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- PDB-6ehm: Model of the Ebola virus nucleocapsid subunit from recombinant vi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ehm | ||||||||||||
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Title | Model of the Ebola virus nucleocapsid subunit from recombinant virus-like particles | ||||||||||||
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![]() | VIRUS LIKE PARTICLE / nucleocapsid / virus-like particle | ||||||||||||
Function / homology | ![]() suppression by virus of host intracellular interferon activity / host cell endomembrane system / viral RNA genome packaging / helical viral capsid / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral budding from plasma membrane / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex ...suppression by virus of host intracellular interferon activity / host cell endomembrane system / viral RNA genome packaging / helical viral capsid / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral budding from plasma membrane / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.3 Å | ||||||||||||
![]() | Wan, W. / Kolesnikova, L. / Clarke, M. / Koehler, A. / Noda, T. / Becker, S. / Briggs, J.A.G. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and assembly of the Ebola virus nucleocapsid. Authors: William Wan / Larissa Kolesnikova / Mairi Clarke / Alexander Koehler / Takeshi Noda / Stephan Becker / John A G Briggs / ![]() ![]() ![]() Abstract: Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles ...Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles virus, and respiratory syncytial virus. Mononegaviruses have non-segmented, single-stranded negative-sense RNA genomes that are encapsidated by nucleoprotein and other viral proteins to form a helical nucleocapsid. The nucleocapsid acts as a scaffold for virus assembly and as a template for genome transcription and replication. Insights into nucleoprotein-nucleoprotein interactions have been derived from structural studies of oligomerized, RNA-encapsidating nucleoprotein, and cryo-electron microscopy of nucleocapsid or nucleocapsid-like structures. There have been no high-resolution reconstructions of complete mononegavirus nucleocapsids. Here we apply cryo-electron tomography and subtomogram averaging to determine the structure of Ebola virus nucleocapsid within intact viruses and recombinant nucleocapsid-like assemblies. These structures reveal the identity and arrangement of the nucleocapsid components, and suggest that the formation of an extended α-helix from the disordered carboxy-terminal region of nucleoprotein-core links nucleoprotein oligomerization, nucleocapsid condensation, RNA encapsidation, and accessory protein recruitment. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.2 KB | Display | ![]() |
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PDB format | ![]() | 31.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 839 KB | Display | ![]() |
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Full document | ![]() | 838.5 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3871MC ![]() 3869C ![]() 3870C ![]() 3872C ![]() 3873C ![]() 3874C ![]() 3875C ![]() 3876C ![]() 6ehlC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 83387.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 28250.811 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: subtomogram averaging |
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Sample preparation
Component | Name: Ebola virus - Mayinga, Zaire, 1976 / Type: VIRUS Details: Recombinantly expressed virus-like particles produced by expression of nucleoprotein, VP24, VP35, VP40. Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||
Virus shell | Name: Nucleocapsid / Diameter: 280 nm | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat 2/1 3C | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.3 sec. / Electron dose: 3.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter upper: 10 eV / Energyfilter lower: -10 eV |
Image scans | Width: 3708 / Height: 3708 / Movie frames/image: 5 / Used frames/image: 1-5 |
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Processing
EM software |
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Image processing | 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. ...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. | |||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: CTF amplitude correction was performed during the wedge-weighted subtomogram averaging step. Type: PHASE FLIPPING ONLY | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1 / Algorithm: BACK PROJECTION Details: Local resolution was estimated using moving window FSC calculations. Resolution varies from 7.3 to 15.2 Angstroms. Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
EM volume selection | Details: 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. Num. of tomograms: 63 / Num. of volumes extracted: 379428 / Reference model: None | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT Details: Nucleoprotein model from Ebola virus nucleoprotein 1-450 was first rigid body fitted into the inner nucleoprotein densities. Densities were then subtracted, and VP24 pdb was then fit into ...Details: Nucleoprotein model from Ebola virus nucleoprotein 1-450 was first rigid body fitted into the inner nucleoprotein densities. Densities were then subtracted, and VP24 pdb was then fit into remaining densities. All models were rigid-body fitted using UCSF Chimera. |