Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 121.93 kDa 
• Atom Count: 7068 
• Residue Count: 950 
• Unique protein chains: 2

3QBV

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

• DOI: 10.2210/pdb3QBV/pdb

• Classification: PROTEIN BINDING/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-01-14 Released: 2012-02-08 
• Deposition Author(s): Kapp, G.T., Remenyi, A., Lim, W.A., Kortemme, T.

---

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 

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

• PubMed: 22403064 
• DOI: 10.1073/pnas.1114487109
• Structures With Same Primary Citation


• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cell division control protein 42 homolog	A, C	178	Homo sapiens	Mutation(s): 2  Gene Names: CDC42 EC: 3.6.5.2
Find proteins for P60953 (Homo sapiens) Go to UniProtKB:  P60953
NIH Common Fund Data Resources
PHAROS  P60953 GTEx  ENSG00000070831

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Intersectin-1	B, D	351	Homo sapiens	Mutation(s): 1  Gene Names: ITSN1, ITSN, SH3D1A
Find proteins for Q15811 (Homo sapiens) Go to UniProtKB:  Q15811
NIH Common Fund Data Resources
PHAROS  Q15811 GTEx  ENSG00000205726

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	A, C	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

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 = 85.46	α = 90
b = 80.062	β = 108.23
c = 94.591	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-14 
• Released Date: 2012-02-08 
Deposition Author(s): Kapp, G.T., Remenyi, A., Lim, W.A., Kortemme, T.

Revision History 

• 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