5YDY | pdb_00005ydy

NMR structure of YAP1-2 WW2 domain with LATS1 PPxY motif complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 5YDY

This is version 1.3 of the entry. See complete history

Literature

Biophysical studies and NMR structure of YAP2 WW domain - LATS1 PPxY motif complexes reveal the basis of their interaction.

Verma, A.Jing-Song, F.Finch-Edmondson, M.L.Velazquez-Campoy, A.Balasegaran, S.Sudol, M.Sivaraman, J.

(2018) Oncotarget 9: 8068-8080

  • DOI: https://doi.org/10.18632/oncotarget.23909
  • Primary Citation Related Structures: 
    5YDX, 5YDY

  • PubMed Abstract: 

    YES-associated protein (YAP) is a major effector protein of the Hippo tumor suppressor pathway, and is phosphorylated by the serine/threonine kinase LATS. Their binding is mediated by the interaction between WW domains of YAP and PPxY motifs of LATS. Their isoforms, YAP2 and LATS1 contain two WW domains and two PPxY motifs respectively. Here, we report the study of the interaction of these domains both in vitro and in human cell lines, to better understand the mechanism of their binding. We show that there is a reciprocal binding preference of YAP2-WW1 with LATS1-PPxY2, and YAP2-WW2 with LATS1-PPxY1. We solved the NMR structures of these complexes and identified several conserved residues that play a critical role in binding. We further created a YAP2 mutant by swapping the WW domains, and found that YAP2 phosphorylation at S127 by LATS1 is not affected by the spatial configuration of its WW domains. This is likely because the region between the PPxY motifs of LATS1 is unstructured, even upon binding with its partner. Based on our observations, we propose possible models for the interaction between YAP2 and LATS1.


  • Organizational Affiliation
    • Department of Biological Sciences, National University of Singapore, Singapore.

Macromolecule Content 

  • Total Structure Weight: 6 kDa 
  • Atom Count: 424 
  • Modeled Residue Count: 54 
  • Deposited Residue Count: 54 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
WW2 domain and PPxY motif complex54Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P46937 (Homo sapiens)
Explore P46937 
Go to UniProtKB:  P46937
PHAROS:  P46937
GTEx:  ENSG00000137693 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46937
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-22
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references