7NX1

TG domain of LTK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of cytokine-mediated activation of ALK family receptors.

De Munck, S.Provost, M.Kurikawa, M.Omori, I.Mukohyama, J.Felix, J.Bloch, Y.Abdel-Wahab, O.Bazan, J.F.Yoshimi, A.Savvides, S.N.

(2021) Nature 600: 143-147

  • DOI: 10.1038/s41586-021-03959-5
  • Primary Citation of Related Structures:  
    7NWZ, 7NX0, 7NX1, 7NX2, 7NX3, 7NX4

  • PubMed Abstract: 
  • Anaplastic lymphoma kinase (ALK) 1 and the related leukocyte tyrosine kinase (LTK) 2 are recently deorphanized receptor tyrosine kinases 3 . Together with their activating cytokines, ALKAL1 and ALKAL2 4-6 (also called FAM150A and FAM150B or AUGβ and AUGα, respectively), they are involved in neural development 7 , cancer 7-9 and autoimmune diseases 10 ...

    Anaplastic lymphoma kinase (ALK) 1 and the related leukocyte tyrosine kinase (LTK) 2 are recently deorphanized receptor tyrosine kinases 3 . Together with their activating cytokines, ALKAL1 and ALKAL2 4-6 (also called FAM150A and FAM150B or AUGβ and AUGα, respectively), they are involved in neural development 7 , cancer 7-9 and autoimmune diseases 10 . Furthermore, mammalian ALK recently emerged as a key regulator of energy expenditure and weight gain 11 , consistent with a metabolic role for Drosophila ALK 12 . Despite such functional pleiotropy and growing therapeutic relevance 13,14 , structural insights into ALK and LTK and their complexes with cognate cytokines have remained scarce. Here we show that the cytokine-binding segments of human ALK and LTK comprise a novel architectural chimera of a permuted TNF-like module that braces a glycine-rich subdomain featuring a hexagonal lattice of long polyglycine type II helices. The cognate cytokines ALKAL1 and ALKAL2 are monomeric three-helix bundles, yet their binding to ALK and LTK elicits similar dimeric assemblies with two-fold symmetry, that tent a single cytokine molecule proximal to the cell membrane. We show that the membrane-proximal EGF-like domain dictates the apparent cytokine preference of ALK. Assisted by these diverse structure-function findings, we propose a structural and mechanistic blueprint for complexes of ALK family receptors, and thereby extend the repertoire of ligand-mediated dimerization mechanisms adopted by receptor tyrosine kinases.


    Organizational Affiliation

    Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium. savvas.savvides@ugent.be.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Leukocyte tyrosine kinase receptorA322Homo sapiensMutation(s): 0 
Gene Names: LTKTYK1
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29376 (Homo sapiens)
Explore P29376 
Go to UniProtKB:  P29376
PHAROS:  P29376
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29376
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTB
Query on BTB

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
TB
Query on TB

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
TERBIUM(III) ION
Tb
HKCRVXUAKWXBLE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.04α = 90
b = 54.46β = 111.284
c = 55.01γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)Belgium--

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references