6UKA | pdb_00006uka

Crystal structure of RHOG and ELMO complex

• PDB DOI: https://doi.org/10.2210/pdb6UKA/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-04 Released: 2020-08-12 
• Deposition Author(s): Jo, C.H., Killoran, R.C., Smith, M.J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.237 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structure of the DOCK2-ELMO1 complex provides insights into regulation of the auto-inhibited state.

Chang, L., Yang, J., Jo, C.H., Boland, A., Zhang, Z., McLaughlin, S.H., Abu-Thuraia, A., Killoran, R.C., Smith, M.J., Cote, J.F., Barford, D.

(2020) Nat Commun 11: 3464-3464

• PubMed: 32651375 
• DOI: https://doi.org/10.1038/s41467-020-17271-9
• Primary Citation Related Structures: 
  6TGB, 6TGC, 6UKA


• PubMed Abstract: 
  

  DOCK (dedicator of cytokinesis) proteins are multidomain guanine nucleotide exchange factors (GEFs) for RHO GTPases that regulate intracellular actin dynamics. DOCK proteins share catalytic (DOCK ^DHR2 ) and membrane-associated (DOCK ^DHR1 ) domains. The structurally-related DOCK1 and DOCK2 GEFs are specific for RAC, and require ELMO (engulfment and cell motility) proteins for function. The N-terminal RAS-binding domain (RBD) of ELMO (ELMO ^RBD ) interacts with RHOG to modulate DOCK1/2 activity. Here, we determine the cryo-EM structures of DOCK2-ELMO1 alone, and as a ternary complex with RAC1, together with the crystal structure of a RHOG-ELMO2 ^RBD complex. The binary DOCK2-ELMO1 complex adopts a closed, auto-inhibited conformation. Relief of auto-inhibition to an active, open state, due to a conformational change of the ELMO1 subunit, exposes binding sites for RAC1 on DOCK2 ^DHR2 , and RHOG and BAI GPCRs on ELMO1. Our structure explains how up-stream effectors, including DOCK2 and ELMO1 phosphorylation, destabilise the auto-inhibited state to promote an active GEF.

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Organizational Affiliation: 
• MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, H3T 1J4, Canada.
Department of Molecular Biology, Science III, University of Geneva, Geneva, Switzerland.
Montreal Institute of Clinical Research (IRCM), Montréal, QC, H2W 1R7, Canada.
Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada.
Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada.
Department of Anatomy and Cell Biology, McGill University, Montréal, QC, H3A 0C7, Canada.
MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 30.91 kDa 
• Atom Count: 2,097 
• Modeled Residue Count: 249 
• Deposited Residue Count: 272 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho-related GTP-binding protein RhoG	A	191	Homo sapiens	Mutation(s): 0  Gene Names: RHOG, ARHG
UniProt & NIH Common Fund Data Resources
Find proteins for P84095 (Homo sapiens) Explore P84095  Go to UniProtKB:  P84095
PHAROS:  P84095 GTEx:  ENSG00000177105

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Engulfment and cell motility protein 2	B	81	Mus musculus	Mutation(s): 0  Gene Names: Elmo2, Kiaa1834
UniProt
Find proteins for Q8BHL5 (Mus musculus) Explore Q8BHL5  Go to UniProtKB:  Q8BHL5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP (Subject of Investigation/LOI)	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.237 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.279	α = 90
b = 40.06	β = 119.71
c = 73.93	γ = 90

Software Package:

Software Name	Purpose
PHENIX	phasing
PHENIX	refinement
PROTEUM PLUS	data collection
PROTEUM PLUS	data scaling
PROTEUM PLUS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Jo, C.H., Killoran, R.C., Smith, M.J.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description