5DC0

CRYSTAL STRUCTURE OF MONOBODY GG3/ABL1 SH2 DOMAIN COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface.

Wojcik, J.Lamontanara, A.J.Grabe, G.Koide, A.Akin, L.Gerig, B.Hantschel, O.Koide, S.

(2016) J.Biol.Chem. 291: 8836-8847

  • DOI: 10.1074/jbc.M115.707901
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bcr-Abl is a constitutively active kinase that causes chronic myelogenous leukemia. We have shown that a tandem fusion of two designed binding proteins, termed monobodies, directed to the interaction interface between the Src homology 2 (SH2) and kin ...

    Bcr-Abl is a constitutively active kinase that causes chronic myelogenous leukemia. We have shown that a tandem fusion of two designed binding proteins, termed monobodies, directed to the interaction interface between the Src homology 2 (SH2) and kinase domains and to the phosphotyrosine-binding site of the SH2 domain, respectively, inhibits the Bcr-Abl kinase activity. Because the latter monobody inhibits processive phosphorylation by Bcr-Abl and the SH2-kinase interface is occluded in the active kinase, it remained undetermined whether targeting the SH2-kinase interface alone was sufficient for Bcr-Abl inhibition. To address this question, we generated new, higher affinity monobodies with single nanomolar KD values targeting the kinase-binding surface of SH2. Structural and mutagenesis studies revealed the molecular underpinnings of the monobody-SH2 interactions. Importantly, the new monobodies inhibited Bcr-Abl kinase activity in vitro and in cells, and they potently induced cell death in chronic myelogenous leukemia cell lines. This work provides strong evidence for the SH2-kinase interface as a pharmacologically tractable site for allosteric inhibition of Bcr-Abl.


    Organizational Affiliation

    From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.,From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, Shohei.Koide@nyumc.org.,From the Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637.,Swiss Institute for Experimental Cancer Research, School of Life Sciences, École polytechnique fédérale de Lausanne, 1015 Lausanne, Switzerland, and oliver.hantschel@epfl.ch.,Swiss Institute for Experimental Cancer Research, School of Life Sciences, École polytechnique fédérale de Lausanne, 1015 Lausanne, Switzerland, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fibronectin
A
93Homo sapiensMutation(s): 0 
Gene Names: FN1 (FN)
Find proteins for P02751 (Homo sapiens)
Go to Gene View: FN1
Go to UniProtKB:  P02751
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase ABL1
B
121Homo sapiensMutation(s): 0 
Gene Names: ABL1 (ABL, JTK7)
EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens)
Go to Gene View: ABL1
Go to UniProtKB:  P00519
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 131.437α = 90.00
b = 37.348β = 98.42
c = 39.705γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM090324
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32GM07281
National Institutes of Health/National Cancer InstituteUnited StatesP30CA014599
Swiss Cancer LeagueSwitzerlandS-3132-02-2013; KLS-3595-02-2015

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 1.2: 2016-05-11
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations