3NTH

Crystal structure of Tudor and Aubergine [R13(me2s)] complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.219 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for methylarginine-dependent recognition of Aubergine by Tudor

Liu, H.P.Wang, J.Y.Huang, Y.Li, Z.Z.Gong, W.M.Lehmann, R.Xu, R.M.

(2010) Genes Dev 24: 1876-1881

  • DOI: https://doi.org/10.1101/gad.1956010
  • Primary Citation of Related Structures:  
    3NTH, 3NTI, 3NTK

  • PubMed Abstract: 

    Piwi proteins are modified by symmetric dimethylation of arginine (sDMA), and the methylarginine-dependent interaction with Tudor domain proteins is critical for their functions in germline development. Cocrystal structures of an extended Tudor domain (eTud) of Drosophila Tudor with methylated peptides of Aubergine, a Piwi family protein, reveal that sDMA is recognized by an asparagine-gated aromatic cage. Furthermore, the unexpected Tudor-SN/p100 fold of eTud is important for sensing the position of sDMA. The structural information provides mechanistic insights into sDMA-dependent Piwi-Tudor interaction, and the recognition of sDMA by Tudor domains in general.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maternal protein tudor172Drosophila melanogasterMutation(s): 0 
Gene Names: tud
UniProt
Find proteins for P25823 (Drosophila melanogaster)
Explore P25823 
Go to UniProtKB:  P25823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25823
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide from AubergineB [auth C]6Drosophila melanogasterMutation(s): 0 
EC: 3.1.26
UniProt
Find proteins for O76922 (Drosophila melanogaster)
Explore O76922 
Go to UniProtKB:  O76922
Entity Groups  
UniProt GroupO76922
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR
B [auth C]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.219 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.012α = 90
b = 48.012β = 90
c = 152.044γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CCP4model building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary