4QT8

Crystal Structure of RON Sema-PSI-IPT1 extracellular domains in complex with MSP beta-chain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report



Literature

Structural basis for the binding specificity of human Recepteur d'Origine Nantais (RON) receptor tyrosine kinase to macrophage-stimulating protein.

Chao, K.L.Gorlatova, N.V.Eisenstein, E.Herzberg, O.

(2014) J Biol Chem 289: 29948-29960

  • DOI: 10.1074/jbc.M114.594341
  • Primary Citation of Related Structures:  
    4QT8

  • PubMed Abstract: 
  • Recepteur d'origine nantais (RON) receptor tyrosine kinase and its ligand, serum macrophage-stimulating protein (MSP), play important roles in inflammation, cell growth, migration, and epithelial to mesenchymal transition during tumor development. Th ...

    Recepteur d'origine nantais (RON) receptor tyrosine kinase and its ligand, serum macrophage-stimulating protein (MSP), play important roles in inflammation, cell growth, migration, and epithelial to mesenchymal transition during tumor development. The binding of mature MSPαβ (disulfide-linked α- and β-chains) to RON ectodomain modulates receptor dimerization, followed by autophosphorylation of tyrosines in the cytoplasmic receptor kinase domains. Receptor recognition is mediated by binding of MSP β-chain (MSPβ) to the RON Sema. Here we report the structure of RON Sema-PSI-IPT1 (SPI1) domains in complex with MSPβ at 3.0 Å resolution. The MSPβ serine protease-like β-barrel uses the degenerate serine protease active site to recognize blades 2, 3, and 4 of the β-propeller fold of RON Sema. Despite the sequence homology between RON and MET receptor tyrosine kinase and between MSP and hepatocyte growth factor, it is well established that there is no cross-reactivity between the two receptor-ligand systems. Comparison of the structure of RON SPI1 in complex with MSPβ and that of MET receptor tyrosine kinase Sema-PSI in complex with hepatocyte growth factor β-chain reveals the receptor-ligand selectivity determinants. Analytical ultracentrifugation studies of the SPI1-MSPβ interaction confirm the formation of a 1:1 complex. SPI1 and MSPαβ also associate primarily as a 1:1 complex with a binding affinity similar to that of SPI1-MSPβ. In addition, the SPI1-MSPαβ ultracentrifuge studies reveal a low abundance 2:2 complex with ∼ 10-fold lower binding affinity compared with the 1:1 species. These results support the hypothesis that the α-chain of MSPαβ mediates RON dimerization.


    Organizational Affiliation

    From the Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850 and the Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742 osnat@umd.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Macrophage-stimulating protein receptorAB669Homo sapiensMutation(s): 5 
Gene Names: MST1RPTK8RON
EC: 2.7.10.1
Find proteins for Q04912 (Homo sapiens)
Explore Q04912 
Go to UniProtKB:  Q04912
NIH Common Fund Data Resources
PHAROS  Q04912
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatocyte growth factor-like proteinCD253Homo sapiensMutation(s): 1 
Gene Names: D3F15S2DNF15S2HGFLMSI1MST1
Find proteins for P26927 (Homo sapiens)
Explore P26927 
Go to UniProtKB:  P26927
NIH Common Fund Data Resources
PHAROS  P26927
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
3 N-Glycosylation Oligosaccharides Interaction
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.585α = 90
b = 63.775β = 90.08
c = 146.049γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2015-04-01
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary