6TUA

The RYK Pseudokinase Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Insights into Pseudokinase Domains of Receptor Tyrosine Kinases.

Sheetz, J.B.Mathea, S.Karvonen, H.Malhotra, K.Chatterjee, D.Niininen, W.Perttila, R.Preuss, F.Suresh, K.Stayrook, S.E.Tsutsui, Y.Radhakrishnan, R.Ungureanu, D.Knapp, S.Lemmon, M.A.

(2020) Mol Cell 79: 390-405.e7

  • DOI: https://doi.org/10.1016/j.molcel.2020.06.018
  • Primary Citation of Related Structures:  
    6TU9, 6TUA

  • PubMed Abstract: 

    Despite their apparent lack of catalytic activity, pseudokinases are essential signaling molecules. Here, we describe the structural and dynamic properties of pseudokinase domains from the Wnt-binding receptor tyrosine kinases (PTK7, ROR1, ROR2, and RYK), which play important roles in development. We determined structures of all pseudokinase domains in this family and found that they share a conserved inactive conformation in their activation loop that resembles the autoinhibited insulin receptor kinase (IRK). They also have inaccessible ATP-binding pockets, occluded by aromatic residues that mimic a cofactor-bound state. Structural comparisons revealed significant domain plasticity and alternative interactions that substitute for absent conserved motifs. The pseudokinases also showed dynamic properties that were strikingly similar to those of IRK. Despite the inaccessible ATP site, screening identified ATP-competitive type-II inhibitors for ROR1. Our results set the stage for an emerging therapeutic modality of "conformational disruptors" to inhibit or modulate non-catalytic functions of pseudokinases deregulated in disease.


  • Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase RYK317Homo sapiensMutation(s): 0 
Gene Names: RYKJTK5A
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P34925 (Homo sapiens)
Explore P34925 
Go to UniProtKB:  P34925
PHAROS:  P34925
GTEx:  ENSG00000163785 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34925
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.645α = 90
b = 47.242β = 97.635
c = 152.741γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-07-29
    Changes: Database references
  • Version 1.2: 2020-08-19
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description