6FAE | pdb_00006fae

The Sec7 domain of IQSEC2 (Brag1) in complex with the small GTPase Arf1

• PDB DOI: https://doi.org/10.2210/pdb6FAE/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-15 Released: 2018-01-17 
• Deposition Author(s): Gray, J., Krojer, T., Fairhead, M., Bountra, C., Arrowsmith, C.H., Edwards, A., Brennan, P., von Delft, F.
• Funding Organization(s): Nuffield Department of Medicine, University of Oxford

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.285 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Literature

Targeting the Small GTPase Superfamily through their Regulatory Proteins.

Gray, J.L., von Delft, F., Brennan, P.

(2019) Angew Chem Int Ed Engl 

• PubMed: 30869179 
• DOI: https://doi.org/10.1002/anie.201900585
• Primary Citation Related Structures: 
  6FAE


• PubMed Abstract: 
  

  The Ras superfamily of small GTPases are guanine-nucleotide-dependent switches essential for numerous cellular processes. Mutations or dysregulation of these proteins are associated with many diseases, but unsuccessful attempts to target the small GTPases directly have resulted in them being classed as "undruggable". The GTP-dependent signaling of these proteins is controlled by their regulators; guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), and in the Rho and Rab subfamilies, guanine nucleotide dissociation inhibitors (GDIs). This review covers the recent small molecule and biologics strategies to target the small GTPases through their regulators. It seeks to critically re-evaluate recent chemical biology practice, such as the presence of PAINs motifs and the cell-based readout using compounds that are weakly potent or of unknown specificity. It highlights the vast scope of potential approaches for targeting the small GTPases in the future through their regulatory proteins.

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Oxford, NDMRB, Old Road Campus, Oxford, OX3 7DQ, UK.
Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7FZ, UK.
Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.
Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa.
Alzheimer's Research (UK) Oxford Drug Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 67.45 kDa 
• Atom Count: 4,017 
• Modeled Residue Count: 492 
• Deposited Residue Count: 584 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IQ motif and SEC7 domain-containing protein 2	A	371	Homo sapiens	Mutation(s): 0  Gene Names: IQSEC2, KIAA0522
UniProt & NIH Common Fund Data Resources
Find proteins for Q5JU85 (Homo sapiens) Explore Q5JU85  Go to UniProtKB:  Q5JU85
PHAROS:  Q5JU85 GTEx:  ENSG00000124313

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor 1	B	213	Homo sapiens	Mutation(s): 0  Gene Names: ARF1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P84077 (Homo sapiens) Explore P84077  Go to UniProtKB:  P84077
PHAROS:  P84077 GTEx:  ENSG00000143761

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.285 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.995	α = 90
b = 92.744	β = 105.53
c = 66.895	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Gray, J., Krojer, T., Fairhead, M., Bountra, C., Arrowsmith, C.H., Edwards, A., Brennan, P., von Delft, F.

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Funding Organization	Location	Grant Number
Nuffield Department of Medicine, University of Oxford	United Kingdom	--

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2019-04-24
  Changes: Data collection, Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references