3QBV

Structure of designed orthogonal interaction between CDC42 and nucleotide exchange domains of intersectin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair.

Kapp, G.T., Liu, S., Stein, A., Wong, D.T., Remenyi, A., Yeh, B.J., Fraser, J.S., Taunton, J., Lim, W.A., Kortemme, T.

(2012) Proc Natl Acad Sci U S A 109: 5277-5282

  • DOI: 10.1073/pnas.1114487109
  • Primary Citation of Related Structures:  
    3QBV

  • PubMed Abstract: 

    • Signaling pathways depend on regulatory protein-protein interactions; controlling these interactions in cells has important applications for reengineering biological functions. As many regulatory proteins are modular, considerable progress in engineering signaling circuits has been made by recombining commonly occurring domains ...

    Signaling pathways depend on regulatory protein-protein interactions; controlling these interactions in cells has important applications for reengineering biological functions. As many regulatory proteins are modular, considerable progress in engineering signaling circuits has been made by recombining commonly occurring domains. Our ability to predictably engineer cellular functions, however, is constrained by complex crosstalk observed in naturally occurring domains. Here we demonstrate a strategy for improving and simplifying protein network engineering: using computational design to create orthogonal (non-crossreacting) protein-protein interfaces. We validated the design of the interface between a key signaling protein, the GTPase Cdc42, and its activator, Intersectin, biochemically and by solving the crystal structure of the engineered complex. The designed GTPase (orthoCdc42) is activated exclusively by its engineered cognate partner (orthoIntersectin), but maintains the ability to interface with other GTPase signaling circuit components in vitro. In mammalian cells, orthoCdc42 activity can be regulated by orthoIntersectin, but not wild-type Intersectin, showing that the designed interaction can trigger complex processes. Computational design of protein interfaces thus promises to provide specific components that facilitate the predictable engineering of cellular functions.

    Organizational Affiliation: 

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 42 homologA, C178Homo sapiensMutation(s): 2 
Gene Names: CDC42
EC: 3.6.5.2
Find proteins for P60953 (Homo sapiens)
Explore P60953 
Go to UniProtKB:  P60953
NIH Common Fund Data Resources
PHAROS:  P60953
GTEx:  ENSG00000070831
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Intersectin-1B, D351Homo sapiensMutation(s): 1 
Gene Names: ITSN1, ITSN, SH3D1A
Find proteins for Q15811 (Homo sapiens)
Explore Q15811 
Go to UniProtKB:  Q15811
NIH Common Fund Data Resources
PHAROS:  Q15811
GTEx:  ENSG00000205726
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
 E [auth A], F [auth C]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.46α = 90
b = 80.062β = 108.23
c = 94.591γ = 90
Software Package:
Software NamePurpose
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-03-21
    Changes: Database references
  • Version 1.2: 2012-04-18
    Changes: Database references
  • Version 1.3: 2012-04-25
    Changes: Database references