3SL9

X-ray structure of Beta catenin in complex with Bcl9

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

An intrinsically labile alpha-helix abutting the BCL9-binding site of beta-catenin is required for its inhibition by carnosic acid.

de la Roche, M., Rutherford, T.J., Gupta, D., Veprintsev, D.B., Saxty, B., Freund, S.M., Bienz, M.

(2012) Nat Commun 3: 680-680

  • DOI: 10.1038/ncomms1680
  • Primary Citation of Related Structures:  
    3SL9, 3SLA

  • PubMed Abstract: 

    • Wnt/β-catenin signalling controls development and tissue homeostasis. Moreover, activated β-catenin can be oncogenic and, notably, drives colorectal cancer. Inhibiting oncogenic β-catenin has proven a formidable challenge. Here we design a screen for small-molecule inhibitors of β-catenin's binding to its cofactor BCL9, and discover five related natural compounds, including carnosic acid from rosemary, which attenuates transcriptional β-catenin outputs in colorectal cancer cells ...

    Wnt/β-catenin signalling controls development and tissue homeostasis. Moreover, activated β-catenin can be oncogenic and, notably, drives colorectal cancer. Inhibiting oncogenic β-catenin has proven a formidable challenge. Here we design a screen for small-molecule inhibitors of β-catenin's binding to its cofactor BCL9, and discover five related natural compounds, including carnosic acid from rosemary, which attenuates transcriptional β-catenin outputs in colorectal cancer cells. Evidence from NMR and analytical ultracentrifugation demonstrates that the carnosic acid response requires an intrinsically labile α-helix (H1) amino-terminally abutting the BCL9-binding site in β-catenin. Similarly, in colorectal cancer cells with hyperactive β-catenin signalling, carnosic acid targets predominantly the transcriptionally active ('oncogenic') form of β-catenin for proteasomal degradation in an H1-dependent manner. Hence, H1 is an 'Achilles' Heel' of β-catenin, which can be exploited for destabilization of oncogenic β-catenin by small molecules, providing proof-of-principle for a new strategy for developing direct inhibitors of oncogenic β-catenin.

    Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Catenin beta-1A,
C [auth B],
E,
G		167Homo sapiensMutation(s): 0 
Gene Names: Beta catenin, CTNNB, CTNNB1, OK/SW-cl.35, PRO2286
UniProt & NIH Common Fund Data Resources
Find proteins for P35222 (Homo sapiens)
Explore P35222 
Go to UniProtKB:  P35222
PHAROS:  P35222
GTEx:  ENSG00000168036 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35222
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
B-cell CLL/lymphoma 9 proteinB [auth C],
D,
F,
H		55Homo sapiensMutation(s): 0 
Gene Names: BCL9
UniProt & NIH Common Fund Data Resources
Find proteins for O00512 (Homo sapiens)
Explore O00512 
Go to UniProtKB:  O00512
PHAROS:  O00512
GTEx:  ENSG00000116128 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00512
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG
Download Ideal Coordinates CCD File 
DA [auth E],
K [auth A],
P [auth C],
V [auth B],
W [auth B]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
FA [auth F],
GA [auth G],
Q [auth B],
R [auth B],
Z [auth E]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
IMD
Query on IMD
Download Ideal Coordinates CCD File 
EA [auth E],
HA [auth G],
IA [auth G],
JA [auth G],
L [auth A],
EA [auth E],
HA [auth G],
IA [auth G],
JA [auth G],
L [auth A],
M [auth A],
X [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
CA [auth E],
I [auth A],
J [auth A],
AA [auth E],
BA [auth E],
CA [auth E],
I [auth A],
J [auth A],
N [auth A],
O [auth C],
S [auth B],
T [auth B],
U [auth B],
Y [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.89α = 90
b = 80.7β = 102
c = 87.94γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2011-06-24 
  • Released Date: 2012-02-29 
    • Deposition Author(s): Gupta, D., Bienz, M.

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Database references