2WKR | pdb_00002wkr

Structure of a photoactivatable Rac1 containing the Lov2 C450M Mutant


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.20 Å
  • R-Value Free:&nbsp
    0.226 (Depositor), 0.220 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.185 (Depositor), 0.180 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.188&nbsp(Depositor)&nbsp

Starting Models: experimental
View more details

wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


Ligand Structure Quality Assessment&nbsp


This is version 1.1 of the entry. See complete&nbsphistory.&nbsp


Literature

A Genetically Encoded Photoactivatable Rac Controls the Motility of Living Cells.

Wu, Y.I.,&nbspFrey, D.,&nbspLungu, O.I.,&nbspJaehrig, A.,&nbspSchlichting, I.,&nbspKuhlman, B.,&nbspHahn, K.M.

(2009) Nature&nbsp461: 104

  • DOI:&nbsphttps://doi.org/10.1038/nature08241
  • Primary Citation of Related Structures: &nbsp
    2WKP, 2WKQ, 2WKR

  • PubMed Abstract:&nbsp

    The precise spatio-temporal dynamics of protein activity are often critical in determining cell behaviour, yet for most proteins they remain poorly understood; it remains difficult to manipulate protein activity at precise times and places within living cells. Protein activity has been controlled by light, through protein derivatization with photocleavable moieties or using photoreactive small-molecule ligands. However, this requires use of toxic ultraviolet wavelengths, activation is irreversible, and/or cell loading is accomplished via disruption of the cell membrane (for example, through microinjection). Here we have developed a new approach to produce genetically encoded photoactivatable derivatives of Rac1, a key GTPase regulating actin cytoskeletal dynamics in metazoan cells. Rac1 mutants were fused to the photoreactive LOV (light oxygen voltage) domain from phototropin, sterically blocking Rac1 interactions until irradiation unwound a helix linking LOV to Rac1. Photoactivatable Rac1 (PA-Rac1) could be reversibly and repeatedly activated using 458- or 473-nm light to generate precisely localized cell protrusions and ruffling. Localized Rac activation or inactivation was sufficient to produce cell motility and control the direction of cell movement. Myosin was involved in Rac control of directionality but not in Rac-induced protrusion, whereas PAK was required for Rac-induced protrusion. PA-Rac1 was used to elucidate Rac regulation of RhoA in cell motility. Rac and Rho coordinate cytoskeletal behaviours with seconds and submicrometre precision. Their mutual regulation remains controversial, with data indicating that Rac inhibits and/or activates Rho. Rac was shown to inhibit RhoA in mouse embryonic fibroblasts, with inhibition modulated at protrusions and ruffles. A PA-Rac crystal structure and modelling revealed LOV-Rac interactions that will facilitate extension of this photoactivation approach to other proteins.


  • Organizational Affiliation:&nbsp

    Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA. [email protected]


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NPH1-1, RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1332Avena sativa,&nbspHomo sapiens
This entity is chimeric
Mutation(s): 4&nbsp
EC:&nbsp2.7.11.1&nbsp(UniProt),&nbsp3.6.5.2&nbsp(UniProt)
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
Find proteins for&nbspO49003&nbsp(Avena sativa)
Explore&nbspO49003&nbsp
Go to UniProtKB: &nbspO49003
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP63000O49003
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands&nbsp4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File&nbsp
B [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File&nbsp
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
CL
Query on CL

Download Ideal Coordinates CCD File&nbsp
E [auth A],
F [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File&nbsp
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.20 Å
  • R-Value Free:&nbsp 0.226 (Depositor), 0.220 (DCC)&nbsp
  • R-Value Work:&nbsp 0.185 (Depositor), 0.180 (DCC)&nbsp
  • R-Value Observed:&nbsp0.188&nbsp(Depositor)&nbsp
Space Group:&nbspP 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.39α = 90
b = 112.39β = 90
c = 69.2γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View&nbspFull Validation Report



Ligand Structure Quality Assessment&nbsp


Entry History&nbsp

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description