+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31296 | |||||||||
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Title | Human Cytomegalovirus, C12 portal | |||||||||
Map data | ||||||||||
Sample |
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Keywords | C12 portal / partially-enveloped capsid / Human Cytomegalovirus / VIRAL PROTEIN | |||||||||
Function / homology | Herpesvirus portal protein / Herpesvirus UL6 like / chromosome organization / Capsid portal protein Function and homology information | |||||||||
Biological species | Human cytomegalovirus / Human betaherpesvirus 5 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Li Z / Yu X / Dong L | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for genome packaging, retention, and ejection in human cytomegalovirus. Authors: Zhihai Li / Jingjing Pang / Lili Dong / Xuekui Yu / Abstract: How the human cytomegalovirus (HCMV) genome-the largest among human herpesviruses-is packaged, retained, and ejected remains unclear. We present the in situ structures of the symmetry-mismatched ...How the human cytomegalovirus (HCMV) genome-the largest among human herpesviruses-is packaged, retained, and ejected remains unclear. We present the in situ structures of the symmetry-mismatched portal and the capsid vertex-specific components (CVSCs) of HCMV. The 5-fold symmetric 10-helix anchor-uncommon among known portals-contacts the portal-encircling DNA, which is presumed to squeeze the portal as the genome packaging proceeds. We surmise that the 10-helix anchor dampens this action to delay the portal reaching a "head-full" packaging state, thus facilitating the large genome to be packaged. The 6-fold symmetric turret, latched via a coiled coil to a helix from a major capsid protein, supports the portal to retain the packaged genome. CVSCs at the penton vertices-presumed to increase inner capsid pressure-display a low stoichiometry, which would aid genome retention. We also demonstrate that the portal and capsid undergo conformational changes to facilitate genome ejection after viral cell entry. | |||||||||
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_31296.map.gz | 6.9 MB | EMDB map data format | |
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Header (meta data) | emd-31296-v30.xml emd-31296.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | emd_31296.png | 28.6 KB | ||
Filedesc metadata | emd-31296.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31296 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31296 | HTTPS FTP |
-Validation report
Summary document | emd_31296_validation.pdf.gz | 594.6 KB | Display | EMDB validaton report |
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Full document | emd_31296_full_validation.pdf.gz | 594.2 KB | Display | |
Data in XML | emd_31296_validation.xml.gz | 5 KB | Display | |
Data in CIF | emd_31296_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31296 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31296 | HTTPS FTP |
-Related structure data
Related structure data | 7et2MC 7et3C 7etjC 7etmC 7etoC 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_31296.map.gz / Format: CCP4 / Size: 8 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: 1.625 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 : Human betaherpesvirus 5
Entire | Name: Human betaherpesvirus 5 |
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Components |
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-Supramolecule #1: Human betaherpesvirus 5
Supramolecule | Name: Human betaherpesvirus 5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10359 / Sci species name: Human betaherpesvirus 5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Macromolecule #1: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Human cytomegalovirus |
Molecular weight | Theoretical: 78.634805 KDa |
Sequence | String: MERNHWNEKS SGAKRSRERD LTLSTIRSIL AADERLRIKA SSYLGVGRGV DDEAVIDIFP TGQTMSFLRL LHGFLGTCRG QSMHQVLRD PCVLRKQLLY GVCKTLFDTI TVRRVAEEWK LHAALFPYRA LDEEDLEQYL LVWSASLRQS VQTGVLGALR D ILYQYADN ...String: MERNHWNEKS SGAKRSRERD LTLSTIRSIL AADERLRIKA SSYLGVGRGV DDEAVIDIFP TGQTMSFLRL LHGFLGTCRG QSMHQVLRD PCVLRKQLLY GVCKTLFDTI TVRRVAEEWK LHAALFPYRA LDEEDLEQYL LVWSASLRQS VQTGVLGALR D ILYQYADN DDYGLYVDWC VTVGLVPLLD VKTKPSEAAE RAQFVRAAVQ RATETHPLAQ DLLQANLALL LQVAERLGAV RV ANAPEVR VFKKVRSERL EAQLRGKHIR LYVAAEPLAY ERDKLLFTTP VAHLHEEILR YDGLCRHQKI CQLLNTFPVK VVT ASRHEL NCKKLVEMME QHDRGSDAKK SIMKFLLNVS DSKSRIGIED SVESFLQDLT PSLVDQNRLL PARGPGGPGV VGPG GAVVG GPAGHVGLLP PPPGPAAPER DIRDLFKKQV IKCLEEQIQS QVDEIQDLRT LNQTWENRVR ELRDLLTRYA SRRED SMSL GARDAELYHL PVLEAVRKAR DAAPFRPLAV EDNRLVANSF FSQFVPGTES LERFLTQLWE NEYFRTFRLR RLVTHQ GAE EAIVYSNYTV ERVTLPYLCH ILALGTLDPV PEAYLQLSFG EIVAAAYDDS KFCRYVELIC SREKARRRQM SREAAGG VP ERGTASSGGP GTLERSAPRR LITADEERRG PERVGRFRNG GPDDPRRAGG PYGFH UniProtKB: Capsid portal protein |
-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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 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: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40903 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |