7MK7

Augmentor domain of augmentor-beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for ligand reception by anaplastic lymphoma kinase.

Li, T.Stayrook, S.E.Tsutsui, Y.Zhang, J.Wang, Y.Li, H.Proffitt, A.Krimmer, S.G.Ahmed, M.Belliveau, O.Walker, I.X.Mudumbi, K.C.Suzuki, Y.Lax, I.Alvarado, D.Lemmon, M.A.Schlessinger, J.Klein, D.E.

(2021) Nature 600: 148-152

  • DOI: https://doi.org/10.1038/s41586-021-04141-7
  • Primary Citation of Related Structures:  
    7LIR, 7LRZ, 7LS0, 7MK7

  • PubMed Abstract: 

    The proto-oncogene ALK encodes anaplastic lymphoma kinase, a receptor tyrosine kinase that is expressed primarily in the developing nervous system. After development, ALK activity is associated with learning and memory 1 and controls energy expenditure, and inhibition of ALK can prevent diet-induced obesity 2 . Aberrant ALK signalling causes numerous cancers 3 . In particular, full-length ALK is an important driver in paediatric neuroblastoma 4,5 , in which it is either mutated 6 or activated by ligand 7 . Here we report crystal structures of the extracellular glycine-rich domain (GRD) of ALK, which regulates receptor activity by binding to activating peptides 8,9 . Fusing the ALK GRD to its ligand enabled us to capture a dimeric receptor complex that reveals how ALK responds to its regulatory ligands. We show that repetitive glycines in the GRD form rigid helices that separate the major ligand-binding site from a distal polyglycine extension loop (PXL) that mediates ALK dimerization. The PXL of one receptor acts as a sensor for the complex by interacting with a ligand-bound second receptor. ALK activation can be abolished through PXL mutation or with PXL-targeting antibodies. Together, these results explain how ALK uses its atypical architecture for its regulation, and suggest new therapeutic opportunities for ALK-expressing cancers such as paediatric neuroblastoma.


  • Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALK and LTK ligand 1,Maltodextrin-binding protein
A, B
421Homo sapiensEscherichia coli
This entity is chimeric
Mutation(s): 9 
Gene Names: ALKAL1malE
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q6UXT8 (Homo sapiens)
Explore Q6UXT8 
Go to UniProtKB:  Q6UXT8
GTEx:  ENSG00000196711 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9Q6UXT8
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC [auth F],
D [auth C]
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.569α = 75.598
b = 56.775β = 77.348
c = 94.408γ = 61.785
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Database references
  • Version 1.2: 2021-12-15
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description