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Yorodumi- EMDB-9368: Atomic structures and deletion mutant reveal different capsid-bin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9368 | ||||||||||||||||||
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Title | Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development | ||||||||||||||||||
Map data | 3-fold sub-particle reconstruction | ||||||||||||||||||
Sample |
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Biological species | Murine cytomegalovirus (strain Smith) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||
Authors | Liu W / Dai XH / Jih J / Chan K / Trang P / Yu XK / Balogun R / Mei Y / Liu FY / Zhou ZH | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: PLoS Pathog / Year: 2019 Title: Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for ...Title: Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development. Authors: Wei Liu / Xinghong Dai / Jonathan Jih / Karen Chan / Phong Trang / Xuekui Yu / Rilwan Balogun / Ye Mei / Fenyong Liu / Z Hong Zhou / Abstract: Cytomegalovirus (CMV) infection causes birth defects and life-threatening complications in immunosuppressed patients. Lack of vaccine and need for more effective drugs have driven widespread ongoing ...Cytomegalovirus (CMV) infection causes birth defects and life-threatening complications in immunosuppressed patients. Lack of vaccine and need for more effective drugs have driven widespread ongoing therapeutic development efforts against human CMV (HCMV), mostly using murine CMV (MCMV) as the model system for preclinical animal tests. The recent publication (Yu et al., 2017, DOI: 10.1126/science.aam6892) of an atomic model for HCMV capsid with associated tegument protein pp150 has infused impetus for rational design of novel vaccines and drugs, but the absence of high-resolution structural data on MCMV remains a significant knowledge gap in such development efforts. Here, by cryoEM with sub-particle reconstruction method, we have obtained the first atomic structure of MCMV capsid with associated pp150. Surprisingly, the capsid-binding patterns of pp150 differ between HCMV and MCMV despite their highly similar capsid structures. In MCMV, pp150 is absent on triplex Tc and exists as a "Λ"-shaped dimer on other triplexes, leading to only 260 groups of two pp150 subunits per capsid in contrast to 320 groups of three pp150 subunits each in a "Δ"-shaped fortifying configuration. Many more amino acids contribute to pp150-pp150 interactions in MCMV than in HCMV, making MCMV pp150 dimer inflexible thus incompatible to instigate triplex Tc-binding as observed in HCMV. While pp150 is essential in HCMV, our pp150-deletion mutant of MCMV remained viable though with attenuated infectivity and exhibiting defects in retaining viral genome. These results thus invalidate targeting pp150, but lend support to targeting capsid proteins, when using MCMV as a model for HCMV pathogenesis and therapeutic studies. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9368.map.gz | 218.7 MB | EMDB map data format | |
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Header (meta data) | emd-9368-v30.xml emd-9368.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_9368.png | 238.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9368 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9368 | HTTPS FTP |
-Validation report
Summary document | emd_9368_validation.pdf.gz | 79.6 KB | Display | EMDB validaton report |
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Full document | emd_9368_full_validation.pdf.gz | 78.7 KB | Display | |
Data in XML | emd_9368_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9368 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9368 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9368.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3-fold sub-particle reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.351 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Murine cytomegalovirus (strain Smith)
Entire | Name: Murine cytomegalovirus (strain Smith) |
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Components |
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-Supramolecule #1: Murine cytomegalovirus (strain Smith)
Supramolecule | Name: Murine cytomegalovirus (strain Smith) / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10367 / Sci species name: Murine cytomegalovirus (strain Smith) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: AGFA SCIENTA FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER Details: 3D reconstruction from extracted 3-fold sub-particles |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 959640 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |