LMP1) is the primary oncoprotein of Epstein-Barr virus (EBV) and plays versatile roles in the EBV life cycle and pathogenesis. Despite decades of extensive research, the molecular basis for LMP1 folding, assembly, and activation remains unclear. Here, we report cryo-electron microscopy structures of LMP1 in two unexpected assemblies: a symmetric homodimer and a higher-order filamentous oligomer. LMP1 adopts a non-canonical and unpredicted fold that supports the formation of a stable homodimer through tight and antiparallel intermolecular packing. LMP1 dimers further assemble side-by-side into higher-order filamentous oligomers, thereby allowing the accumulation and specific organization of the flexible cytoplasmic tails for efficient recruitment of downstream factors. Super-resolution microscopy and cellular functional assays demonstrate that mutations at both dimeric and oligomeric interfaces disrupt LMP1 higher-order assembly and block multiple LMP1-mediated signaling pathways. Our research provides a framework for understanding the mechanism of LMP1 and for developing potential therapies targeting EBV-associated diseases.
History
DepositionDec 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Latent membrane protein 1
E: Latent membrane protein 1
F: Latent membrane protein 1
A: Latent membrane protein 1
B: Latent membrane protein 1
D: Latent membrane protein 1


Theoretical massNumber of molelcules
Total (without water)112,3776
Polymers112,3776
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
Latent membrane protein 1 / Protein p63


Mass: 18729.418 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human gammaherpesvirus 4 (Epstein-Barr virus)
Gene: LMP1, LMP-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7T6U2

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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: LMP1 oligomer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Human gammaherpesvirus 4 (Epstein-Barr virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.1_4122: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10157152 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038124
ELECTRON MICROSCOPYf_angle_d0.68511124
ELECTRON MICROSCOPYf_dihedral_angle_d3.8551008
ELECTRON MICROSCOPYf_chiral_restr0.0371422
ELECTRON MICROSCOPYf_plane_restr0.0021206

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