5YGD

Crystal structure of Drosophila melanogaster Papi extended Tudor domain (D287A) in complex with Piwi N-terminal R10me2s peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the sequence-specific recognition of Piwi byDrosophilaPapi

Zhang, Y.Liu, W.Li, R.Gu, J.Wu, P.Peng, C.Ma, J.Wu, L.Yu, Y.Huang, Y.

(2018) Proc Natl Acad Sci U S A 115: 3374-3379

  • DOI: 10.1073/pnas.1717116115
  • Primary Citation of Related Structures:  
    5YGB, 5YGD, 5YGC, 5YGF

  • PubMed Abstract: 
  • The Tudor domain-containing (Tdrd) family proteins play a critical role in transposon silencing in animal gonads by recognizing the symmetrically dimethylated arginine (sDMA) on the (G/A)R motif of the N-terminal of PIWI family proteins via the eTud domains ...

    The Tudor domain-containing (Tdrd) family proteins play a critical role in transposon silencing in animal gonads by recognizing the symmetrically dimethylated arginine (sDMA) on the (G/A)R motif of the N-terminal of PIWI family proteins via the eTud domains. Papi, also known as "Tdrd2," is involved in Zucchini-mediated PIWI-interacting RNA (piRNA) 3'-end maturation. Intriguingly, a recent study showed that, in papi mutant flies, only Piwi-bound piRNAs increased in length, and not Ago3-bound or Aub-bound piRNAs. However, the molecular and structural basis of the Papi-Piwi complex is still not fully understood, which limits mechanistic understanding of the function of Papi in piRNA biogenesis. In the present study, we determined the crystal structures of Papi-eTud in the apo form and in complex with a peptide containing unmethylated or dimethylated R10 residues. Structural and biochemical analysis showed that the Papi interaction region on the Drosophila Piwi contains an RGRRR motif (R7-R11) distinct from the consensus (G/A)R motif recognized by canonical eTud. Mass spectrometry results indicated that Piwi is the major binding partner of Papi in vivo. The papi mutant flies suffered from both fertility and transposon-silencing defects, supporting the important role conferred to Papi in piRNA 3' processing through direct interaction with Piwi proteins.


    Organizational Affiliation

    Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GH18329pA223Drosophila melanogasterMutation(s): 1 
Gene Names: papiDmel\CG7082CG7082Dmel_CG7082Tdrd2
UniProt
Find proteins for Q9VQ91 (Drosophila melanogaster)
Explore Q9VQ91 
Go to UniProtKB:  Q9VQ91
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ASP-GLN-GLY-ARG-GLY-ARG-2MR-ARG-PRO-LEU-ASNB [auth D]11Drosophila melanogasterMutation(s): 0 
Gene Names: piwiCG6122
EC: 3.1.26
UniProt
Find proteins for Q9VKM1 (Drosophila melanogaster)
Explore Q9VKM1 
Go to UniProtKB:  Q9VKM1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2MR
Query on 2MR
B [auth D]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.472α = 90
b = 72.472β = 90
c = 50.311γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2017-09-22 
  • Released Date: 2018-03-14 
  • Deposition Author(s): Zhang, Y.H., Huang, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references