8HIB | pdb_00008hib

The crystal structure of Pygo2-LDB1-SSBP2 triple complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.246 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of the interaction between BCL9-Pygo and LDB-SSBP complexes in assembling the Wnt enhanceosome.

Wang, H.Bienz, M.Yan, X.X.Xu, W.

(2023) Nat Commun 14: 3702-3702

  • DOI: https://doi.org/10.1038/s41467-023-39439-9
  • Primary Citation of Related Structures:  
    8HIB

  • PubMed Abstract: 

    The Wnt enhanceosome is responsible for transactivation of Wnt-responsive genes and a promising therapeutic target for treatment of numerous cancers with Adenomatous Polyposis Coli (APC) or β-catenin mutations. How the Wnt enhanceosome is assembled remains poorly understood. Here we show that B-cell lymphoma 9 protein (BCL9), Pygopus (Pygo), LIM domain-binding protein 1 (LDB1) and single-stranded DNA-binding protein (SSBP) form a stable core complex within the Wnt enhanceosome. Their mutual interactions rely on a highly conserved N-terminal asparagine proline phenylalanine (NPF) motif of Pygo, through which the BCL9-Pygo complex binds to the LDB-SSBP core complex. Our crystal structure of a ternary complex comprising the N-terminus of human Pygo2, LDB1 and SSBP2 reveals a single LDB1-SSBP2 complex binding simultaneously to two Pygo2 molecules via their NPF motifs. These interactions critically depend on the NPF motifs which bind to a deep groove formed between LDB1 and SSBP2, potentially constituting a binding site for drugs blocking Wnt/β-catenin signaling. Analysis of human cell lines lacking LDB or Pygo supports the functional relevance of the Pygo-LDB1-SSBP2 interaction for Wnt/β-catenin-dependent transcription.


  • Organizational Affiliation
    • School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LIM domain-binding protein 1A [auth V]230Homo sapiensMutation(s): 0 
Gene Names: LDB1CLIM2
UniProt & NIH Common Fund Data Resources
Find proteins for Q86U70 (Homo sapiens)
Explore Q86U70 
Go to UniProtKB:  Q86U70
PHAROS:  Q86U70
GTEx:  ENSG00000198728 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86U70
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Single-stranded DNA-binding protein 2B [auth A],
C [auth B]
94Homo sapiensMutation(s): 0 
Gene Names: SSBP2SSDP2
UniProt & NIH Common Fund Data Resources
Find proteins for P81877 (Homo sapiens)
Explore P81877 
Go to UniProtKB:  P81877
PHAROS:  P81877
GTEx:  ENSG00000145687 
Entity Groups  
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UniProt GroupP81877
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pygopus homolog 227Homo sapiensMutation(s): 0 
Gene Names: PYGO2PP7910
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRQ0 (Homo sapiens)
Explore Q9BRQ0 
Go to UniProtKB:  Q9BRQ0
PHAROS:  Q9BRQ0
GTEx:  ENSG00000163348 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BRQ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.499α = 90
b = 104.499β = 90
c = 252.274γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB37030302
Chinese Academy of SciencesChina2021kf01
National Natural Science Foundation of China (NSFC)China32000862
National Natural Science Foundation of China (NSFC)China32171218
Other governmentBX20200351

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2024-12-11
    Changes: Database references, Structure summary