3NTI

Crystal structure of Tudor and Aubergine [R15(me2s)] complex

• PDB DOI: https://doi.org/10.2210/pdb3NTI/pdb

• Classification: TRANSCRIPTION
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-05 Released: 2010-09-15 
• Deposition Author(s): Liu, H.P., Huang, Y., Li, Z.Z., Gong, W.M., Xu, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.276 
• R-Value Work: 0.239 

Starting Model: experimental

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

• PubMed: 20713507 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 21.04 kDa 
• Atom Count: 1,360 
• Modelled Residue Count: 170 
• Deposited Residue Count: 185 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maternal protein tudor	A	172	Drosophila melanogaster	Mutation(s): 0  Gene Names: tud
UniProt
Find proteins for P25823 (Drosophila melanogaster) Explore P25823  Go to UniProtKB:  P25823

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide from Aubergine	B [auth C]	13	Drosophila melanogaster	Mutation(s): 0  EC: 3.1.26
UniProt
Find proteins for O76922 (Drosophila melanogaster) Explore O76922  Go to UniProtKB:  O76922

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2MR	B [auth C]	L-PEPTIDE LINKING	C8 H18 N4 O2		ARG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.276 
• R-Value Work: 0.239 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.79	α = 90
b = 48.79	β = 90
c = 152.159	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Liu, H.P., Huang, Y., Li, Z.Z., Gong, W.M., Xu, R.M.

Revision History  

• 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