6BW3

Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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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:  
    6BW3, 6BW4

  • 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, lacking the N-terminus containing the PR-SET domain (ΔPR) ...

    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, University of Toronto, Toronto, ON, M5G 1L7, Canada.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-binding protein RBBP4C [auth A],
A [auth C]
427Homo sapiensMutation(s): 0 
Gene Names: RBBP4RBAP48
UniProt & NIH Common Fund Data Resources
Find proteins for Q09028 (Homo sapiens)
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Go to UniProtKB:  Q09028
PHAROS:  Q09028
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UniProt GroupQ09028
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MDS1 and EVI1 complex locus protein MDS1B, D12Homo sapiensMutation(s): 0 
Gene Names: MECOMEVI1MDS1PRDM3
EC: 2.1.1.367
UniProt & NIH Common Fund Data Resources
Find proteins for Q03112 (Homo sapiens)
Explore Q03112 
Go to UniProtKB:  Q03112
PHAROS:  Q03112
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03112
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.979α = 90
b = 59.822β = 94.55
c = 101.773γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

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