Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71816.43 
• Atom Count: 3639 
• Residue Count: 638 
• Unique protein chains: 2

5UPL

CDC42 binds PAK4 via an extended GTPase-effector inteface - 2 peptide: PAK4FL, CDC42 - UNREFINED

• DOI: 10.2210/pdb5UPL/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2017-02-03 Released: 2017-12-27 
• Deposition Author(s): Ha, B.H., Boggon, T.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.003 Å
• R-Value Free: 0.310 
• R-Value Work: 0.257 

Literature

CDC42 binds PAK4 via an extended GTPase-effector interface.

Ha, B.H., Boggon, T.J.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 531-536

• PubMed: 29295922 
• DOI: 10.1073/pnas.1717437115
• Primary Citation of Related Structures:  
  5UPK


• PubMed Abstract: 
  

The p21-activated kinase (PAK) group of serine/threonine kinases are downstream effectors of RHO GTPases and play important roles in regulation of the actin cytoskeleton, cell growth, survival, polarity, and development. Here we probe the interaction of the type II PAK, PAK4, with RHO GTPases. Using solution scattering we find that the full-length PAK4 heterodimer with CDC42 adopts primarily a compact organization. X-ray crystallography reveals the molecular nature of the interaction between PAK4 and CDC42 and shows that in addition to the canonical PAK4 CDC42/RAC interactive binding (CRIB) domain binding to CDC42 there are unexpected contacts involving the PAK4 kinase C-lobe, CDC42, and the PAK4 polybasic region. These additional interactions modulate kinase activity and increase the binding affinity of CDC42 for full-length PAK4 compared with the CRIB domain alone. We therefore show that the interaction of CDC42 with PAK4 can influence kinase activity in a previously unappreciated manner.

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Organizational Affiliation: 

Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Serine/threonine-protein kinase PAK 4	A	453	Homo sapiens	Mutation(s): 0  Gene Names: PAK4 (KIAA1142) EC: 2.7.11.1
Find proteins for O96013 (Homo sapiens) Go to Gene View: PAK4 Go to UniProtKB:  O96013

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Cell division control protein 42 homolog	B	185	Homo sapiens	Mutation(s): 0  Gene Names: CDC42
Find proteins for P60953 (Homo sapiens) Go to Gene View: CDC42 Go to UniProtKB:  P60953

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.003 Å
• R-Value Free: 0.310 
• R-Value Work: 0.257 
• Space Group: P 6₃
• Diffraction Data DOI: 
  10.15785/SBGRID/532 SBGrid

Unit Cell:

Length (Å)	Angle (°)
a = 141.652	α = 90.00
b = 141.652	β = 90.00
c = 62.093	γ = 120.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-02-03 
• Released Date: 2017-12-27 
• Deposition Author(s): Ha, B.H., Boggon, T.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	R01GM102262

Revision History 

• Version 1.0: 2017-12-27
  Type: Initial release
• Version 1.1: 2018-01-17
  Type: Author supporting evidence, Database references
• Version 1.2: 2018-01-24
  Type: Database references