5UPK

CDC42 binds PAK4 via an extended GTPase-effector interface - 3 peptide: PAK4cat, PAK4-N45, CDC42


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1073/pnas.1717437115
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PAK 4
A
48Homo sapiensMutation(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
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PAK 4
B
346Homo sapiensMutation(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: 3
MoleculeChainsSequence LengthOrganismDetails
Cell division control protein 42 homolog
C
185Homo sapiensMutation(s): 1 
Gene Names: CDC42
Find proteins for P60953 (Homo sapiens)
Go to Gene View: CDC42
Go to UniProtKB:  P60953
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
C
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 58.465α = 90.00
b = 61.621β = 91.57
c = 85.791γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM102262

Revision History 

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