7K3K

Crystal structure of dLC8 in complex with Panoramix TQT peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex.

Schnabl, J.Wang, J.Hohmann, U.Gehre, M.Batki, J.Andreev, V.I.Purkhauser, K.Fasching, N.Duchek, P.Novatchkova, M.Mechtler, K.Plaschka, C.Patel, D.J.Brennecke, J.

(2021) Genes Dev 35: 392-409

  • DOI: https://doi.org/10.1101/gad.347989.120
  • Primary Citation of Related Structures:  
    7K3J, 7K3K, 7K3L

  • PubMed Abstract: 

    Nuclear Argonaute proteins, guided by their bound small RNAs to nascent target transcripts, mediate cotranscriptional silencing of transposons and repetitive genomic loci through heterochromatin formation. The molecular mechanisms involved in this process are incompletely understood. Here, we show that the SFiNX complex, a silencing mediator downstream from nuclear Piwi-piRNA complexes in Drosophila , facilitates cotranscriptional silencing as a homodimer. The dynein light chain protein Cut up/LC8 mediates SFiNX dimerization, and its function can be bypassed by a heterologous dimerization domain, arguing for a constitutive SFiNX dimer. Dimeric, but not monomeric SFiNX, is capable of forming molecular condensates in a nucleic acid-stimulated manner. Mutations that prevent SFiNX dimerization result in loss of condensate formation in vitro and the inability of Piwi to initiate heterochromatin formation and silence transposons in vivo. We propose that multivalent SFiNX-nucleic acid interactions are critical for heterochromatin establishment at piRNA target loci in a cotranscriptional manner.


  • Organizational Affiliation

    Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain 1, cytoplasmic89Drosophila melanogasterMutation(s): 0 
Gene Names: ctpCdlc1ddlc1CG6998
UniProt
Find proteins for Q24117 (Drosophila melanogaster)
Explore Q24117 
Go to UniProtKB:  Q24117
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ24117
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein panoramix14Drosophila melanogasterMutation(s): 0 
Gene Names: PanxCG9754
UniProt
Find proteins for Q9W2H9 (Drosophila melanogaster)
Explore Q9W2H9 
Go to UniProtKB:  Q9W2H9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9W2H9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.639α = 90
b = 45.639β = 90
c = 202.717γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM124165
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description