5WNO

Crystal structure of C. elegans LET-23 kinase domain complexed with AMP-PNP

  • Classification: TRANSFERASE
  • Organism(s): Caenorhabditis elegans
  • Expression System: Spodoptera frugiperda
  • Mutation(s): No 

  • Deposited: 2017-08-01 Released: 2018-01-31 
  • Deposition Author(s): Liu, L., Thaker, T.M., Jura, N.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Susan G. Komen Foundation, National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Regulation of Kinase Activity in the Caenorhabditis elegans EGF Receptor, LET-23.

Liu, L.Thaker, T.M.Freed, D.M.Frazier, N.Malhotra, K.Lemmon, M.A.Jura, N.

(2018) Structure 26: 270-281.e4

  • DOI: 10.1016/j.str.2017.12.012
  • Primary Citation of Related Structures:  
    5WNO

  • PubMed Abstract: 
  • In the active HER receptor dimers, kinases play distinct roles; one is the catalytically active kinase and the other is its allosteric activator. This specialization enables signaling by the catalytically inactive HER3, which functions exclusively as ...

    In the active HER receptor dimers, kinases play distinct roles; one is the catalytically active kinase and the other is its allosteric activator. This specialization enables signaling by the catalytically inactive HER3, which functions exclusively as an allosteric activator upon heterodimerization with other HER receptors. It is unclear whether the allosteric activation mechanism evolved before HER receptors functionally specialized. We determined the crystal structure of the kinase domain of the only EGF receptor in Caenorhabditis elegans, LET-23. Our structure of a non-human EGFR kinase reveals autoinhibitory features conserved in the human counterpart. Strikingly, mutations within the putative allosteric dimer interface abrogate activity of the isolated LET-23 kinase and of the full-length receptor despite these regions being only partially conserved with human EGFR. Our results indicate that ancestral EGFRs have built-in features that poise them for allosteric activation that could facilitate emergence of the catalytically dead, yet functional, orthologs.


    Organizational Affiliation

    Cardiovascular Research Institute, University of California - San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California - San Francisco, San Francisco, CA 94158, USA. Electronic address: natalia.jura@ucsf.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor tyrosine-protein kinase let-23A330Caenorhabditis elegansMutation(s): 0 
Gene Names: let-23kin-7ZK1067.1
EC: 2.7.10.1
Find proteins for P24348 (Caenorhabditis elegans)
Explore P24348 
Go to UniProtKB:  P24348
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.097α = 90
b = 77.978β = 90
c = 106.207γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM109176
Susan G. Komen FoundationUnited StatesCCR14299947
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesF32CA216928

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence