5WNO | pdb_00005wno

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 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1016/j.str.2017.12.012
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 38.48 kDa 
  • Atom Count: 2,484 
  • Modeled Residue Count: 302 
  • Deposited Residue Count: 330 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor tyrosine-protein kinase let-23330Caenorhabditis elegansMutation(s): 0 
Gene Names: let-23kin-7ZK1067.1
EC: 2.7.10.1
UniProt
Find proteins for P24348 (Caenorhabditis elegans)
Explore P24348 
Go to UniProtKB:  P24348
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24348
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP

Query on ANP



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
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



Ligand Structure Quality Assessment 


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  (Full details and data files)

  • 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
  • Version 1.3: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.4: 2024-12-25
    Changes: Advisory, Derived calculations, Structure summary