7RX9 | pdb_00007rx9

Structure of autoinhibited P-Rex1

• PDB DOI: https://doi.org/10.2210/pdb7RX9/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Tequatrovirus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-08-22 Released: 2022-08-10 
• Deposition Author(s): Ellisdon, A.M., Chang, Y.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free: 
  0.262 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Structure of the metastatic factor P-Rex1 reveals a two-layered autoinhibitory mechanism.

Chang, Y.G., Lupton, C.J., Bayly-Jones, C., Keen, A.C., D'Andrea, L., Lucato, C.M., Steele, J.R., Venugopal, H., Schittenhelm, R.B., Whisstock, J.C., Halls, M.L., Ellisdon, A.M.

(2022) Nat Struct Mol Biol 29: 767-773

• PubMed: 35864164 
• DOI: https://doi.org/10.1038/s41594-022-00804-9
• Primary Citation Related Structures: 
  7RX9, 7SYF


• PubMed Abstract: 
  

  P-Rex (PI(3,4,5)P ₃ -dependent Rac exchanger) guanine nucleotide exchange factors potently activate Rho GTPases. P-Rex guanine nucleotide exchange factors are autoinhibited, synergistically activated by Gβγ and PI(3,4,5)P ₃ binding and dysregulated in cancer. Here, we use X-ray crystallography, cryogenic electron microscopy and crosslinking mass spectrometry to determine the structural basis of human P-Rex1 autoinhibition. P-Rex1 has a bipartite structure of N- and C-terminal modules connected by a C-terminal four-helix bundle that binds the N-terminal Pleckstrin homology (PH) domain. In the N-terminal module, the Dbl homology (DH) domain catalytic surface is occluded by the compact arrangement of the DH-PH-DEP1 domains. Structural analysis reveals a remarkable conformational transition to release autoinhibition, requiring a 126° opening of the DH domain hinge helix. The off-axis position of Gβγ and PI(3,4,5)P ₃ binding sites further suggests a counter-rotation of the P-Rex1 halves by 90° facilitates PH domain uncoupling from the four-helix bundle, releasing the autoinhibited DH domain to drive Rho GTPase signaling.

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Organizational Affiliation: 
• Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail].
Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria, Australia.
Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria, Australia.
EMBL Australia, Monash University, Melbourne, Victoria, Australia.
ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, cross-linking

Macromolecule Content 

• Total Structure Weight: 70.6 kDa 
• Atom Count: 3,555 
• Modeled Residue Count: 432 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein, Endolysin chimera	A	606	Homo sapiens, Tequatrovirus T4	Mutation(s): 0  Gene Names: PREX1, KIAA1415 EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
Find proteins for Q8TCU6 (Homo sapiens) Explore Q8TCU6  Go to UniProtKB:  Q8TCU6
PHAROS:  Q8TCU6 GTEx:  ENSG00000124126
UniProt Groups	Q8TCU6P00720

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.22 Å
• R-Value Free:  0.262 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.256	α = 90
b = 151.256	β = 90
c = 94.287	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Ellisdon, A.M., Chang, Y.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1128120
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1146578

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description