3KYS | pdb_00003kys

Crystal structure of human YAP and TEAD complex

• PDB DOI: https://doi.org/10.2210/pdb3KYS/pdb

• Classification: TRANSCRIPTION/PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-07 Released: 2010-02-23 
• Deposition Author(s): Li, Z., Zhao, B., Wang, P., Chen, F., Dong, Z., Yang, H., Guan, K.L., Xu, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.266 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Structural insights into the YAP and TEAD complex

Li, Z., Zhao, B., Wang, P., Chen, F., Dong, Z., Yang, H., Guan, K.L., Xu, Y.

(2010) Genes Dev 24: 235-240

• PubMed: 20123905 
• DOI: https://doi.org/10.1101/gad.1865810
• Primary Citation Related Structures: 
  3KYS


• PubMed Abstract: 
  

  The Yes-associated protein (YAP) transcriptional coactivator is a key regulator of organ size and a candidate human oncogene inhibited by the Hippo tumor suppressor pathway. The TEAD family of transcription factors binds directly to and mediates YAP-induced gene expression. Here we report the three-dimensional structure of the YAP (residues 50-171)-TEAD1 (residues 194-411) complex, in which YAP wraps around the globular structure of TEAD1 and forms extensive interactions via three highly conserved interfaces. Interface 3, including YAP residues 86-100, is most critical for complex formation. Our study reveals the biochemical nature of the YAP-TEAD interaction, and provides a basis for pharmacological intervention of YAP-TEAD hyperactivation in human diseases.

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Organizational Affiliation: 
• School of Life Sciences, Fudan University, Shanghai 200433, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 77.68 kDa 
• Atom Count: 4,286 
• Modeled Residue Count: 518 
• Deposited Residue Count: 688 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional enhancer factor TEF-1	A, C	219	Homo sapiens	Mutation(s): 0  Gene Names: TEAD1, TCF13, TEF1
UniProt & NIH Common Fund Data Resources
Find proteins for P28347 (Homo sapiens) Explore P28347  Go to UniProtKB:  P28347
PHAROS:  P28347 GTEx:  ENSG00000187079

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
65 kDa Yes-associated protein	B, D	125	Homo sapiens	Mutation(s): 0  Gene Names: YAP1, YAP65
UniProt & NIH Common Fund Data Resources
Find proteins for P46937 (Homo sapiens) Explore P46937  Go to UniProtKB:  P46937
PHAROS:  P46937 GTEx:  ENSG00000137693

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
P1L	A, C	L-PEPTIDE LINKING	C19 H37 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.266 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.643	α = 90
b = 110.503	β = 90
c = 165.695	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MAR345dtb	data collection
SOLVE	phasing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Li, Z., Zhao, B., Wang, P., Chen, F., Dong, Z., Yang, H., Guan, K.L., Xu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	30870493

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-10-07
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2025-03-26
  Changes: Data collection, Database references, Structure summary