|Entry||Database: EMDB / ID: 0383|
|Title||Atomic structure of Non-Structural protein 1 of bluetongue virus|
|Map data||Non-Structural protein 1 of bluetongue virus, primary map|
|Sample||Non-structural protein 1 (tubule):|
Non-structural protein 1
|Function / homology||Orbivirus non-structural protein NS1/hydrophobic tubular protein / Orbivirus non-structural protein NS1, or hydrophobic tubular protein / NS1|
Function and homology information
|Source||Bluetongue virus (serotype 1 / isolate South Africa) / Bluetongue virus 23|
|Method||helical reconstruction / cryo EM / 4 Å resolution|
|Authors||Kerviel A / Ge P / Lai M / Jih J / Boyce M / Zhang X / Zhou ZH / Roy P|
|Citation||Journal: Nat Microbiol / Year: 2019|
Title: Atomic structure of the translation regulatory protein NS1 of bluetongue virus.
Authors: Adeline Kerviel / Peng Ge / Mason Lai / Jonathan Jih / Mark Boyce / Xing Zhang / Z Hong Zhou / Polly Roy
|Validation Report||PDB-ID: 6n9y|
SummaryFull reportAbout validation report
|Date||Deposition: Dec 4, 2018 / Header (metadata) release: Jan 16, 2019 / Map release: Mar 13, 2019 / Last update: Mar 13, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||emd_0383.map.gz (map file in CCP4 format, 32001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.07 Å|
CCP4 map header:
-Entire Non-structural protein 1 (tubule)
|Entire||Name: Non-structural protein 1 (tubule) / Number of components: 2|
-Component #1: protein, Non-structural protein 1 (tubule)
|Protein||Name: Non-structural protein 1 (tubule) / Recombinant expression: No|
|Source||Species: Bluetongue virus (serotype 1 / isolate South Africa)|
-Component #2: protein, Non-structural protein 1
|Protein||Name: Non-structural protein 1 / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 64.554984 kDa|
|Source||Species: Bluetongue virus 23|
|Specimen||Specimen state: helical array / Method: cryo EM|
|Helical parameters||Axial symmetry: D2 (2*2 fold dihedral) / Delta z: 8.83 Å / Delta phi: -17.5 deg.|
|Sample solution||pH: 7.5|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE|
-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: 6 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 QUANTUM (4k x 4k)|
|Image acquisition||Number of digital images: 5006|
|Processing||Method: helical reconstruction|
|3D reconstruction||Algorithm: BACK PROJECTION / Software: RELION / Resolution: 4 Å / Resolution method: OTHER|
-Atomic model buiding
|Modeling #1||Refinement space: REAL|
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-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
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