The C-terminal RRM domain of Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 (E329A/E330A/E332A)

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Structural and biochemical insights into small RNA 3' end trimming by Arabidopsis SDN1.

Chen, J.Liu, L.You, C.Gu, J.Ruan, W.Zhang, L.Gan, J.Cao, C.Huang, Y.Chen, X.Ma, J.

(2018) Nat Commun 9: 3585-3585

  • DOI: https://doi.org/10.1038/s41467-018-05942-7
  • Primary Citation of Related Structures:  
    5Z9X, 5Z9Z

  • PubMed Abstract: 

    A family of DEDDh 3'→5' exonucleases known as Small RNA Degrading Nucleases (SDNs) initiates the turnover of ARGONAUTE1 (AGO1)-bound microRNAs in Arabidopsis by trimming their 3' ends. Here, we report the crystal structure of Arabidopsis SDN1 (residues 2-300) in complex with a 9 nucleotide single-stranded RNA substrate, revealing that the DEDDh domain forms rigid interactions with the N-terminal domain and binds 4 nucleotides from the 3' end of the RNA via its catalytic pocket. Structural and biochemical results suggest that the SDN1 C-terminal domain adopts an RNA Recognition Motif (RRM) fold and is critical for substrate binding and enzymatic processivity of SDN1. In addition, SDN1 interacts with the AGO1 PAZ domain in an RNA-independent manner in vitro, enabling it to act on AGO1-bound microRNAs. These extensive structural and biochemical studies may shed light on a common 3' end trimming mechanism for 3'→5' exonucleases in the metabolism of small non-coding RNAs.

  • Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Small RNA degrading nuclease 1103Arabidopsis thalianaMutation(s): 3 
Gene Names: SDN1At3g50100F3A4.180
EC: 3.1
Find proteins for A3KPE8 (Arabidopsis thaliana)
Explore A3KPE8 
Go to UniProtKB:  A3KPE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3KPE8
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.132α = 90
b = 65.62β = 90
c = 74.73γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChinaNSFC 31230041

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references