6GVC | pdb_00006gvc

Structure of ArhGAP12 bound to G-Actin

• PDB DOI: https://doi.org/10.2210/pdb6GVC/pdb

• Classification: HYDROLASE
• Organism(s): Oryctolagus cuniculus, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-20 Released: 2019-03-27 
• Deposition Author(s): Mouilleron, S., Treisman, R., Diring, J.
• Funding Organization(s): European Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

RPEL-family rhoGAPs link Rac/Cdc42 GTP loading to G-actin availability.

Diring, J., Mouilleron, S., McDonald, N.Q., Treisman, R.

(2019) Nat Cell Biol 21: 845-855

• PubMed: 31209295 
• DOI: https://doi.org/10.1038/s41556-019-0337-y
• Primary Citation Related Structures: 
  6GVC


• PubMed Abstract: 
  

  RPEL proteins, which contain the G-actin-binding RPEL motif, coordinate cytoskeletal processes with actin dynamics. We show that the ArhGAP12- and ArhGAP32-family GTPase-activating proteins (GAPs) are RPEL proteins. We determine the structure of the ArhGAP12/G-actin complex, and show that G-actin contacts the RPEL motif and GAP domain sequences. G-actin inhibits ArhGAP12 GAP activity, and this requires the G-actin contacts identified in the structure. In B16 melanoma cells, ArhGAP12 suppresses basal Rac and Cdc42 activity, F-actin assembly, invadopodia formation and experimental metastasis. In this setting, ArhGAP12 mutants defective for G-actin binding exhibit more effective downregulation of Rac GTP loading following HGF stimulation and enhanced inhibition of Rac-dependent processes, including invadopodia formation. Potentiation or disruption of the G-actin/ArhGAP12 interaction, by treatment with the actin-binding drugs latrunculin B or cytochalasin D, has corresponding effects on Rac GTP loading. The interaction of G-actin with RPEL-family rhoGAPs thus provides a negative feedback loop that couples Rac activity to actin dynamics.

---

Organizational Affiliation: 
• Signalling and Transcription Group, The Francis Crick Institute, London, UK.
Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK.
Signalling and Structural Biology Group, The Francis Crick Institute, London, UK.
Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, UK.
Signalling and Transcription Group, The Francis Crick Institute, London, UK. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 279.27 kDa 
• Atom Count: 18,354 
• Modeled Residue Count: 2,308 
• Deposited Residue Count: 2,432 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A [auth B], B [auth A], C, D	377	Oryctolagus cuniculus	Mutation(s): 0  EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho GTPase-activating protein 12	E [auth R], F [auth Q], G [auth S], H [auth T]	231	Mus musculus	Mutation(s): 0  Gene Names: Arhgap12
UniProt & NIH Common Fund Data Resources
Find proteins for Q8C0D4 (Mus musculus) Explore Q8C0D4  Go to UniProtKB:  Q8C0D4
IMPC:  MGI:1922665

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	K [auth B], O [auth A], S [auth C], W [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
LAB	J [auth B], N [auth A], R [auth C], V [auth D]	LATRUNCULIN B C20 H29 N O5 S NSHPHXHGRHSMIK-JRIKCGFMSA-N
EDO	AA [auth S], BA [auth S], I [auth B], M [auth A], Q [auth C], U [auth D], Y [auth R], Z [auth Q]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	L [auth B], P [auth A], T [auth C], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.65	α = 90
b = 130.24	β = 111.17
c = 109.3	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Mouilleron, S., Treisman, R., Diring, J.

---

Funding Organization	Location	Grant Number
European Research Council	United Kingdom	268690

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2019-10-23
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description