+
Open data
-
Basic information
Entry | Database: PDB / ID: 7et3 | ||||||
---|---|---|---|---|---|---|---|
Title | C5 portal vertex in the enveloped virion capsid | ||||||
![]() |
| ||||||
![]() | VIRAL PROTEIN / C5 portal vertex / enveloped capsid | ||||||
Function / homology | ![]() T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / viral release from host cell / chromosome organization / viral process / viral capsid / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm ...T=16 icosahedral viral capsid / viral genome packaging / viral tegument / viral capsid assembly / viral release from host cell / chromosome organization / viral process / viral capsid / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell cytoplasm / cysteine-type deubiquitinase activity / host cell nucleus / structural molecule activity / proteolysis / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
![]() | Li, Z. / Yu, X. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.9 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1.6 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 233.1 KB | Display | |
Data in CIF | ![]() | 369.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31297MC ![]() 7et2C ![]() 7etjC ![]() 7etmC ![]() 7etoC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 | ![]()
| x 5
2 |
|
3 | ![]()
|
Symmetry | Point symmetry: (Schoenflies symbol: C5 (5 fold cyclic)) |
-
Components
-Triplex capsid protein ... , 2 types, 6 molecules hInogm
#1: Protein | Mass: 34635.750 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 33071.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Protein , 4 types, 14 molecules HP1RSTijaBCDYZ
#2: Protein | Mass: 253541.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A3G6XL22, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #6: Protein | | Mass: 112829.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 8495.924 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 154048.906 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Capsid vertex component ... , 2 types, 3 molecules MNO
#4: Protein | Mass: 68567.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#5: Protein | Mass: 71269.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
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 |
---|---|
Source (natural) | Organism: ![]() ![]() |
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 |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
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 |
---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23136 / Symmetry type: POINT |