7LIR

Structure of the invertebrate ALK GRD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

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This is version 1.2 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 tyrosine kinase receptor homolog scd-2
A, B
350Caenorhabditis elegansMutation(s): 0 
Gene Names: scd-2T10H9.2
EC: 2.7.10.1
UniProt
Find proteins for O76411 (Caenorhabditis elegans)
Explore O76411 
Go to UniProtKB:  O76411
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76411
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
C
6N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G51784HB
GlyCosmos:  G51784HB
GlyGen:  G51784HB
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, F, I
2N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G35446HX
GlyCosmos:  G35446HX
GlyGen:  G35446HX
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
G
5N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G93904UY
GlyCosmos:  G93904UY
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H
3N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO
GlyCosmos:  G62182OO
GlyGen:  G62182OO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.339α = 90
b = 224.339β = 90
c = 114.525γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesK22 CA215821
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA248532

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