5MTM

Monobody Mb(Lck_3) bound to Lck-SH2 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.405 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies.

Kukenshoner, T.Schmit, N.E.Bouda, E.Sha, F.Pojer, F.Koide, A.Seeliger, M.Koide, S.Hantschel, O.

(2017) J. Mol. Biol. 429: 1364-1380

  • DOI: 10.1016/j.jmb.2017.03.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The binding of Src-homology 2 (SH2) domains to phosphotyrosine (pY) sites is critical for the autoinhibition and substrate recognition of the eight Src family kinases (SFKs). The high sequence conservation of the 120 human SH2 domains poses a signifi ...

    The binding of Src-homology 2 (SH2) domains to phosphotyrosine (pY) sites is critical for the autoinhibition and substrate recognition of the eight Src family kinases (SFKs). The high sequence conservation of the 120 human SH2 domains poses a significant challenge to selectively perturb the interactions of even the SFK SH2 family against the rest of the SH2 domains. We have developed synthetic binding proteins, termed monobodies, for six of the SFK SH2 domains with nanomolar affinity. Most of these monobodies competed with pY ligand binding and showed strong selectivity for either the SrcA (Yes, Src, Fyn, Fgr) or SrcB subgroup (Lck, Lyn, Blk, Hck). Interactome analysis of intracellularly expressed monobodies revealed that they bind SFKs but no other SH2-containing proteins. Three crystal structures of monobody-SH2 complexes unveiled different and only partly overlapping binding modes, which rationalized the observed selectivity and enabled structure-based mutagenesis to modulate inhibition mode and selectivity. In line with the critical roles of SFK SH2 domains in kinase autoinhibition and T-cell receptor signaling, monobodies binding the Src and Hck SH2 domains selectively activated respective recombinant kinases, whereas an Lck SH2-binding monobody inhibited proximal signaling events downstream of the T-cell receptor complex. Our results show that SFK SH2 domains can be targeted with unprecedented potency and selectivity using monobodies. They are excellent tools for dissecting SFK functions in normal development and signaling and to interfere with aberrant SFK signaling networks in cancer cells.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, 430 East 29th Street, New York, NY 10016, USA; Department of Medicine, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA.,Department of Pharmacological Sciences, Stony Brook University, BST 8-140, Stony Brook, NY 11794-8651, USA.,Protein Crystallography Core Facility, School of Life Sciences, École polytechnique fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland. Electronic address: oliver.hantschel@epfl.ch.,Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, 430 East 29th Street, New York, NY 10016, USA; Department of Medicine, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 430 East 29th Street, New York, NY 10016, USA. Electronic address: Shohei.Koide@nyumc.org.,Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase Lck
A
116Homo sapiensMutation(s): 0 
Gene Names: LCK
EC: 2.7.10.2
Find proteins for P06239 (Homo sapiens)
Go to Gene View: LCK
Go to UniProtKB:  P06239
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Monobody Mb(Lck_3)
B
95N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.405 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.834α = 90.00
b = 81.834β = 90.00
c = 105.961γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Source and taxonomy, Structure summary
  • Version 1.3: 2019-10-16
    Type: Data collection