7MKK | pdb_00007mkk

Crystal structure of Drosophila Panoramix in complex with Sov NTD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.260 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7MKK

This is version 1.2 of the entry. See complete history

Literature

Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery.

Andreev, V.I.Yu, C.Wang, J.Schnabl, J.Tirian, L.Gehre, M.Handler, D.Duchek, P.Novatchkova, M.Baumgartner, L.Meixner, K.Sienski, G.Patel, D.J.Brennecke, J.

(2022) Nat Struct Mol Biol 29: 130-142

  • DOI: https://doi.org/10.1038/s41594-022-00721-x
  • Primary Citation Related Structures: 
    7MKK

  • PubMed Abstract: 

    Nuclear Argonaute proteins, guided by small RNAs, mediate sequence-specific heterochromatin formation. The molecular principles that link Argonaute-small RNA complexes to cellular heterochromatin effectors on binding to nascent target RNAs are poorly understood. Here, we explain the mechanism by which the PIWI-interacting RNA (piRNA) pathway connects to the heterochromatin machinery in Drosophila. We find that Panoramix, a corepressor required for piRNA-guided heterochromatin formation, is SUMOylated on chromatin in a Piwi-dependent manner. SUMOylation, together with an amphipathic LxxLL motif in Panoramix's intrinsically disordered repressor domain, are necessary and sufficient to recruit Small ovary (Sov), a multi-zinc-finger protein essential for general heterochromatin formation and viability. Structure-guided mutations that eliminate the Panoramix-Sov interaction or that prevent SUMOylation of Panoramix uncouple Sov from the piRNA pathway, resulting in viable but sterile flies in which Piwi-targeted transposons are derepressed. Thus, Piwi engages the heterochromatin machinery specifically at transposon loci by coupling recruitment of a corepressor to nascent transcripts with its SUMOylation.


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

Macromolecule Content 

  • Total Structure Weight: 49.41 kDa 
  • Atom Count: 3,072 
  • Modeled Residue Count: 370 
  • Deposited Residue Count: 424 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ovary, isoform AA [auth B],
C [auth A],
E,
G
78Drosophila melanogasterMutation(s): 0 
Gene Names: sovDmel\CG14438EM25fs(1)M105l(1)6Dcl(1)EA42l(1)EM25CG14438Dmel_CG14438
UniProt
Find proteins for Q9W3W6 (Drosophila melanogaster)
Explore Q9W3W6 
Go to UniProtKB:  Q9W3W6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9W3W6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein panoramixB [auth C],
D,
F,
H
28Drosophila 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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.260 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.389α = 90
b = 127.389β = 90
c = 96.012γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata 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: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-03-02
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection