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Yorodumi- EMDB-32353: CryoEM structure of open form ZmRDR2 at 3.5 Angstroms resolution -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32353 | |||||||||
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Title | CryoEM structure of open form ZmRDR2 at 3.5 Angstroms resolution | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information transposable element silencing by siRNA-mediated heterochromatin formation / gene silencing by siRNA-directed DNA methylation / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / RNA binding Similarity search - Function | |||||||||
Biological species | Zea mays (maize) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Du X / Yang Z / Du J | |||||||||
Funding support | China, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32353.map.gz | 85.4 MB | EMDB map data format | |
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Header (meta data) | emd-32353-v30.xml emd-32353.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_32353.png | 50.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32353 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32353 | HTTPS FTP |
-Validation report
Summary document | emd_32353_validation.pdf.gz | 344.7 KB | Display | EMDB validaton report |
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Full document | emd_32353_full_validation.pdf.gz | 344.3 KB | Display | |
Data in XML | emd_32353_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_32353_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32353 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32353 | HTTPS FTP |
-Related structure data
Related structure data | 7w88MC 7w82C 7w84C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32353.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.74 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : RNA-dependent RNA polymerase 2 in open form
Entire | Name: RNA-dependent RNA polymerase 2 in open form |
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Components |
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-Supramolecule #1: RNA-dependent RNA polymerase 2 in open form
Supramolecule | Name: RNA-dependent RNA polymerase 2 in open form / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Zea mays (maize) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: RNA-dependent RNA polymerase
Macromolecule | Name: RNA-dependent RNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase |
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Source (natural) | Organism: Zea mays (maize) |
Molecular weight | Theoretical: 126.277297 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: AMGSMSTAAP APGSTATVRV SNIPASAIAA ELLAFFDSAV TIAGATFACE IVAAHRGWLS RGHGFVQFDS SAAATHAIDL ASSGRLPPF LGSCLSVSPA RADLLPRAPD LSLRAASASL ILGNRVAERE LEVAYSCDGV RAEVIPRMRR VDLYLKHDSQ S YKLEVLFE ...String: AMGSMSTAAP APGSTATVRV SNIPASAIAA ELLAFFDSAV TIAGATFACE IVAAHRGWLS RGHGFVQFDS SAAATHAIDL ASSGRLPPF LGSCLSVSPA RADLLPRAPD LSLRAASASL ILGNRVAERE LEVAYSCDGV RAEVIPRMRR VDLYLKHDSQ S YKLEVLFE DINECFGCHL DGTGAILLQL TYAPRIHIAI SGSTVKSRFT DDRFHACKED AKFAWVRALD FTPNSSFGEC ST LVLKLSK GASVSYILES LPFSGELGEL AIASMDVFGS SSNVVPLVDC PNGFSVPYEV LFRLNSLVHM GKLVARHVNA DLF KVLEDL SIDTLRRIFE KMSKLKSTCY EPLQFIRHEA HSMNMRKKAL SNKRESGKLM RCYRIHITPS KIYCLGPEEE VSNY VVKYH SEYASDFARV TFVDEDWSKL SPNALSARTE QGFFSKPLKT GLYHRILSIL KEGFCIGPKK YEFLAFSASQ LRGNS VWMF ASNSSLTAEN IRRWMGHFED IRSVSKCAAR MGQLFSSSRQ TFEVSSYDVE VIPDIEVTTD GTKYIFSDGI GKISTR FAR QVAKLIGLDP AHPPSAFQIR YGGYKGVITI DPTSFFNLSL RPSMKKFESK STMLNITNWS KSQPCYVNRE IISLLST LG IKDEVFESMQ QDDMHESDGM LTNKEAALSV LGKIGGGDTK TAADMLLQGY EPSSEPYLLM ILKAHRANRL TDIRTRCK I HVQKGRVLIG CLDETCKLEY GQVYIRITKN HKEQKYSEQP FFCNDDGKTA VIVGKVAITK NPCLHPGDVR VLEAVYDPG LDARGLIDCV VFPQRGERPH PNECSGGDLD GDLFFITWDD KLIPEKVDAP MDYTATRPRI MDHAVTLEEI QKHFVSYMIN DTLGAISTA HLIHADRDPL KARSPECVQL AALHSMAVDF AKTGAPAEMP LALRPREFPD FMERWERPMY VSNGVLGKLY R AALRHAAD AAALLPAGPP SCVYDPDLEV AGFDEFLDAA EERYEAYAER LGALMTYYSA EREDEILTGN IRNKLVYLRR DN KRYFEMK DRIIAAVDAL HAEVRGWLRA CKEDDASRVA SAWYHVTYHP DRRGEKRFWS FPWIICDTLL AIKAARRCRK RVE DAAVPM DCDGS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 177075 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-7w88: |