+
Open data
-
Basic information
Entry | Database: PDB / ID: 6rpo | ||||||
---|---|---|---|---|---|---|---|
Title | bat circovirus without DNA VLP | ||||||
![]() | bat circovirus capsid protein | ||||||
![]() | VIRUS LIKE PARTICLE / bat circovirus without DNA VLP | ||||||
Function / homology | Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein / viral capsid assembly / T=1 icosahedral viral capsid / symbiont entry into host cell / virion attachment to host cell / Capsid protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å | ||||||
![]() | Forwood, J.K. / Luque, D. / Mata, C.P. / Das, S. / Raidal, S. | ||||||
![]() | ![]() Title: bat circovirus without DNA VLP Authors: Forwood, J.K. / Luque, D. / Mata, C.P. / Das, S. / Raidal, S. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 49.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 34.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4979MC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 | ![]()
| x 60
-
Components
#1: Protein | Mass: 27754.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Bat circovirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 1.42 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE |
Virus shell | Diameter: 200 nm / Triangulation number (T number): 1 |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: LEICA EM CPC / 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: OTHER / Nominal magnification: 47170 X / Nominal defocus max: 3500 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 57 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1474 |
Image scans | Movie frames/image: 32 |
-
Processing
Software | Name: PHENIX / Version: dev_3311: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 124275 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58147 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 83 / Protocol: OTHER / Space: REAL |