+Open data
-Basic information
Entry | Database: PDB / ID: 6m6i | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of HSV2 B-capsid portal vertex | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN / HSV2 / Portal vertex / Complex | ||||||
Function / homology | Function and homology information T=16 icosahedral viral capsid / viral capsid assembly / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding Similarity search - Function | ||||||
Biological species | Human herpesvirus 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.05 Å | ||||||
Authors | Wang, X.X. / Wang, N. | ||||||
Citation | Journal: Protein Cell / Year: 2020 Title: Structures of the portal vertex reveal essential protein-protein interactions for Herpesvirus assembly and maturation. Authors: Nan Wang / Wenyuan Chen / Ling Zhu / Dongjie Zhu / Rui Feng / Jialing Wang / Bin Zhu / Xinzheng Zhang / Xiaoqing Chen / Xianjie Liu / Runbin Yan / Dongyao Ni / Grace Guoying Zhou / Hongrong ...Authors: Nan Wang / Wenyuan Chen / Ling Zhu / Dongjie Zhu / Rui Feng / Jialing Wang / Bin Zhu / Xinzheng Zhang / Xiaoqing Chen / Xianjie Liu / Runbin Yan / Dongyao Ni / Grace Guoying Zhou / Hongrong Liu / Zihe Rao / Xiangxi Wang / | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6m6i.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6m6i.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 6m6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/6m6i ftp://data.pdbj.org/pub/pdb/validation_reports/m6/6m6i | HTTPS FTP |
---|
-Related structure data
Related structure data | 30125MC 6m6gC 6m6hC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 5
2 |
|
3 |
|
Symmetry | Point symmetry: (Schoenflies symbol: C5 (5 fold cyclic)) |
-Components
-Protein , 2 types, 12 molecules ABCDEFLMNOPQ
#1: Protein | Mass: 149399.359 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: P89442 #6: Protein | Mass: 12147.707 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I257 |
---|
-Coiled coils chain ... , 2 types, 2 molecules GH
#2: Protein | Mass: 6911.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 |
---|---|
#3: Protein | Mass: 7081.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 |
-Triplex capsid protein ... , 2 types, 3 molecules IJK
#4: Protein | Mass: 34373.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I239 #5: Protein | | Mass: 50566.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I260 |
---|
-Details
Sequence details | Sequence for Coiled coils chains could not be identified. |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human alphaherpesvirus 2 / Type: VIRUS / Entity ID: all / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Human alphaherpesvirus 2 |
Details of virus | Empty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION |
Buffer solution | pH: 7.4 |
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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM | ||||||||||||
Electron lens | Mode: DARK FIELD | ||||||||||||
Image recording |
|
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22158 / Symmetry type: POINT |