+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38343 | |||||||||
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Title | Structure of EBV LMP1 oligomer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | EBV latent membrane protein 1 / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information symbiont-mediated activation of host NF-kappaB cascade / 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 Similarity search - Function | |||||||||
Biological species | Human gammaherpesvirus 4 (Epstein-Barr virus) / human gammaherpesvirus 4 (Epstein-Barr virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.52 Å | |||||||||
Authors | Gao P / Huang JF | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38343.map.gz | 565.4 MB | EMDB map data format | |
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Header (meta data) | emd-38343-v30.xml emd-38343.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38343_fsc.xml | 17.8 KB | Display | FSC data file |
Images | emd_38343.png | 51.6 KB | ||
Filedesc metadata | emd-38343.cif.gz | 5 KB | ||
Others | emd_38343_half_map_1.map.gz emd_38343_half_map_2.map.gz | 556.8 MB 556.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38343 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38343 | HTTPS FTP |
-Validation report
Summary document | emd_38343_validation.pdf.gz | 963.5 KB | Display | EMDB validaton report |
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Full document | emd_38343_full_validation.pdf.gz | 963 KB | Display | |
Data in XML | emd_38343_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | emd_38343_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38343 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38343 | HTTPS FTP |
-Related structure data
Related structure data | 8xh7MC 8xh6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_38343.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.52 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_38343_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38343_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : LMP1 oligomer
Entire | Name: LMP1 oligomer |
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Components |
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-Supramolecule #1: LMP1 oligomer
Supramolecule | Name: LMP1 oligomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Human gammaherpesvirus 4 (Epstein-Barr virus) |
-Macromolecule #1: Latent membrane protein 1
Macromolecule | Name: Latent membrane protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: human gammaherpesvirus 4 (Epstein-Barr virus) |
Molecular weight | Theoretical: 18.729418 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SIGLALLLLL LALLFWLYIV MSNWTGGALL VLYSFALMLI IIILIIFIFR RDLLCPLGGL GLLLLMITLL LIALWNLHGQ ALYLGIVLF IFGCLLVLGL WIYFLEILWR LGATIWQLLA FILAFFLAII LLIIALYLQQ NWWTLLVDLL WLLLFMAILI W MY UniProtKB: Latent membrane protein 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |