7W82 | pdb_00007w82

Crystal structure of maize RDR2

• PDB DOI: https://doi.org/10.2210/pdb7W82/pdb

• Classification: PLANT PROTEIN
• Organism(s): Zea mays
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2021-12-07 Released: 2022-06-08 
• Deposition Author(s): Du, X., Yang, Z., Du, J.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.270 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Structure of plant RNA-DEPENDENT RNA POLYMERASE 2, an enzyme involved in small interfering RNA production.

Du, X., Yang, Z., Ariza, A.J.F., Wang, Q., Xie, G., Li, S., Du, J.

(2022) Plant Cell 34: 2140-2149

• PubMed: 35188193 
• DOI: https://doi.org/10.1093/plcell/koac067
• Primary Citation Related Structures: 
  7W82, 7W84, 7W88


• PubMed 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 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.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen 518060, China.
Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, China.
California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA.
Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.
Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China.
Biophysics Graduate Group, University of California, Berkeley, California 94720, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 115.39 kDa 
• Atom Count: 7,492 
• Modeled Residue Count: 944 
• Deposited Residue Count: 1,024 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-dependent RNA polymerase	A	1,024	Zea mays	Mutation(s): 5  Gene Names: mop1, 100502460, ZEAMMB73_Zm00001d003378 EC: 2.7.7.48
UniProt
Find proteins for Q19VG2 (Zea mays) Explore Q19VG2  Go to UniProtKB:  Q19VG2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.270 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.036	α = 90
b = 149.036	β = 90
c = 345.473	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Du, X., Yang, Z., Du, J.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Structure summary