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- EMDB-32351: CryoEM structure of apo form ZmRDR2 at 3.4 Angstroms resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-32351
TitleCryoEM structure of apo form ZmRDR2 at 3.4 Angstroms resolution
Map data
Sample
  • Organelle or cellular component: RNA-dependent RNA polymerase 2 in apo form
    • Protein or peptide: RNA-dependent RNA polymerase
Function / homology
Function and homology information


retrotransposon silencing by siRNA-directed DNA methylation / nuclear RNA-directed RNA polymerase complex / siRNA processing / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / RNA binding
Similarity search - Function
RNA-dependent RNA polymerase, eukaryotic-type / RNA dependent RNA polymerase / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA-dependent RNA polymerase
Similarity search - Component
Biological speciesZea mays (maize)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDu X / Yang Z / Du J
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: 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
DepositionDec 7, 2021-
Header (metadata) releaseJun 8, 2022-
Map releaseJun 8, 2022-
UpdateJun 8, 2022-
Current statusJun 8, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32351.png

Downloads & links

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Map

FileDownload / File: emd_32351.map.gz / Format: CCP4 / Size: 76.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.66 Å
Density
Contour LevelBy AUTHOR: 5.33
Minimum - Maximum0.0 - 13.403012
Average (Standard dev.)0.18389075 (±0.71170753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions272272272
Spacing272272272
CellA=B=C: 179.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : RNA-dependent RNA polymerase 2 in apo form

EntireName: RNA-dependent RNA polymerase 2 in apo form
Components
  • Organelle or cellular component: RNA-dependent RNA polymerase 2 in apo form
    • Protein or peptide: RNA-dependent RNA polymerase

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Supramolecule #1: RNA-dependent RNA polymerase 2 in apo form

SupramoleculeName: RNA-dependent RNA polymerase 2 in apo form / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Zea mays (maize)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: RNA-dependent RNA polymerase

MacromoleculeName: RNA-dependent RNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 126.277297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7w82

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 273512
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-7w84:
CryoEM structure of apo form ZmRDR2 at 3.4 Angstroms resolution

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