3AX1

Molecular insights into miRNA processing by Arabidopsis Serrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular insights into miRNA processing by Arabidopsis thaliana SERRATE

Machida, S.Chen, H.Y.Yuan, Y.A.

(2011) Nucleic Acids Res. 39: 7828-7836

  • DOI: 10.1093/nar/gkr428

  • PubMed Abstract: 
  • In plant, primary transcripts (pri-miRNAs) transcribed from miRNA genes by RNA polymerase II are first processed into stem-loop pre-miRNAs and further chopped into ∼21 nt long miRNAs by RNase III-like enzyme DCL1. SERRATE (SE) protein is an essential ...

    In plant, primary transcripts (pri-miRNAs) transcribed from miRNA genes by RNA polymerase II are first processed into stem-loop pre-miRNAs and further chopped into ∼21 nt long miRNAs by RNase III-like enzyme DCL1. SERRATE (SE) protein is an essential component for miRNA processing by assisting DCL1 for accurate cleavage. Here we report the crystal structure of Arabidopsis SE core (residues 194-543) at 2.7 Å. SE core adopts the 'walking man-like' topology with N-terminal α helices, C-terminal non-canonical zinc-finger domain and novel Middle domain resembling the leading leg, the lagging leg and the body, respectively. Pull-down assay shows that SE core provides the platform for HYL1 and DCL1 binding, whereas in vitro RNA binding and in vivo mutant rescue experiments suggest that the non-canonical zinc-finger domain coupled with C-terminal tail binds miRNA precursors. SE presumably works as a scaffold-like protein capable of binding both protein and RNA to guide the positioning of miRNA precursor toward DCL1 catalytic site within miRNA processing machinery in plant.


    Organizational Affiliation

    Department of Biological Sciences, National University of Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serrate RNA effector molecule
A
358Arabidopsis thalianaGene Names: SE
Find proteins for Q9ZVD0 (Arabidopsis thaliana)
Go to UniProtKB:  Q9ZVD0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.965α = 90.00
b = 80.663β = 90.00
c = 112.670γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
SHARPphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-13
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references