5OC7 | pdb_00005oc7

Crystal structure of the pleckstrin-homology domain of Bcr-Abl in complex with monobody Mb(Bcr-PH_4).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.204 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.174 (Depositor) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structural and functional dissection of the DH and PH domains of oncogenic Bcr-Abl tyrosine kinase.

Reckel, S.Gehin, C.Tardivon, D.Georgeon, S.Kukenshoner, T.Lohr, F.Koide, A.Buchner, L.Panjkovich, A.Reynaud, A.Pinho, S.Gerig, B.Svergun, D.Pojer, F.Guntert, P.Dotsch, V.Koide, S.Gavin, A.C.Hantschel, O.

(2017) Nat Commun 8: 2101-2101

  • DOI: https://doi.org/10.1038/s41467-017-02313-6
  • Primary Citation Related Structures: 
    5N6R, 5N7E, 5OC7

  • PubMed Abstract: 

    The two isoforms of the Bcr-Abl tyrosine kinase, p210 and p190, are associated with different leukemias and have a dramatically different signaling network, despite similar kinase activity. To provide a molecular rationale for these observations, we study the Dbl-homology (DH) and Pleckstrin-homology (PH) domains of Bcr-Abl p210, which constitute the only structural differences to p190. Here we report high-resolution structures of the DH and PH domains and characterize conformations of the DH-PH unit in solution. Our structural and functional analyses show no evidence that the DH domain acts as a guanine nucleotide exchange factor, whereas the PH domain binds to various phosphatidylinositol-phosphates. PH-domain mutants alter subcellular localization and result in decreased interactions with p210-selective interaction partners. Hence, the PH domain, but not the DH domain, plays an important role in the formation of the differential p210 and p190 Bcr-Abl signaling networks.


  • Organizational Affiliation
    • Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 51.54 kDa 
  • Atom Count: 3,599 
  • Modeled Residue Count: 404 
  • Deposited Residue Count: 450 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Breakpoint cluster region protein,pleckstrin-homology domain of Bcr-AblA [auth D],
B [auth A]
133Homo sapiensMutation(s): 0 
Gene Names: BCRBCR1D22S11
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11274 (Homo sapiens)
Explore P11274 
Go to UniProtKB:  P11274
PHAROS:  P11274
GTEx:  ENSG00000186716 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11274
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
monobody Mb(Bcr-PH_4)C,
D [auth B]
92synthetic constructMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IP2
(Subject of Investigation/LOI)

Query on IP2



Download:Ideal Coordinates CCD File
F [auth D]D-MYO-INOSITOL-4,5-BISPHOSPHATE
C6 H14 O12 P2
MCKAJXMRULSUKI-UZAAGFTCSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth D]
G [auth A]
H [auth A]
I [auth A]
J [auth C]
E [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth C],
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.204 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.174 (Depositor) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.683α = 62.74
b = 62.606β = 84.77
c = 67.378γ = 89.29
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_140913

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description