3RYT

The Plexin A1 intracellular region in complex with Rac1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.58 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.270 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Plexins Are GTPase-Activating Proteins for Rap and Are Activated by Induced Dimerization.

Wang, Y., He, H., Srivastava, N., Vikarunnessa, S., Chen, Y.B., Jiang, J., Cowan, C.W., Zhang, X.

(2012) Sci Signal 5: ra6-ra6

  • DOI: 10.1126/scisignal.2002636
  • Primary Citation of Related Structures:  
    3RYT

  • PubMed Abstract: 

    • Plexins are cell surface receptors that bind to semaphorins and transduce signals that regulate neuronal development, immune responses, and other processes. Signaling through plexins has been proposed to rely on specific guanosine triphosphatase (GTPase)-activating protein (GAP) activity for R-Ras and M-Ras ...

    Plexins are cell surface receptors that bind to semaphorins and transduce signals that regulate neuronal development, immune responses, and other processes. Signaling through plexins has been proposed to rely on specific guanosine triphosphatase (GTPase)-activating protein (GAP) activity for R-Ras and M-Ras. Activation of this GAP activity of plexins appears to require simultaneous binding of semaphorin to the plexin extracellular domain and of the Rho GTPases Rac1 or Rnd1 to the cytoplasmic region. However, GAP activity of plexins has eluded detection in several recent studies. We show that the purified cytoplasmic region of plexin uses a noncanonical catalytic mechanism to act as a GAP for Rap, but not for R-Ras or M-Ras. The RapGAP activity of plexins was autoinhibited and was activated by induced dimerization. Biochemical and crystallographic analyses demonstrated that binding of Rho GTPases did not directly contribute to activation of plexin RapGAP activity. Semaphorin stimulated the RapGAP activity of full-length plexin in cells, which was required for plexin-mediated neuronal growth cone collapse. Together, these findings define a pathway for plexin signaling and provide insights into the mechanism for semaphorin-induced activation of plexins.

    Organizational Affiliation: 

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75063, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plexin-A1A, B626Mus musculusMutation(s): 0 
Gene Names: Kiaa4053, Plexin A1, Plxna1
Find proteins for P70206 (Mus musculus)
Explore P70206 
Go to UniProtKB:  P70206
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related C3 botulinum toxin substrate 1C180Homo sapiensMutation(s): 1 
Gene Names: MIG5, RAC1, TC25
EC: 3.6.5.2
Find proteins for P63000 (Homo sapiens)
Explore P63000 
Go to UniProtKB:  P63000
NIH Common Fund Data Resources
PHAROS:  P63000
GTEx:  ENSG00000136238
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP
Download Ideal Coordinates CCD File 
 E [auth C]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
 D [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.58 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.270 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.783α = 90
b = 110.783β = 90
c = 265.628γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2011-05-11 
  • Released Date: 2012-01-18 
    • Deposition Author(s): Zhang, X., He, H.

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2012-02-01
    Changes: Database references