6BW4

Crystal structure of RBBP4 in complex with PRDM16 N-terminal peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex.

Ivanochko, D.Halabelian, L.Henderson, E.Savitsky, P.Jain, H.Marcon, E.Duan, S.Hutchinson, A.Seitova, A.Barsyte-Lovejoy, D.Filippakopoulos, P.Greenblatt, J.Lima-Fernandes, E.Arrowsmith, C.H.

(2019) Nucleic Acids Res. 47: 1225-1238

  • DOI: 10.1093/nar/gky1192
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aberrant isoform expression of chromatin-associated proteins can induce epigenetic programs related to disease. The MDS1 and EVI1 complex locus (MECOM) encodes PRDM3, a protein with an N-terminal PR-SET domain, as well as a shorter isoform, EVI1, lac ...

    Aberrant isoform expression of chromatin-associated proteins can induce epigenetic programs related to disease. The MDS1 and EVI1 complex locus (MECOM) encodes PRDM3, a protein with an N-terminal PR-SET domain, as well as a shorter isoform, EVI1, lacking the N-terminus containing the PR-SET domain (ΔPR). Imbalanced expression of MECOM isoforms is observed in multiple malignancies, implicating EVI1 as an oncogene, while PRDM3 has been suggested to function as a tumor suppressor through an unknown mechanism. To elucidate functional characteristics of these N-terminal residues, we compared the protein interactomes of the full-length and ΔPR isoforms of PRDM3 and its closely related paralog, PRDM16. Unlike the ΔPR isoforms, both full-length isoforms exhibited a significantly enriched association with components of the NuRD chromatin remodeling complex, especially RBBP4. Typically, RBBP4 facilitates chromatin association of the NuRD complex by binding to histone H3 tails. We show that RBBP4 binds to the N-terminal amino acid residues of PRDM3 and PRDM16, with a dissociation constant of 3.0 μM, as measured by isothermal titration calorimetry. Furthermore, high-resolution X-ray crystal structures of PRDM3 and PRDM16 N-terminal peptides in complex with RBBP4 revealed binding to RBBP4 within the conserved histone H3-binding groove. These data support a mechanism of isoform-specific interaction of PRDM3 and PRDM16 with the NuRD chromatin remodeling complex.


    Organizational Affiliation

    Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 2M9, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-binding protein RBBP4
C, A
427Homo sapiensMutation(s): 0 
Gene Names: RBBP4 (RBAP48)
Find proteins for Q09028 (Homo sapiens)
Go to Gene View: RBBP4
Go to UniProtKB:  Q09028
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PR domain zinc finger protein 16
B, D
12Homo sapiensMutation(s): 0 
Gene Names: PRDM16 (KIAA1675, MEL1, PFM13)
EC: 2.1.1.-
Find proteins for Q9HAZ2 (Homo sapiens)
Go to Gene View: PRDM16
Go to UniProtKB:  Q9HAZ2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 76.034α = 90.00
b = 59.862β = 94.55
c = 101.843γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2019-10-09
    Type: Data collection, Database references