[English] 日本語
Yorodumi- PDB-7xr2: 3.1 Angstrom cryoEM icosahedral reconstruction of mud crab reovirus -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xr2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 3.1 Angstrom cryoEM icosahedral reconstruction of mud crab reovirus | |||||||||
Components |
| |||||||||
Keywords | VIRUS / Reovirus / ds-RNA virus | |||||||||
Function / homology | VP3 / VP11 / VP12 Function and homology information | |||||||||
Biological species | Scylla serrata reovirus SZ-2007 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Zhang, Q. / Gao, Y. | |||||||||
Funding support | China, 2items
| |||||||||
Citation | Journal: PLoS Pathog / Year: 2023 Title: The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization. Authors: Qinfen Zhang / Yuanzhu Gao / Matthew L Baker / Shanshan Liu / Xudong Jia / Haidong Xu / Jianguo He / Jason T Kaelber / Shaoping Weng / Wen Jiang / Abstract: Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell ...Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell and carry out genome replication and transcription inside the virion. Several cryo-electron microscopy (cryo-EM) structures of reoviruses with 9, 10 or 11 segmented dsRNA genomes have revealed insights into genome arrangement and transcription. However, the structure and genome arrangement of 12-segmented Reovirales members remain poorly understood. Using cryo-EM, we determined the structure of mud crab reovirus (MCRV), a 12-segmented dsRNA virus that is a putative member of Reovirales in the non-turreted Sedoreoviridae family, to near-atomic resolutions with icosahedral symmetry (3.1 Å) and without imposing icosahedral symmetry (3.4 Å). These structures revealed the organization of the major capsid proteins in two layers: an outer T = 13 layer consisting of VP12 trimers and unique VP11 clamps, and an inner T = 1 layer consisting of VP3 dimers. Additionally, ten RNA dependent RNA polymerases (RdRp) were well resolved just below the VP3 layer but were offset from the 5-fold axes and arranged with D5 symmetry, which has not previously been seen in other members of Reovirales. The N-termini of VP3 were shown to adopt four unique conformations; two of which anchor the RdRps, while the other two conformations are likely involved in genome organization and capsid stability. Taken together, these structures provide a new level of understanding for capsid stabilization and genome organization of segmented dsRNA viruses. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7xr2.cif.gz | 924.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7xr2.ent.gz | 783.2 KB | Display | PDB format |
PDBx/mmJSON format | 7xr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xr2_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7xr2_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7xr2_validation.xml.gz | 156.1 KB | Display | |
Data in CIF | 7xr2_validation.cif.gz | 237.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/7xr2 ftp://data.pdbj.org/pub/pdb/validation_reports/xr/7xr2 | HTTPS FTP |
-Related structure data
Related structure data | 33403MC 7xr3C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 97019.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Scylla serrata reovirus SZ-2007 / References: UniProt: E9LEU6 #2: Protein | Mass: 23750.701 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Scylla serrata reovirus SZ-2007 / References: UniProt: G9BDA7 #3: Protein | Mass: 29730.963 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Scylla serrata reovirus SZ-2007 / References: UniProt: G9BDA8 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Scylla serrata reovirus SZ-2007 / Type: VIRUS / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: Scylla serrata reovirus SZ-2007 |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Scylla serrata |
Buffer solution | pH: 7.4 |
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: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 / Nominal magnification: 75000 X / Calibrated magnification: 128440 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 600 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 80 K |
Image recording | Average exposure time: 1.1 sec. / Electron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3595 |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 1-16 |
-Processing
Software | Name: PHENIX / Version: 1.14rc1_3161: / Classification: refinement | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 58095 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58095 / Algorithm: FOURIER SPACE / Symmetry type: POINT |