6CDY | pdb_00006cdy

Crystal structure of TEAD complexed with its inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6CDY/pdb

• Classification: transcription/transcription inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-09 Released: 2020-07-01 
• Deposition Author(s): LIU, S., HAN, X., LUO, X.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.255 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Lats1/2 Sustain Intestinal Stem Cells and Wnt Activation through TEAD-Dependent and Independent Transcription.

Li, Q., Sun, Y., Jarugumilli, G.K., Liu, S., Dang, K., Cotton, J.L., Xiol, J., Chan, P.Y., DeRan, M., Ma, L., Li, R., Zhu, L.J., Li, J.H., Leiter, A.B., Ip, Y.T., Camargo, F.D., Luo, X., Johnson, R.L., Wu, X., Mao, J.

(2020) Cell Stem Cell 26: 675-692.e8

• PubMed: 32259481 
• DOI: https://doi.org/10.1016/j.stem.2020.03.002
• Primary Citation Related Structures: 
  6CDY


• PubMed Abstract: 
  

  Intestinal homeostasis is tightly regulated by complex yet poorly understood signaling networks. Here, we demonstrate that Lats1/2, the core Hippo kinases, are essential to maintain Wnt pathway activity and intestinal stem cells. Lats1/2 deletion leads to loss of intestinal stem cells but drives Wnt-uncoupled crypt expansion. To explore the function of downstream transcriptional enhanced associate domain (TEAD) transcription factors, we identified a selective small-molecule reversible inhibitor of TEAD auto-palmitoylation that directly occupies its lipid-binding site and inhibits TEAD-mediated transcription in vivo. Combining this chemical tool with genetic and proteomics approaches, we show that intestinal Wnt inhibition by Lats deletion is Yes-associated protein (YAP)/transcriptional activator with PDZ-binding domain (TAZ) dependent but TEAD independent. Mechanistically, nuclear YAP/TAZ interact with Groucho/Transducin-Like Enhancer of Split (TLE) to block Wnt/T-cell factor (TCF)-mediated transcription, and dual inhibition of TEAD and Lats suppresses Wnt-uncoupled Myc upregulation and epithelial over-proliferation in Adenomatous polyposis coli (APC)-mutated intestine. Our studies highlight a pharmacological approach to inhibit TEAD palmitoylation and have important implications for targeting Wnt and Hippo signaling in human malignancies.

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Organizational Affiliation: 
• Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.
Departments of Pharmacology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
Stem Cell Program, Department of Hematology/Oncology, Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA.
Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
Division of Basic Science Research, Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA. Electronic address: [e-mail].
Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.72 kDa 
• Atom Count: 3,412 
• Modeled Residue Count: 400 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional enhancer factor TEF-4	A, B	240	Homo sapiens	Mutation(s): 0  Gene Names: TEAD2, TEF4
UniProt & NIH Common Fund Data Resources
Find proteins for Q15562 (Homo sapiens) Explore Q15562  Go to UniProtKB:  Q15562
PHAROS:  Q15562 GTEx:  ENSG00000074219

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EY1 (Subject of Investigation/LOI)	C [auth A], D [auth B]	2-[(4H-1,2,4-triazol-3-yl)sulfanyl]-N-{4-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]phenyl}acetamide C20 H24 N4 O S UUKXOVBCMOZQNC-PVGDPBLGSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EY1	BindingDB:  6CDY	IC50: 710 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.255 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.464	α = 90
b = 61.64	β = 117.4
c = 80.421	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): LIU, S., HAN, X., LUO, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK107651

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2022-03-23
  Changes: Author supporting evidence, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Refinement description