3NTK

Crystal structure of Tudor

PDB DOI: https://doi.org/10.2210/pdb3NTK/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.238
R-Value Work: 0.210

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 20713507 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 38.4 kDa
Atom Count: 2,852
Modelled Residue Count: 335
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maternal protein tudor	A, B	169	Drosophila melanogaster	Mutation(s): 0 Gene Names: tud
UniProt
Find proteins for P25823 (Drosophila melanogaster) Explore P25823 Go to UniProtKB: P25823
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25823
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.238
R-Value Work: 0.210
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.145	α = 90
b = 47.262	β = 106.24
c = 85.404	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
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-09-15

Deposition Author(s):

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: 2023-12-27
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.