3K2M

Crystal Structure of Monobody HA4/Abl1 SH2 Domain Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain.

Wojcik, J.Hantschel, O.Grebien, F.Kaupe, I.Bennett, K.L.Barkinge, J.Jones, R.B.Koide, A.Superti-Furga, G.Koide, S.

(2010) Nat.Struct.Mol.Biol. 17: 519-527

  • DOI: 10.1038/nsmb.1793

  • PubMed Abstract: 
  • Interactions between Src homology 2 (SH2) domains and phosphotyrosine sites regulate tyrosine kinase signaling networks. Selective perturbation of these interactions is challenging due to the high homology among the 120 human SH2 domains. Using an im ...

    Interactions between Src homology 2 (SH2) domains and phosphotyrosine sites regulate tyrosine kinase signaling networks. Selective perturbation of these interactions is challenging due to the high homology among the 120 human SH2 domains. Using an improved phage-display selection system, we generated a small antibody mimic (or 'monobody'), termed HA4, that bound to the Abelson (Abl) kinase SH2 domain with low nanomolar affinity. SH2 protein microarray analysis and MS of intracellular HA4 interactors showed HA4's specificity, and a crystal structure revealed how this specificity is achieved. HA4 disrupted intramolecular interactions of Abl involving the SH2 domain and potently activated the kinase in vitro. Within cells, HA4 inhibited processive phosphorylation activity of Abl and also inhibited STAT5 activation. This work provides a design guideline for highly specific and potent inhibitors of a protein interaction domain and shows their utility in mechanistic and cellular investigations.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene tyrosine-protein kinase ABL1
A, B
112Homo sapiensGene Names: ABL1 (ABL, JTK7)
EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens)
Go to Gene View: ABL1
Go to UniProtKB:  P00519
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Monobody HA4
C, D
101N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.625α = 90.00
b = 88.181β = 90.00
c = 131.081γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description