+Open data
-Basic information
Entry | Database: PDB / ID: 7w88 | ||||||
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Title | CryoEM structure of open form ZmRDR2 at 3.5 Angstroms resolution | ||||||
Components | RNA-dependent RNA polymerase | ||||||
Keywords | PLANT PROTEIN / RDR2 / RdDM / RNA polymerase | ||||||
Function / homology | Function and homology information gene silencing by siRNA-directed DNA methylation / siRNA-mediated retrotransposon silencing by heterochromatin formation / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / RNA binding Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Du, X. / Yang, Z. / Du, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Plant Cell / Year: 2022 Title: Structure of plant RNA-DEPENDENT RNA POLYMERASE 2, an enzyme involved in small interfering RNA production. Authors: Xuan Du / Zhenlin Yang / Alfredo Jose Florez Ariza / Qian Wang / Guohui Xie / Sisi Li / Jiamu Du / Abstract: In plants, the biogenesis of small interfering RNA (siRNA) requires a family of RNA-dependent RNA polymerases that convert single-stranded RNA (ssRNA) into double-stranded RNA (dsRNA), which is ...In plants, the biogenesis of small interfering RNA (siRNA) requires a family of RNA-dependent RNA polymerases that convert single-stranded RNA (ssRNA) into double-stranded RNA (dsRNA), which is subsequently cleaved into defined lengths by Dicer endonucleases. Here, we determined the structure of maize (Zea mays) RNA-DEPENDENT RNA POLYMERASE 2 (ZmRDR2) in the closed and open conformations. The core catalytic region of ZmRDR2 possesses the canonical DNA-dependent RNA polymerase (DdRP) catalytic sites, pointing to a shared RNA production mechanism between DdRPs and plant RDR-family proteins. Apo-ZmRDR2 adopts a highly compact structure, representing an inactive closed conformation. By contrast, adding RNA induced a significant conformational change in the ZmRDR2 Head domain that opened the RNA binding tunnel, suggesting this is an active elongation conformation of ZmRDR2. Overall, our structural studies trapped both the active and inactive conformations of ZmRDR2, providing insights into the molecular mechanism of dsRNA synthesis during plant siRNA production. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w88.cif.gz | 170.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w88.ent.gz | 135.1 KB | Display | PDB format |
PDBx/mmJSON format | 7w88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w88_validation.pdf.gz | 699.4 KB | Display | wwPDB validaton report |
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Full document | 7w88_full_validation.pdf.gz | 719.6 KB | Display | |
Data in XML | 7w88_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 7w88_validation.cif.gz | 46.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/7w88 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/7w88 | HTTPS FTP |
-Related structure data
Related structure data | 32353MC 7w82C 7w84C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 126277.297 Da / Num. of mol.: 1 / Mutation: E966A,E967A,E970A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: mop1, 100502460, ZEAMMB73_Zm00001d003378 / Plasmid: pFastHTB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q19VG2, RNA-directed RNA polymerase |
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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: RNA-dependent RNA polymerase 2 in open form / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Zea mays (maize) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 177075 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
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