|Entry||Database: EMDB / ID: 3521|
|Title||Near-atomic resolution structure of a plant geminivirus determined by electron cryo-microscopy|
|Sample||African cassava mosaic virus - [West Kenya 844]:|
virus / Capsid proteinCapsid
|Function / homology||Geminivirus AR1 coat protein / Geminivirus AR1/BR1 coat protein / Geminivirus coat protein/nuclear export factor BR1 family / T=1 icosahedral viral capsid / viral penetration into host nucleus / viral entry into host cell / host cell nucleus / structural molecule activity / DNA binding / metal ion binding / Capsid protein|
Function and homology information
|Source||African cassava mosaic virus - [West Kenya 844]|
|Method||single particle reconstruction / cryo EM / 4.2 Å resolution|
|Authors||Bottcher B / Hipp K / Grimm C / Jeske H|
|Citation||Journal: Structure / Year: 2017|
Title: Near-Atomic Resolution Structure of a Plant Geminivirus Determined by Electron Cryomicroscopy.
Authors: Katharina Hipp / Clemens Grimm / Holger Jeske / Bettina Böttcher
Abstract: African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its ...African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its 22 capsomers interact within a half-capsid or across the waist is unknown thus far. Using electron cryo-microscopy and image processing, we determined the virion structure with a resolution of 4.2 Å and built an atomic model for its capsid protein. The inter-capsomer contacts mediated by the flexible N termini and loop regions differed within the half-capsids and at the waist, explaining partly the unusual twin structure. The tip of the pentameric capsomer is sealed by a plug formed by a turn region harboring the evolutionary conserved residue Y193. Basic amino acid residues inside the capsid form a positively charged pocket next to the five-fold axis of the capsomer suitable for binding DNA. Within this pocket, density most likely corresponding to DNA was resolved.
|Validation Report||PDB-ID: 6ek5|
SummaryFull reportAbout validation report
|Date||Deposition: Dec 1, 2016 / Header (metadata) release: Aug 2, 2017 / Map release: Aug 2, 2017 / Last update: Mar 28, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_3521.map.gz (map file in CCP4 format, 108001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.57 Å|
CCP4 map header:
|File||emd_3521_msk_1.map ( map file in CCP4 format, 108001 KB )|
|Projections & Slices|
|Data type||Image stored as Reals|
|Space group number||1|
-Entire African cassava mosaic virus - [West Kenya 844]
|Entire||Name: African cassava mosaic virus - [West Kenya 844] / Number of components: 2|
|Mass||Theoretical: 3.3 MDa|
-Component #1: virus, African cassava mosaic virus - [West Kenya 844]
|Virus||Name: African cassava mosaic virus - [West Kenya 844] / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN|
|Mass||Theoretical: 3.3 MDa|
|Species||Species: African cassava mosaic virus - [West Kenya 844]|
|Source (natural)||Host Species: Manihot esculenta (cassava)|
-Component #2: protein, Capsid protein
|Protein||Name: Capsid proteinCapsid / Recombinant expression: No|
|Mass||Theoretical: 24.094891 kDa|
|Source (engineered)||Expression System: African cassava mosaic virus (isolate West Kenyan 844)|
Strain: isolate West Kenyan 844
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||pH: 8|
|Support film||Quantifoil R1.2/1.3 + 2nm C. Glow discharged for 30-60 s with 25-28 MicroAmp (Quorum Tec Mini Sputter coater SC7620) and used within 1 hour|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 1 %|
Details: Samples (3 ?l) were applied to the glow discharged grids, incubated for 60 s on the grid, blotted and plunge frozen in liquid ethane using a Vitrobot IV (FEI, Eindhoven, The Netherlands) at 4?C with 100% humidity and blotting from both sides for 3 s with blot force 7
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 94000 X (nominal) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Image acquisition||Number of digital images: 934|
Details: data acquisition with a cs-corrected FEI Titan Krios on a Falcon II direct detector at 300 kV. Data was acquired at a primary magnification of 94,000 (calibrated pixel size of 1.57 A) and with a total dose of 25 e/A2 in 17 frames. In total 1,108 movies were recorded of which 934 movies were used for further processing. The movie frames were averaged after motion correction and dose weightin
-Atomic model buiding
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi