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 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1073/pnas.1801253115
  • Primary Citation of Related Structures:  
    5XWR

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-binding protein RBBP4
A, B
443Homo sapiensMutation(s): 0 
Gene Names: RBBP4RBAP48
UniProt & NIH Common Fund Data Resources
Find proteins for Q09028 (Homo sapiens)
Explore Q09028 
Go to UniProtKB:  Q09028
GTEx:  ENSG00000162521 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09028
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MET-SER-ARG-ARG-LYS-GLN-ALA-LYS-PRO-GLN-HIS-ILE
C, D
12Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJQ4 (Homo sapiens)
Explore Q9UJQ4 
Go to UniProtKB:  Q9UJQ4
GTEx:  ENSG00000101115 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJQ4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.84α = 90
b = 59.86β = 93.7
c = 101.529γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description