5XWR

Crystal Structure of RBBP4-peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Targeting cancer addiction for SALL4 by shifting its transcriptome with a pharmacologic peptide.

Liu, B.H.Jobichen, C.Chia, C.S.B.Chan, T.H.M.Tang, J.P.Chung, T.X.Y.Li, J.Poulsen, A.Hung, A.W.Koh-Stenta, X.Tan, Y.S.Verma, C.S.Tan, H.K.Wu, C.S.Li, F.Hill, J.Joy, J.Yang, H.Chai, L.Sivaraman, J.Tenen, D.G.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E7119-E7128

  • DOI: 10.1073/pnas.1801253115

  • PubMed Abstract: 
  • Sal-like 4 (SALL4) is a nuclear factor central to the maintenance of stem cell pluripotency and is a key component in hepatocellular carcinoma, a malignancy with no effective treatment. In cancer cells, SALL4 associates with nucleosome remodeling dea ...

    Sal-like 4 (SALL4) is a nuclear factor central to the maintenance of stem cell pluripotency and is a key component in hepatocellular carcinoma, a malignancy with no effective treatment. In cancer cells, SALL4 associates with nucleosome remodeling deacetylase (NuRD) to silence tumor-suppressor genes, such as PTEN. Here, we determined the crystal structure of an amino-terminal peptide of SALL4(1-12) complexed to RBBp4, the chaperone subunit of NuRD, at 2.7 Å, and subsequent design of a potent therapeutic SALL4 peptide (FFW) capable of antagonizing the SALL4-NURD interaction using systematic truncation and amino acid substitution studies. FFW peptide disruption of the SALL4-NuRD complex resulted in unidirectional up-regulation of transcripts, turning SALL4 from a dual transcription repressor-activator mode to singular transcription activator mode. We demonstrate that FFW has a target affinity of 23 nM, and displays significant antitumor effects, inhibiting tumor growth by 85% in xenograft mouse models. Using transcriptome and survival analysis, we discovered that the peptide inhibits the transcription-repressor function of SALL4 and causes massive up-regulation of transcripts that are beneficial to patient survival. This study supports the SALL4-NuRD complex as a drug target and FFW as a viable drug candidate, showcasing an effective strategy to accurately target oncogenes previously considered undruggable.


    Organizational Affiliation

    Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-binding protein RBBP4
A, B
443Homo 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
MET-SER-ARG-ARG-LYS-GLN-ALA-LYS-PRO-GLN-HIS-ILE
C, D
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.840α = 90.00
b = 59.860β = 93.70
c = 101.529γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-18
    Type: Data collection, Database references
  • Version 1.2: 2018-08-08
    Type: Data collection, Database references