6GE3

X-ray structure of TEAD4 (wildtype) complexed with YAP (wildtype): The role of residual flexibility and water molecules in the adaptation of a bound intrinsically disordered protein to mutations at a binding interface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Adaptation of the bound intrinsically disordered protein YAP to mutations at the YAP:TEAD interface.

Mesrouze, Y.Bokhovchuk, F.Izaac, A.Meyerhofer, M.Zimmermann, C.Fontana, P.Schmelzle, T.Erdmann, D.Furet, P.Kallen, J.Chene, P.

(2018) Protein Sci 27: 1810-1820

  • DOI: 10.1002/pro.3493
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Many interactions between proteins are mediated by intrinsically disordered regions (IDRs). Intrinsically disordered proteins (IDPs) do not adopt a stable three-dimensional structure in their unbound form, but they become more structured upon binding ...

    Many interactions between proteins are mediated by intrinsically disordered regions (IDRs). Intrinsically disordered proteins (IDPs) do not adopt a stable three-dimensional structure in their unbound form, but they become more structured upon binding to their partners. In this communication, we study how a bound IDR adapts to mutations, preventing the formation of hydrogen bonds at the binding interface that needs a precise positioning of the interacting residues to be formed. We use as a model the YAP:TEAD interface, where one YAP (IDP) and two TEAD residues form hydrogen bonds via their side chain. Our study shows that the conformational flexibility of bound YAP and the reorganization of water molecules at the interface help to reduce the energetic constraints created by the loss of H-bonds at the interface. The residual flexibility/dynamic of bound IDRs and water might, therefore, be a key for the adaptation of IDPs to different interface landscapes and to mutations occurring at binding interfaces.


    Organizational Affiliation

    Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional enhancer factor TEF-3A219Homo sapiensMutation(s): 0 
Gene Names: TEAD4RTEF1TCF13L1TEF3
Find proteins for Q15561 (Homo sapiens)
Explore Q15561 
Go to UniProtKB:  Q15561
NIH Common Fund Data Resources
PHAROS  Q15561
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcriptional coactivator YAP1L41Homo sapiensMutation(s): 0 
Gene Names: YAP1YAP65
Find proteins for P46937 (Homo sapiens)
Explore P46937 
Go to UniProtKB:  P46937
NIH Common Fund Data Resources
PHAROS  P46937
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download CCD File 
A
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.149α = 90
b = 59.149β = 90
c = 158.999γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-04-25 
  • Released Date: 2018-09-19 
  • Deposition Author(s): Kallen, J.

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references