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- PDB-6uka: Crystal structure of RHOG and ELMO complex -

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Basic information

Entry
Database: PDB / ID: 6uka
TitleCrystal structure of RHOG and ELMO complex
Components
  • Engulfment and cell motility protein 2ELMO2
  • Rho-related GTP-binding protein RhoG
KeywordsSIGNALING PROTEIN / RHOG / ELMO / RBD / complex / CELL ADHESION
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / : / regulation of ruffle assembly / neutrophil degranulation / regulation of neutrophil migration / engulfment of apoptotic cell / Regulation of actin dynamics for phagocytic cup formation / cortical cytoskeleton organization / cell projection assembly ...small GTPase binding => GO:0031267 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / : / regulation of ruffle assembly / neutrophil degranulation / regulation of neutrophil migration / engulfment of apoptotic cell / Regulation of actin dynamics for phagocytic cup formation / cortical cytoskeleton organization / cell projection assembly / VEGFA-VEGFR2 Pathway / activation of GTPase activity / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of small GTPase mediated signal transduction / establishment or maintenance of cell polarity / Rac protein signal transduction / Rho protein signal transduction / phagocytosis / GPVI-mediated activation cascade / cell chemotaxis / secretory granule membrane / actin filament organization / cell projection / cell motility / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / cell-cell adhesion / receptor tyrosine kinase binding / SH3 domain binding / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / cell cortex / regulation of cell shape / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / actin cytoskeleton organization / vesicle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / focal adhesion / intracellular membrane-bounded organelle / GTPase activity / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / protein kinase binding / positive regulation of DNA-templated transcription / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rho-related GTP-binding protein RhoG / Engulfment and cell motility protein 2 / ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / Pleckstrin homology domain / Small GTPase Rho / small GTPase Rho family profile. ...Rho-related GTP-binding protein RhoG / Engulfment and cell motility protein 2 / ELMO domain / ELMO/CED-12 family / ELMO domain profile. / ELMO, armadillo-like helical domain / ELMO, armadillo-like helical domain / Pleckstrin homology domain / Small GTPase Rho / small GTPase Rho family profile. / Pleckstrin homology domain / Small GTPase / Ras family / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Rho-related GTP-binding protein RhoG / Engulfment and cell motility protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJo, C.H. / Killoran, R.C. / Smith, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the DOCK2-ELMO1 complex provides insights into regulation of the auto-inhibited state.
Authors: Leifu Chang / Jing Yang / Chang Hwa Jo / Andreas Boland / Ziguo Zhang / Stephen H McLaughlin / Afnan Abu-Thuraia / Ryan C Killoran / Matthew J Smith / Jean-Francois Côté / David Barford /
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) ...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) and membrane-associated (DOCK) 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) 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 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, 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.
History
DepositionOct 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho-related GTP-binding protein RhoG
B: Engulfment and cell motility protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9134
Polymers30,3672
Non-polymers5472
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, Kd value = 8
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.279, 40.060, 73.930
Angle α, β, γ (deg.)90.000, 119.710, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Rho-related GTP-binding protein RhoG


Mass: 21334.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOG, ARHG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: P84095
#2: Protein Engulfment and cell motility protein 2 / ELMO2 / Protein ced-12 homolog A


Mass: 9032.248 Da / Num. of mol.: 1 / Fragment: Ras-binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Elmo2, Kiaa1834 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8BHL5
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M CHES, 0.95M sodium citrate / PH range: 8.5 - 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.34165 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34165 Å / Relative weight: 1
ReflectionResolution: 2.4→27.01 Å / Num. obs: 38996 / % possible obs: 93.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 17.88 Å2 / Rmerge(I) obs: 0.1131 / Net I/σ(I): 13.42
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.2591 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 466 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998phasing
PHENIX1.13_2998refinement
PROTEUM PLUSdata collection
PROTEUM PLUSdata scaling
PROTEUM PLUSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A2B

1a2b


Resolution: 2.4→27.01 Å / SU ML: 0.2833 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4928
RfactorNum. reflection% reflection
Rfree0.2366 1820 10.04 %
Rwork0.1856 --
obs0.1909 18135 92.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.54 Å2
Refinement stepCycle: LAST / Resolution: 2.4→27.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 33 126 2097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342013
X-RAY DIFFRACTIONf_angle_d0.6442755
X-RAY DIFFRACTIONf_chiral_restr0.0552317
X-RAY DIFFRACTIONf_plane_restr0.0033350
X-RAY DIFFRACTIONf_dihedral_angle_d15.91671198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.29461340.23261215X-RAY DIFFRACTION89.1
2.46-2.540.3081420.25081261X-RAY DIFFRACTION92.91
2.54-2.620.34121350.23731246X-RAY DIFFRACTION92.75
2.62-2.710.31511380.23981270X-RAY DIFFRACTION94.05
2.71-2.820.27081340.23381227X-RAY DIFFRACTION90.55
2.82-2.950.27411360.24071194X-RAY DIFFRACTION88.43
2.95-3.10.29291360.21231206X-RAY DIFFRACTION88.52
3.1-3.30.22381380.19471216X-RAY DIFFRACTION91.06
3.3-3.550.26911380.17491282X-RAY DIFFRACTION93.79
3.55-3.910.19241500.16021275X-RAY DIFFRACTION94.87
3.91-4.470.19231480.13321306X-RAY DIFFRACTION97.06
4.47-5.630.17781470.13681302X-RAY DIFFRACTION96.6
5.63-27.010.17331440.15571315X-RAY DIFFRACTION96.62

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