[English] 日本語
Yorodumi- EMDB-3870: Cryo-electron tomogram of Ebola virus nucleoprotein, residues 1-450 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3870 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-electron tomogram of Ebola virus nucleoprotein, residues 1-450 | ||||||||||||
Map data | A 4x binned representative tomogram of recombinant nucleocapsid-like assemblies of Ebola virus nucleoprotein, residues 1-450. | ||||||||||||
Sample | Nucleocapsid != Ebola virus - Mayinga, Zaire, 1976 Nucleocapsid
| ||||||||||||
Biological species | Ebola virus - Mayinga, Zaire, 1976 | ||||||||||||
Method | electron tomography / cryo EM | ||||||||||||
Authors | Wan W / Kolesnikova L / Clarke M / Koehler A / Noda T / Becker S / Briggs JAG | ||||||||||||
Funding support | Germany, 3 items
| ||||||||||||
Citation | Journal: Nature / Year: 2017 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3870.map.gz | 34 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3870-v30.xml emd-3870.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_3870.png | 255.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3870 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3870 | HTTPS FTP |
-Validation report
Summary document | emd_3870_validation.pdf.gz | 188.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3870_full_validation.pdf.gz | 187.5 KB | Display | |
Data in XML | emd_3870_validation.xml.gz | 2.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3870 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3870 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_3870.map.gz / Format: CCP4 / Size: 204.9 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | A 4x binned representative tomogram of recombinant nucleocapsid-like assemblies of Ebola virus nucleoprotein, residues 1-450. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Nucleocapsid
Entire | Name: Nucleocapsid |
---|---|
Components |
|
-Supramolecule #1: Ebola virus - Mayinga, Zaire, 1976
Supramolecule | Name: Ebola virus - Mayinga, Zaire, 1976 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 128952 / Sci species name: Ebola virus - Mayinga, Zaire, 1976 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
---|---|
Host system | Organism: Homo sapiens (human) / Recombinant cell: HEK 293T |
Virus shell | Shell ID: 1 / Name: Nucleocapsid / Diameter: 280.0 Å |
-Macromolecule #1: Ebola virus nucleoprotein, residues 1-450
Macromolecule | Name: Ebola virus nucleoprotein, residues 1-450 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Ebola virus - Mayinga, Zaire, 1976 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDSRPQKIWM APSLTESDMD YHKILTAGLS VQQGIVRQRV IPVYQVNNLE EICQLIIQAF EAGVDFQESA DSFLLMLCLH HAYQGDYKLF LESGAVKYLE GHGFRFEVKK RDGVKRLEEL LPAVSSGKNI KRTLAAMPEE ETTEANAGQF LSFASLFLPK LVVGEKACLE ...String: MDSRPQKIWM APSLTESDMD YHKILTAGLS VQQGIVRQRV IPVYQVNNLE EICQLIIQAF EAGVDFQESA DSFLLMLCLH HAYQGDYKLF LESGAVKYLE GHGFRFEVKK RDGVKRLEEL LPAVSSGKNI KRTLAAMPEE ETTEANAGQF LSFASLFLPK LVVGEKACLE KVQRQIQVHA EQGLIQYPTA WQSVGHMMVI FRLMRTNFLI KFLLIHQGMH MVAGHDANDA VISNSVAQAR FSGLLIVKTV LDHILQKTER GVRLHPLART AKVKNEVNSF KAALSSLAKH GEYAPFARLL NLSGVNNLEH GLFPQLSAIA LGVATAHGST LAGVNVGEQY QQLREAATEA EKQLQQYAES RELDHLGLDD QEKKILMNFH QKKNEISFQQ TNAMVTLRKE RLAKLTEAIT AASLPKTSGH YDDDDDIPFP GPINDDDNPG HQDDDPTDSQ |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | electron tomography |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.4 Component:
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: C-flat 2/1 3C / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK II | |||||||||||||||
Sectioning | Other: NO SECTIONING | |||||||||||||||
Fiducial marker | Manufacturer: UMC Utrecht / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: -10 eV / Energy filter - Upper energy threshold: 10 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3708 pixel / Digitization - Dimensions - Height: 3708 pixel / Digitization - Frames/image: 1-5 / Average exposure time: 1.0 sec. / Average electron dose: 2.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-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. | ||||||
---|---|---|---|---|---|---|---|
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD / Software - details: weighted back projection / Number images used: 41 | ||||||
CTF correction | Software:
|