|Entry||Database: EMDB / ID: 3869|
|Title||The structure of Ebola virus nucleoprotein (residues 1-450) in nucleocapsid-like assemblies|
|Sample||Ebola virus - Mayinga, Zaire, 1976|
|Source||Ebola virus - Mayinga, Zaire, 1976 / virus|
|Map data||Subtomogram averaging of recombinantly expressed Ebola Nucleoprotein (NP), residues 1-450|
|Method||subtomogram averaging, at 6.6 Å resolution|
|Authors||Wan W / Kolesnikova L|
|Validation Report||PDB-ID: 6ehl|
SummaryFull reportAbout validation report
|Date||Deposition: Sep 13, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 8, 2017 / Last update: Nov 8, 2017|
Downloads & links
|File||emd_3869.map.gz (map file in CCP4 format, 28312 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.78 Å|
CCP4 map header:
-Entire Ebola virus - Mayinga, Zaire, 1976
|Entire||Name: Ebola virus - Mayinga, Zaire, 1976 / Number of components: 2|
-Component #1: virus, Ebola virus - Mayinga, Zaire, 1976
|Virus||Name: Ebola virus - Mayinga, Zaire, 1976 / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: Ebola virus - Mayinga, Zaire, 1976 / virus|
|Source (engineered)||Expression System: Homo sapiens / human / Cell of expression system: HEK 293T|
|Shell #1||Name of element: Nucleocapsid / Diameter: 280 Å|
-Component #2: protein, Nucleoprotein
|Protein||Name: Nucleoprotein / Recombinant expression: No|
|Mass||Theoretical: 83.3875 kDa|
|Source (engineered)||Expression System: Zaire ebolavirus (strain Mayinga-76) / virus|
|Specimen state||helical array|
|Sample solution||pH: 7.4|
|Vitrification||Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 %|
-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: 2.4 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 81000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4500 nm / Energy filter: Gatan Quantum 967 LS / Energy window: -10-10 eV|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -60 - 60 deg.|
|Camera||Detector: GATAN K2 QUANTUM (4k x 4k)|
|Processing||Method: subtomogram averaging / Applied symmetry: C1 (asymmetric)|
Details: Frames were aligned using K2Align software, based off the MotionCorr algorithm. Tomograms were reconstructed with IMOD, using stripwise CTF-correction and weighted back projection. Subtomogram averaging was performed using scripts derived from TOM, AV3, and DYNAMO.
|3D reconstruction||Algorithm: BACK PROJECTION / Software: TOM/AV3|
CTF correction: CTF amplitude correction was performed during the wedge-weighted subtomogram averaging step.
Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Local resolution was estimated using moving window FSC calculations.
Euler angles: Iterative angular search was performed via maximization of a modified constrained cross-correlation function.
-Atomic model buiding
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
-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 / EM Navigator (legacy version) / Yorodumi (legacy version)
+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 / EM Navigator (legacy version) / Yorodumi (legacy version)
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi