Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 123.95 kDa 
• Atom Count: 8565 
• Modelled Residue Count: 1040 
• Deposited Residue Count: 1080 
• Unique protein chains: 2

1KI1

Guanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42

• PDB DOI: 10.2210/pdb1KI1/pdb

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


• Deposited: 2001-12-02 Released: 2002-05-29 
• Deposition Author(s): Snyder, J.T., Pruitt, W.M., Der, C.J., Sondek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.247 
• R-Value Work: 0.231 

Literature

Structural basis for the selective activation of Rho GTPases by Dbl exchange factors.

Snyder, J.T., Worthylake, D.K., Rossman, K.L., Betts, L., Pruitt, W.M., Siderovski, D.P., Der, C.J., Sondek, J.

(2002) Nat Struct Biol 9: 468-475

• PubMed: 12006984 
• DOI: 10.1038/nsb796
• Primary Citation of Related Structures:  
  1KI1, 1LB1


• PubMed Abstract: 
  

Activation of Rho-family GTPases involves the removal of bound GDP and the subsequent loading of GTP, all catalyzed by guanine nucleotide exchange factors (GEFs) of the Dbl-family. Despite high sequence conservation among Rho GTPases, Dbl proteins possess a wide spectrum of discriminatory potentials for Rho-family members. To rationalize this specificity, we have determined crystal structures of the conserved, catalytic fragments (Dbl and pleckstrin homology domains) of the exchange factors intersectin and Dbs in complex with their cognate GTPases, Cdc42 and RhoA, respectively. Structure-based mutagenesis of intersectin and Dbs reveals the key determinants responsible for promoting exchange activity in Cdc42, Rac1 and RhoA. These findings provide critical insight into the structural features necessary for the proper pairing of Dbl-exchange factors with Rho GTPases and now allow for the detailed manipulation of signaling pathways mediated by these oncoproteins in vivo.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Program in Molecular and Cellular Biophysics, Chapel Hill, North Carolina 27599, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G25K GTP-binding protein, placental isoform	A, C	188	Homo sapiens	Mutation(s): 1  Gene Names: CDC42 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P60953 (Homo sapiens) Explore P60953  Go to UniProtKB:  P60953
PHAROS:  P60953 GTEx:  ENSG00000070831

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
intersectin long form	B, D	352	Homo sapiens	Mutation(s): 0  Gene Names: ITSN1, ITSN, SH3D1A
UniProt & NIH Common Fund Data Resources
Find proteins for Q15811 (Homo sapiens) Explore Q15811  Go to UniProtKB:  Q15811
PHAROS:  Q15811 GTEx:  ENSG00000205726

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.247 
• R-Value Work: 0.231 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.37	α = 90
b = 79.23	β = 111.51
c = 116.41	γ = 90

Software Package:

Software Name	Purpose
SHELXS	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-12-02 
• Released Date: 2002-05-29 
Deposition Author(s): Snyder, J.T., Pruitt, W.M., Der, C.J., Sondek, J.

Revision History  

• Version 1.0: 2002-05-29
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations