5Z9X

Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 in complex with an RNA substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1038/s41467-018-05942-7
  • Primary Citation of Related Structures:  

  • 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 (residu ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Small RNA degrading nuclease 1
A
409Arabidopsis thalianaMutation(s): 0 
Gene Names: SDN1
EC: 3.1.-.-
Find proteins for A3KPE8 (Arabidopsis thaliana)
Go to UniProtKB:  A3KPE8
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*GP*CP*CP*CP*AP*UP*UP*AP*G)-3')R10Arabidopsis thaliana
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, R
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.252 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.993α = 90.00
b = 87.993β = 90.00
c = 178.639γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Science Foundation of ChinaChinaNSFC 31230041

Revision History 

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