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Yorodumi- PDB-6jc3: The Cryo-EM structure of nucleoprotein-RNA complex of Newcastle d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jc3 | ||||||
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Title | The Cryo-EM structure of nucleoprotein-RNA complex of Newcastle disease virus | ||||||
Components |
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Keywords | NUCLEAR PROTEIN/RNA / self-capping helical structure complex / NUCLEAR PROTEIN / NUCLEAR PROTEIN-RNA complex | ||||||
Function / homology | Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / host cell cytoplasm / structural molecule activity / RNA binding / RNA / Nucleocapsid Function and homology information | ||||||
Biological species | Avian avulavirus 1 Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||
Authors | Song, X. / Shan, H. / Zhu, Y. / Ding, W. / Ouyang, S. / Shen, Q.T. / Liu, Z.J. | ||||||
Citation | Journal: Elife / Year: 2019 Title: Self-capping of nucleoprotein filaments protects the Newcastle disease virus genome. Authors: Xiyong Song / Hong Shan / Yanping Zhu / Shunlin Hu / Ling Xue / Yong Chen / Wei Ding / Tongxin Niu / Jian Gu / Songying Ouyang / Qing-Tao Shen / Zhi-Jie Liu / Abstract: Non-segmented negative-strand RNA viruses, such as measles, ebola and Newcastle disease viruses (NDV), encapsidate viral genomic RNAs into helical nucleocapsids, which serve as the template for viral ...Non-segmented negative-strand RNA viruses, such as measles, ebola and Newcastle disease viruses (NDV), encapsidate viral genomic RNAs into helical nucleocapsids, which serve as the template for viral replication and transcription. Here, the clam-shaped nucleocapsid structure, where the NDV viral genome is sequestered, was determined at 4.8 Å resolution by cryo-electron microscopy. The clam-shaped structure is composed of two single-turn spirals packed in a back-to-back mode. This tightly packed structure functions as a seed for the assembly of a nucleocapsid from both directions, facilitating the growth of double-headed filaments with two separate RNA strings inside. Disruption of this structure by mutations in its loop interface yielded a single-headed unfunctional filament. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6jc3.cif.gz | 173.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jc3.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 6jc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jc3_validation.pdf.gz | 992.6 KB | Display | wwPDB validaton report |
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Full document | 6jc3_full_validation.pdf.gz | 1008.4 KB | Display | |
Data in XML | 6jc3_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 6jc3_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/6jc3 ftp://data.pdbj.org/pub/pdb/validation_reports/jc/6jc3 | HTTPS FTP |
-Related structure data
Related structure data | 9793MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 43830.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Avian avulavirus 1 / Gene: NP, N / Production host: Escherichia coli (E. coli) / References: UniProt: D6R3F6 |
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#2: RNA chain | Mass: 1792.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ternary complex of nucleoprotein-RNA of Newcastle disease virus Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Newcastle disease virus |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: GLOW DISCHARGED |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 41 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75290 / Symmetry type: POINT |