4M8N

Crystal Structure of PlexinC1/Rap1B Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin.

Wang, Y.Pascoe, H.G.Brautigam, C.A.He, H.Zhang, X.

(2013) Elife 2: e01279-e01279

  • DOI: 10.7554/eLife.01279
  • Primary Citation of Related Structures:  
    4M8M, 4M8N

  • PubMed Abstract: 
  • Plexins are cell surface receptors that bind semaphorins and transduce signals for regulating neuronal axon guidance and other processes. Plexin signaling depends on their cytoplasmic GTPase activating protein (GAP) domain, which specifically inactivates the Ras homolog Rap through an ill-defined non-canonical catalytic mechanism ...

    Plexins are cell surface receptors that bind semaphorins and transduce signals for regulating neuronal axon guidance and other processes. Plexin signaling depends on their cytoplasmic GTPase activating protein (GAP) domain, which specifically inactivates the Ras homolog Rap through an ill-defined non-canonical catalytic mechanism. The plexin GAP is activated by semaphorin-induced dimerization, the structural basis for which remained unknown. Here we present the crystal structures of the active dimer of zebrafish PlexinC1 cytoplasmic region in the apo state and in complex with Rap. The structures show that the dimerization induces a large-scale conformational change in plexin, which opens the GAP active site to allow Rap binding. Plexin stabilizes the switch II region of Rap in an unprecedented conformation, bringing Gln63 in Rap into the active site for catalyzing GTP hydrolysis. The structures also explain the unique Rap-specificity of plexins. Mutational analyses support that these mechanisms underlie plexin activation and signaling. DOI:http://dx.doi.org/10.7554/eLife.01279.001.


    Organizational Affiliation

    Department of Pharmacology , University of Texas Southwestern Medical Center , Dallas , United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PlexinC1 Intracellular RegionA, B, C, D599Danio rerioMutation(s): 0 
Gene Names: Plexin C1plxnc1
UniProt
Find proteins for Q5RGW1 (Danio rerio)
Explore Q5RGW1 
Go to UniProtKB:  Q5RGW1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5RGW1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rap-1bE, F, G, H199Homo sapiensMutation(s): 0 
Gene Names: OK/SW-cl.11Rap 1BRAP1B
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61224 (Homo sapiens)
Explore P61224 
Go to UniProtKB:  P61224
PHAROS:  P61224
GTEx:  ENSG00000127314 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61224
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.276α = 91.09
b = 84.734β = 95.15
c = 138.752γ = 90.32
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2014-01-15
    Changes: Database references