3GQL

Crystal Structure of activated receptor tyrosine kinase in complex with substrates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

The selectivity of receptor tyrosine kinase signaling is controlled by a secondary SH2 domain binding site.

Bae, J.H.Lew, E.D.Yuzawa, S.Tome, F.Lax, I.Schlessinger, J.

(2009) Cell 138: 514-524

  • DOI: https://doi.org/10.1016/j.cell.2009.05.028
  • Primary Citation of Related Structures:  
    3GQI, 3GQL

  • PubMed Abstract: 

    SH2 domain-mediated interactions represent a crucial step in transmembrane signaling by receptor tyrosine kinases. SH2 domains recognize phosphotyrosine (pY) in the context of particular sequence motifs in receptor phosphorylation sites. However, the modest binding affinity of SH2 domains to pY containing peptides may not account for and likely represents an oversimplified mechanism for regulation of selectivity of signaling pathways in living cells. Here we describe the crystal structure of the activated tyrosine kinase domain of FGFR1 in complex with a phospholipase Cgamma fragment. The structural and biochemical data and experiments with cultured cells show that the selectivity of phospholipase Cgamma binding and signaling via activated FGFR1 are determined by interactions between a secondary binding site on an SH2 domain and a region in FGFR1 kinase domain in a phosphorylation independent manner. These experiments reveal a mechanism for how SH2 domain selectivity is regulated in vivo to mediate a specific cellular process.


  • Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Basic fibroblast growth factor receptor 1
A, B, C
326Homo sapiensMutation(s): 1 
Gene Names: FGFBRFGFR1FLGFLT2
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11362 (Homo sapiens)
Explore P11362 
Go to UniProtKB:  P11362
PHAROS:  P11362
GTEx:  ENSG00000077782 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11362
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GQL
Query on GQL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
(E)-[4-(3,5-difluorophenyl)-3H-pyrrolo[2,3-b]pyridin-3-ylidene](3-methoxyphenyl)methanol
C21 H14 F2 N2 O2
HQMUBYFTZASKLP-ZZEZOPTASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.252 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.168α = 90
b = 78.265β = 110.55
c = 98.458γ = 90
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-21
    Changes: Data collection