3BDL

Crystal structure of a truncated human Tudor-SN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing.

Li, C.L., Yang, W.Z., Chen, Y.P., Yuan, H.S.

(2008) Nucleic Acids Res 36: 3579-3589

  • DOI: 10.1093/nar/gkn236
  • Primary Citation of Related Structures:  
    3BDL

  • PubMed Abstract: 

    • Human Tudor-SN is involved in the degradation of hyper-edited inosine-containing microRNA precursors, thus linking the pathways of RNA interference and editing. Tudor-SN contains four tandem repeats of staphylococcal nuclease-like domains (SN1-SN4) followed by a tudor and C-terminal SN domain (SN5) ...

    Human Tudor-SN is involved in the degradation of hyper-edited inosine-containing microRNA precursors, thus linking the pathways of RNA interference and editing. Tudor-SN contains four tandem repeats of staphylococcal nuclease-like domains (SN1-SN4) followed by a tudor and C-terminal SN domain (SN5). Here, we showed that Tudor-SN requires tandem repeats of SN domains for its RNA binding and cleavage activity. The crystal structure of a 64-kD truncated form of human Tudor-SN further shows that the four domains, SN3, SN4, tudor and SN5, assemble into a crescent-shaped structure. A concave basic surface formed jointly by SN3 and SN4 domains is likely involved in RNA binding, where citrate ions are bound at the putative RNase active sites. Additional modeling studies provide a structural basis for Tudor-SN's preference in cleaving RNA containing multiple I.U wobble-paired sequences. Collectively, these results suggest that tandem repeats of SN domains in Tudor-SN function as a clamp to capture RNA substrates.

    Organizational Affiliation: 

    Institute of Molecular Biology, Academia Sinica and Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Staphylococcal nuclease domain-containing protein 1A570Homo sapiensMutation(s): 0 
Gene Names: SND1, TDRD11
EC: 3.1.31.1
Find proteins for Q7KZF4 (Homo sapiens)
Explore Q7KZF4 
Go to UniProtKB:  Q7KZF4
NIH Common Fund Data Resources
PHAROS:  Q7KZF4
GTEx:  ENSG00000197157
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT
Download Ideal Coordinates CCD File 
 B [auth A], C [auth A], D [auth A], E [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.405α = 90
b = 91.929β = 91.26
c = 88.042γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2007-11-15 
  • Released Date: 2008-08-26 
    • Deposition Author(s): Li, C.L.

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance