+Open data
-Basic information
Entry | Database: PDB / ID: 7etm | ||||||
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Title | C6 portal vertex in the enveloped virion capsid | ||||||
Components | Portal protein | ||||||
Keywords | VIRAL PROTEIN / C6 portal vertex / enveloped capsid | ||||||
Function / homology | Herpesvirus portal protein / Herpesvirus UL6 like / chromosome organization / Capsid portal protein Function and homology information | ||||||
Biological species | Human cytomegalovirus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.9 Å | ||||||
Authors | Li, Z. / Yu, X. | ||||||
Funding support | China, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7etm.cif.gz | 1003.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7etm.ent.gz | 839.3 KB | Display | PDB format |
PDBx/mmJSON format | 7etm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/7etm ftp://data.pdbj.org/pub/pdb/validation_reports/et/7etm | HTTPS FTP |
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-Related structure data
Related structure data | 31299MC 7et2C 7et3C 7etjC 7etoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 78634.805 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Human cytomegalovirus / References: UniProt: Q6RXD3 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human betaherpesvirus 5 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Human betaherpesvirus 5 |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22087 / Symmetry type: POINT |