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Yorodumi- EMDB-23388: Structure of human transfer RNA visualized in the cytomegalovirus... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23388 | ||||||||||||||||||
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Title | Structure of human transfer RNA visualized in the cytomegalovirus, a DNA virus | ||||||||||||||||||
Map data | C2 2-fold sub-particle reconstruction of HCMV virion particles | ||||||||||||||||||
Sample |
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Keywords | HCMV / tRNA / VIRUS | ||||||||||||||||||
Function / homology | host cell viral assembly compartment / Herpesvirus UL11/UL32 / Herpesvirus large structural phosphoprotein UL32 / viral tegument / host cell cytoplasmic vesicle / host cell perinuclear region of cytoplasm / host cell nucleus / structural molecule activity / Large structural phosphoprotein Function and homology information | ||||||||||||||||||
Biological species | Homo sapiens (human) / Human cytomegalovirus (strain AD169) / Human herpesvirus 5 strain AD169 | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||
Authors | Liu YT / Strugatsky D | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structure of human cytomegalovirus virion reveals host tRNA binding to capsid-associated tegument protein pp150. Authors: Yun-Tao Liu / David Strugatsky / Wei Liu / Z Hong Zhou / Abstract: Under the Baltimore nucleic acid-based virus classification scheme, the herpesvirus human cytomegalovirus (HCMV) is a Class I virus, meaning that it contains a double-stranded DNA genome-and no RNA. ...Under the Baltimore nucleic acid-based virus classification scheme, the herpesvirus human cytomegalovirus (HCMV) is a Class I virus, meaning that it contains a double-stranded DNA genome-and no RNA. Here, we report sub-particle cryoEM reconstructions of HCMV virions at 2.9 Å resolution revealing structures resembling non-coding transfer RNAs (tRNAs) associated with the virion's capsid-bound tegument protein, pp150. Through deep sequencing, we show that these RNA sequences match human tRNAs, and we built atomic models using the most abundant tRNA species. Based on our models, tRNA recruitment is mediated by the electrostatic interactions between tRNA phosphate groups and the helix-loop-helix motif of HCMV pp150. The specificity of these interactions may explain the absence of such tRNA densities in murine cytomegalovirus and other human herpesviruses. | ||||||||||||||||||
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_23388.map.gz | 113.9 MB | EMDB map data format | |
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Header (meta data) | emd-23388-v30.xml emd-23388.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_23388.png | 174.8 KB | ||
Filedesc metadata | emd-23388.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23388 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23388 | HTTPS FTP |
-Validation report
Summary document | emd_23388_validation.pdf.gz | 798 KB | Display | EMDB validaton report |
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Full document | emd_23388_full_validation.pdf.gz | 797.6 KB | Display | |
Data in XML | emd_23388_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_23388_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23388 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23388 | HTTPS FTP |
-Related structure data
Related structure data | 7lj3MC 7livC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_23388.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | C2 2-fold sub-particle reconstruction of HCMV virion particles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 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 : Transfer RNA visualized in the cytomegalovirus, a DNA virus
Entire | Name: Transfer RNA visualized in the cytomegalovirus, a DNA virus |
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Components |
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-Supramolecule #1: Transfer RNA visualized in the cytomegalovirus, a DNA virus
Supramolecule | Name: Transfer RNA visualized in the cytomegalovirus, a DNA virus type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #3: RNA
Supramolecule | Name: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: Human herpesvirus 5 strain AD169
Supramolecule | Name: Human herpesvirus 5 strain AD169 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1 / NCBI-ID: 10360 / Sci species name: Human herpesvirus 5 strain AD169 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Macromolecule #1: Tegument protein pp150
Macromolecule | Name: Tegument protein pp150 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Human cytomegalovirus (strain AD169) / Strain: AD169 |
Molecular weight | Theoretical: 33.232418 KDa |
Sequence | String: MSLQFIGLQR RDVVALVNFL RHLTQKPDVD LEAHPKILKK CGEKRLHRRT VLFNELMLWL GYYRELRFHN PDLSSVLEEF EVRCVAVAR RGYTYPFGDR GKARDHLAVL DRTEFDTDVR HDAEIVERAL VSAVILAKMS VRETLVTAIG QTEPIAFVHL K DTEVQRIE ...String: MSLQFIGLQR RDVVALVNFL RHLTQKPDVD LEAHPKILKK CGEKRLHRRT VLFNELMLWL GYYRELRFHN PDLSSVLEEF EVRCVAVAR RGYTYPFGDR GKARDHLAVL DRTEFDTDVR HDAEIVERAL VSAVILAKMS VRETLVTAIG QTEPIAFVHL K DTEVQRIE ENLEGVRRNM FCVKPLDLNL DRHANTALVN AVNKLVYTGR LIMNVRRSWE ELERKCLARI QERCKLLVKE LR MCLSFDS NYCRNILKHA VENGDSADTL LELLIEDFDI YVDSFPQS UniProtKB: Large structural phosphoprotein |
-Macromolecule #2: RNA (75-MER)
Macromolecule | Name: RNA (75-MER) / type: rna / ID: 2 / Number of copies: 3 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.077223 KDa |
Sequence | String: UCCCUGGUGG UCUAGUGGUU AGGAUUCGGC GCUCUCACCG CCGCGGCCCG GGUUCGAUUC CCGGUCAGGG AACCA GENBANK: GENBANK: M31637.1 |
-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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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: 35.0 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: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43666 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |