3ADJ | pdb_00003adj

Structure of Arabidopsis HYL1 and its molecular implications for miRNA processing

• PDB DOI: https://doi.org/10.2210/pdb3ADJ/pdb

• Classification: GENE REGULATION
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-22 Released: 2010-05-26 
• Deposition Author(s): Yuan, Y.A., Chen, H.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.322 (Depositor), 0.311 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

Literature

Structure of arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing

Yang, S.W., Chen, H.Y., Yang, J., Machida, S., Chua, N.H., Yuan, Y.A.

(2010) Structure 18: 594-605

• PubMed: 20462493 
• DOI: https://doi.org/10.1016/j.str.2010.02.006
• Primary Citation Related Structures: 
  3ADG, 3ADI, 3ADJ, 3ADL


• PubMed Abstract: 
  

  The Arabidopsis HYPONASTIC LEAVES1 (HYL1) is a double-stranded RNA-binding protein that forms a complex with DICER-LIKE1 (DCL1) and SERRATE to facilitate processing of primary miRNAs into microRNAs (miRNAs). However, the structural mechanisms of miRNA maturation by this complex are poorly understood. Here, we present the crystal structures of double-stranded RNA binding domains (dsRBD1 and dsRBD2) of HYL1 and HYL1 dsRBD1 (HR1)/dsRNA complex as well as human TRBP2 dsRBD2 (TR2)/dsRNA complex for comparison analysis. Structural and functional study demonstrates that both HR1 and TR2 are canonical dsRBDs for dsRNA binding, whereas HR2 of HYL1 is a non-canonical dsRBD harboring a putative dimerization interface. Domain swapping within the context of HYL1 demonstrates that TR2 can supplant the function of HR1 in vitro and in vivo. Further biochemical analyses suggest that HYL1 probably binds to the miRNA/miRNA( *) region of precursors as a dimer mediated by HR2.

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Organizational Affiliation: 
• Host-Pathogen Interaction Group, Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 8.28 kDa 
• Atom Count: 552 
• Modeled Residue Count: 72 
• Deposited Residue Count: 76 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F21M12.9 protein	A	76	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for O04492 (Arabidopsis thaliana) Explore O04492  Go to UniProtKB:  O04492

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.322 (Depositor), 0.311 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.108	α = 90
b = 46.108	β = 90
c = 33.318	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-26 
Deposition Author(s): Yuan, Y.A., Chen, H.Y.

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description