[English] 日本語
Yorodumi
- PDB-6ehl: Model of the Ebola virus nucleoprotein in recombinant nucleocapsi... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6ehl
TitleModel of the Ebola virus nucleoprotein in recombinant nucleocapsid-like assemblies
DescriptorNucleoprotein
KeywordsVIRUS LIKE PARTICLE / nucleocapsid
Specimen sourceZaire ebolavirus (strain Mayinga-76) / virus / ZEBOV
MethodElectron microscopy (6.6 Å resolution / Helical array / Subtomogram averaging)
AuthorsWan, W. / Kolesnikova, L. / Clarke, M. / Koehler, A. / Noda, T. / Becker, S. / Briggs, J.A.G.
CitationNature, 2017

Nature, 2017
Structure and assembly of the Ebola virus nucleocapsid
Wan, W. / Kolesnikova, L. / Clarke, M. / Koehler, A. / Noda, T. / Becker, S. / Briggs, J.A.G.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 13, 2017 / Release: Nov 8, 2017

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-3869
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)83,3881
Polyers83,3881
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Polypeptide(L)Nucleoprotein / Nucleocapsid protein / Protein N / Coordinate model: Cα atoms only


Mass: 83387.500 Da / Num. of mol.: 1 / Mutation: Truncation mutant (residues 1-450)
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / virus
References: UniProt: P18272

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: SUBTOMOGRAM AVERAGING

-
Sample preparation

ComponentName: Ebola virus - Mayinga, Zaire, 1976 / Type: VIRUS / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Source (recombinant)Cell: HEK 293T / Organism: Homo sapiens
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRUS-LIKE PARTICLE
Virus shellName: Nucleocapsid / Diameter: 280 Å
Buffer solutionpH: 7.4
Buffer component
IDConc.UnitsNameFormulaBuffer ID
1137mMsodium chlorideNaCl1
22.7mMpotassium chlorideKCl1
310mMdisodium phosphateNa2PO41
41.8mMmonopotassium phosphateKH2PO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: C-flat 2/1 3C
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 5 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 2.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 1
EM imaging opticsEnergyfilter name: Gatan Quantum 967 LS / Energyfilter upper: 10 eV / Energyfilter lower: -10 eV
Image scansDimension width: 3708 / Dimension height: 3708 / Movie frames/image: 5 / Used frames/image: 1-5

-
Processing

EM software
IDNameVersionCategoryDetailsImage processing IDImaging IDFitting ID
1Amira4VOLUME SELECTIONplacing spline points1
2MATLAB/TOMVOLUME SELECTIONsubtomogram extraction1
3SerialEMIMAGE ACQUISITION1
5CTFFIND4CTF CORRECTIONdefocus determination1
6CTFPHASEFLIPCTF CORRECTIONCTF-correction1
9UCSF ChimeraMODEL FITTINGRigid body fit1
11CootMODEL REFINEMENTBuilding missing regions1
12MDFF/NAMDMODEL REFINEMENTFlexible fitting1
14TOM/AV3FINAL EULER ASSIGNMENT1
16TOM/AV3RECONSTRUCTION1
Image processingDetails: 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.
CTF correctionDetails: CTF amplitude correction was performed during the wedge-weighted subtomogram averaging step.
Type: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 1 / Algorithm: BACK PROJECTION
Details: Local resolution was estimated using moving window FSC calculations.
Number of class averages: 1 / Symmetry type: POINT
EM volume selectionDetails: Points along the helical axis were manually placed to define a spline. A cylindrical grid as defined at a given radius from the spline; grid spacing was chosen to provide ~4x oversampling.
Number of tomograms: 63 / Number of volumes extracted: 488916 / Reference model: None
Atomic model buildingDetails: Crystal structure was rigid-body fitted into density using Chimera. Missing regions of the structure was built using ideal secondary structures in coot. These were then flexibly fit using MDFF and NAMD.
Ref protocol: FLEXIBLE FIT

+
About Yorodumi

-
News

-
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.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
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)

Read more

-
Yorodumi

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

Read more