5J8Y | pdb_00005j8y

Crystal structure of the Scm-SAM and Sfmbt-SAM heterodimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.277 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.265 (DCC) 
  • R-Value Observed: 
    0.256 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Molecular basis of PRC1 targeting to Polycomb response elements by PhoRC.

Frey, F.Sheahan, T.Finkl, K.Stoehr, G.Mann, M.Benda, C.Muller, J.

(2016) Genes Dev 30: 1116-1127

  • DOI: https://doi.org/10.1101/gad.279141.116
  • Primary Citation Related Structures: 
    5J8Y

  • PubMed Abstract: 

    Polycomb group (PcG) protein complexes repress transcription by modifying target gene chromatin. In Drosophila, this repression requires association of PcG protein complexes with cis-regulatory Polycomb response elements (PREs), but the interactions permitting formation of these assemblies are poorly understood. We show that the Sfmbt subunit of the DNA-binding Pho-repressive complex (PhoRC) and the Scm subunit of the canonical Polycomb-repressive complex 1 (PRC1) directly bind each other through their SAM domains. The 1.9 Å crystal structure of the Scm-SAM:Sfmbt-SAM complex reveals the recognition mechanism and shows that Sfmbt-SAM lacks the polymerization capacity of the SAM domains of Scm and its PRC1 partner subunit, Ph. Functional analyses in Drosophila demonstrate that Sfmbt-SAM and Scm-SAM are essential for repression and that PhoRC DNA binding is critical to initiate PRC1 association with PREs. Together, this suggests that PRE-tethered Sfmbt-SAM nucleates PRC1 recruitment and that Scm-SAM/Ph-SAM-mediated polymerization then results in the formation of PRC1-compacted chromatin.


  • Organizational Affiliation
    • Laboratory of Chromatin Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;

Macromolecule Content 

  • Total Structure Weight: 38.08 kDa 
  • Atom Count: 2,495 
  • Modeled Residue Count: 295 
  • Deposited Residue Count: 338 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polycomb protein Scm
A, B
80Drosophila melanogasterMutation(s): 0 
Gene Names: ScmCG9495
UniProt
Find proteins for Q9VHA0 (Drosophila melanogaster)
Explore Q9VHA0 
Go to UniProtKB:  Q9VHA0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VHA0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Polycomb protein Sfmbt
C, D
89Drosophila melanogasterMutation(s): 0 
Gene Names: SfmbtCG16975
UniProt
Find proteins for Q9VK33 (Drosophila melanogaster)
Explore Q9VK33 
Go to UniProtKB:  Q9VK33
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VK33
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.277 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.265 (DCC) 
  • R-Value Observed: 0.256 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.956α = 90
b = 53.97β = 109.22
c = 61.455γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB1064
European UnionGermany277899

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Author supporting evidence, Data collection, Database references, Refinement description