5FI0 | pdb_00005fi0

Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1

  • Classification:&nbspPROTEIN BINDING
  • Organism(s):&nbspHomo sapiens
  • Expression System:&nbspEscherichia coli BL21(DE3)
  • Mutation(s):&nbspNo&nbsp

  • Deposited:&nbsp2015-12-22&nbspReleased:&nbsp2016-04-20&nbsp
  • Deposition Author(s):&nbspCash, J.N., Tesmer, J.J.G.
  • Funding Organization(s):&nbspNational Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), American Cancer Society

Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp3.28 Å
  • R-Value Free:&nbsp
    0.235 (Depositor), 0.240 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.190 (Depositor), 0.190 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.192&nbsp(Depositor)&nbsp

Starting Models: experimental
View more details

wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


This is version 1.5 of the entry. See complete&nbsphistory.&nbsp


Literature

Structural and Biochemical Characterization of the Catalytic Core of the Metastatic Factor P-Rex1 and Its Regulation by PtdIns(3,4,5)P3.

Cash, J.N.,&nbspDavis, E.M.,&nbspTesmer, J.J.

(2016) Structure&nbsp24: 730-740

  • DOI:&nbsphttps://doi.org/10.1016/j.str.2016.02.022
  • Primary Citation of Related Structures: &nbsp
    5D27, 5D3V, 5D3W, 5D3X, 5D3Y, 5FI0, 5FI1

  • PubMed Abstract:&nbsp

    Phosphatidylinositol 3,4,5-trisphosphate (PIP3)-dependent Rac exchanger 1 (P-Rex1) is a Rho guanine nucleotide exchange factor synergistically activated by PIP3 and Gβγ that plays an important role in the metastasis of breast, prostate, and skin cancer, making it an attractive therapeutic target. However, the molecular mechanisms behind P-Rex1 regulation are poorly understood. We determined structures of the P-Rex1 pleckstrin homology (PH) domain bound to the headgroup of PIP3 and resolved that PIP3 binding to the PH domain is required for P-Rex1 activity in cells but not for membrane localization, which points to an allosteric activation mechanism by PIP3. We also determined structures of the P-Rex1 tandem Dbl homology/PH domains in complexes with two of its substrate GTPases, Rac1 and Cdc42. Collectively, this study provides important molecular insights into P-Rex1 regulation and tools for targeting the PIP3-binding pocket of P-Rex1 with a new generation of cancer chemotherapeutic agents.


  • Organizational Affiliation:&nbsp
    • Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein,Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein
A, C, E, G
374Homo sapiensMutation(s): 0&nbsp
Gene Names:&nbspPREX1,&nbspKIAA1415
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspQ8TCU6&nbsp(Homo sapiens)
Explore&nbspQ8TCU6&nbsp
Go to UniProtKB: &nbspQ8TCU6
PHAROS: &nbspQ8TCU6
GTEx: &nbspENSG00000124126&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TCU6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related C3 botulinum toxin substrate 1
B, D, F, H
195Homo sapiensMutation(s): 0&nbsp
Gene Names:&nbspRAC1,&nbspTC25,&nbspMIG5
EC:&nbsp3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP63000&nbsp(Homo sapiens)
Explore&nbspP63000&nbsp
Go to UniProtKB: &nbspP63000
PHAROS: &nbspP63000
GTEx: &nbspENSG00000136238&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63000
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp3.28 Å
  • R-Value Free:&nbsp 0.235 (Depositor), 0.240 (DCC)&nbsp
  • R-Value Work:&nbsp 0.190 (Depositor), 0.190 (DCC)&nbsp
  • R-Value Observed:&nbsp0.192&nbsp(Depositor)&nbsp
Space Group:&nbspP 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.373α = 90
b = 107.053β = 90
c = 323.568γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View&nbspFull Validation Report



Entry History&nbsp& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL086865
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL122416
American Cancer SocietyUnited StatesPF-14-224-01-DMC

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2016-05-18
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description