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Yorodumi- PDB-3ja5: Genome and RdRp structure within the capsid of no-transcribing cy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ja5 | ||||||
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Title | Genome and RdRp structure within the capsid of no-transcribing cypovirus | ||||||
Components | RNA-dependent RNA polymerase | ||||||
Keywords | TRANSFERASE / non-transcribing cypovirus / RNA-dependent RNA polymerase / dsRNA virus / icosahedral virus | ||||||
Function / homology | RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / viral genome replication / RNA-dependent RNA polymerase activity / RNA binding / RNA-dependent RNA polymerase Function and homology information | ||||||
Biological species | Bombyx mori cypovirus 1 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å | ||||||
Authors | Liu, H. / Cheng, L. | ||||||
Citation | Journal: Science / Year: 2015 Title: Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus. Authors: Hongrong Liu / Lingpeng Cheng / Abstract: Double-stranded RNA (dsRNA) viruses possess a segmented dsRNA genome and a number of RNA-dependent RNA polymerases (RdRps) enclosed in a capsid. Until now, the precise structures of genomes and RdRps ...Double-stranded RNA (dsRNA) viruses possess a segmented dsRNA genome and a number of RNA-dependent RNA polymerases (RdRps) enclosed in a capsid. Until now, the precise structures of genomes and RdRps within the capsids have been unknown. Here we report the structures of RdRps and associated RNAs within nontranscribing and transcribing cypoviruses (NCPV and TCPV, respectively), using a combination of cryo-electron microscopy (cryo-EM) and a symmetry-mismatch reconstruction method. The RdRps and associated RNAs appear to exhibit a pseudo-D3 symmetric organization in both NCPV and TCPV. However, the molecular interactions between RdRps and the genomic RNA were found to differ in these states. Our work provides insight into the mechanisms of the replication and transcription in dsRNA viruses and paves a way for structural determination of lower-symmetry complexes enclosed in higher-symmetry structures. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3ja5.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ja5.ent.gz | 24.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ja5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ja5_validation.pdf.gz | 675.7 KB | Display | wwPDB validaton report |
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Full document | 3ja5_full_validation.pdf.gz | 675.3 KB | Display | |
Data in XML | 3ja5_validation.xml.gz | 20 KB | Display | |
Data in CIF | 3ja5_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/3ja5 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/3ja5 | HTTPS FTP |
-Related structure data
Related structure data | 6322MC 6321C 3ja4C 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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Symmetry | Point symmetry: (Schoenflies symbol: D3 (2x3 fold dihedral)) |
-Components
#1: Protein | Mass: 138830.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q6RJR5 |
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-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: Bombyx mori cypovirus 1 / Type: VIRUS |
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Details of virus | Empty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Homo sapiens |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Apr 10, 2010 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 125390 X / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN HELIUM / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
-Processing
EM software | Name: MRC / Category: 3D reconstruction / Details: Symmetry-Mismatch-Reconstruction | ||||||||||||
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CTF correction | Details: Each particle | ||||||||||||
Symmetry | Point symmetry: D3 (2x3 fold dihedral) | ||||||||||||
3D reconstruction | Method: cross-correlation coefficient / Resolution: 12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28000 Details: (Single particle details: Symmetry-mismatch reconstruction of icosahedral with D3 symmetry imposed) (Single particle--Applied symmetry: D3) Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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