3IXS

Ring1B C-terminal domain/RYBP C-terminal domain Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Polycomb Group Targeting through Different Binding Partners of RING1B C-Terminal Domain.

Wang, R.Taylor, A.B.Leal, B.Z.Chadwell, L.V.Ilangovan, U.Robinson, A.K.Schirf, V.Hart, P.J.Lafer, E.M.Demeler, B.Hinck, A.P.McEwen, D.G.Kim, C.A.

(2010) Structure 18: 966-975

  • DOI: https://doi.org/10.1016/j.str.2010.04.013
  • Primary Citation of Related Structures:  
    3GS2, 3IXS

  • PubMed Abstract: 

    RING1B, a Polycomb Group (PcG) protein, binds methylated chromatin through its association with another PcG protein called Polycomb (Pc). However, RING1B can associate with nonmethylated chromatin suggesting an alternate mechanism for RING1B interaction with chromatin. Here, we demonstrate that two proteins with little sequence identity between them, the Pc cbox domain and RYBP, bind the same surface on the C-terminal domain of RING1B (C-RING1B). Pc cbox and RYBP each fold into a nearly identical, intermolecular beta sheet with C-RING1B and a loop structure which are completely different in the two proteins. Both the beta sheet and loop are required for stable binding and transcription repression. Further, a mutation engineered to disrupt binding on the Drosophila dRING1 protein prevents chromatin association and PcG function in vivo. These results suggest that PcG targeting to different chromatin locations relies, in part, on binding partners of C-RING1B that are diverse in sequence and structure.


  • Organizational Affiliation

    Department of Biochemistry, University of Texas Health Science Center at San Antonio, MSC 7760, 7703 Floyd Curl Drive, San Antonio, TX 78229-3990, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RING2
A, C, E, G, I
A, C, E, G, I, K
111Homo sapiensMutation(s): 1 
Gene Names: BAP1DINGHIPI3RING1BRNF2
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99496 (Homo sapiens)
Explore Q99496 
Go to UniProtKB:  Q99496
PHAROS:  Q99496
GTEx:  ENSG00000121481 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99496
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RING1 and YY1-binding protein
B, D, F, H, J
B, D, F, H, J, L
37Homo sapiensMutation(s): 0 
Gene Names: DEDAFRYBPYEAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N488 (Homo sapiens)
Explore Q8N488 
Go to UniProtKB:  Q8N488
PHAROS:  Q8N488
GTEx:  ENSG00000163602 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N488
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.894α = 100.88
b = 56.549β = 90.61
c = 100.352γ = 100.49
Software Package:
Software NamePurpose
SHARPphasing
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-02-21
    Changes: Data collection