3IXS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.str.2010.04.013
  • Primary Citation of Related Structures:  

  • 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 interact ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RING2
A, C, E, G, I, K
111Homo sapiensMutation(s): 1 
Gene Names: RNF2 (BAP1, DING, HIPI3, RING1B)
EC: 2.3.2.27
Find proteins for Q99496 (Homo sapiens)
Go to Gene View: RNF2
Go to UniProtKB:  Q99496
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RING1 and YY1-binding protein
B, D, F, H, J, L
37Homo sapiensMutation(s): 0 
Gene Names: RYBP (DEDAF, YEAF1)
Find proteins for Q8N488 (Homo sapiens)
Go to Gene View: RYBP
Go to UniProtKB:  Q8N488
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHE
Query on NHE

Download SDF File 
Download CCD File 
C
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
N-CYCLOHEXYLTAURINE; CHES
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C, E, H
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • 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
d*TREKdata reduction
SHARPphasing
PHENIXrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance