6GE4

TEAD4 (216-434);E263A COMPLEXED WITH YAP PEPTIDE (60-100) AND MYRISTOATE (COVALENTLY BOUND) AT 1.97A (P41212 CRYSTAL FORM); MYRISTOYLATION WAS DONE BY ADDING MYR-COA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  

  • 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.,Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland.,Chemical Biology & Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional enhancer factor TEF-3
A
219Homo sapiensMutation(s): 1 
Gene Names: TEAD4 (RTEF1, TCF13L1, TEF3)
Find proteins for Q15561 (Homo sapiens)
Go to Gene View: TEAD4
Go to UniProtKB:  Q15561
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcriptional coactivator YAP1
L
41Homo sapiensMutation(s): 0 
Gene Names: YAP1 (YAP65)
Find proteins for P46937 (Homo sapiens)
Go to Gene View: YAP1
Go to UniProtKB:  P46937
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
A
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.224 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.033α = 90.00
b = 59.033β = 90.00
c = 159.129γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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: 2018-10-03
    Type: Data collection
  • Version 1.2: 2018-10-31
    Type: Data collection, Database references