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- EMDB-10498: CryoEM structure of the ternary DOCK2-ELMO1-RAC1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-10498
TitleCryoEM structure of the ternary DOCK2-ELMO1-RAC1 complex
Map data
SampleTernary complex of DOCK2-ELMO1-RAC1
  • Dedicator of cytokinesis protein 2
  • Engulfment and cell motility protein 1ELMO1
  • Ras-related C3 botulinum toxin substrate 1
Function / homology
Function and homology information


alpha-beta T cell proliferation / membrane raft polarization / myeloid dendritic cell activation involved in immune response / establishment of T cell polarity / guanyl-nucleotide exchange factor complex / regulation of respiratory burst / macropinocytosis / regulation of neutrophil migration / localization within membrane / regulation of hydrogen peroxide metabolic process ...alpha-beta T cell proliferation / membrane raft polarization / myeloid dendritic cell activation involved in immune response / establishment of T cell polarity / guanyl-nucleotide exchange factor complex / regulation of respiratory burst / macropinocytosis / regulation of neutrophil migration / localization within membrane / regulation of hydrogen peroxide metabolic process / Rac guanyl-nucleotide exchange factor activity / negative regulation of interleukin-23 production / engulfment of apoptotic cell / immunological synapse formation / negative regulation of receptor-mediated endocytosis / mast cell chemotaxis / Rho GDP-dissociation inhibitor binding / Rac protein signal transduction / negative thymic T cell selection / ruffle assembly / cortical cytoskeleton organization / cell projection assembly / ruffle organization / regulation of nitric oxide biosynthetic process / small monomeric GTPase / positive thymic T cell selection / positive regulation of neutrophil chemotaxis / hepatocyte growth factor receptor signaling pathway / thioesterase binding / motor neuron axon guidance / regulation of lamellipodium assembly / positive regulation of cell-substrate adhesion / positive regulation of Rho protein signal transduction / positive regulation of lamellipodium assembly / lamellipodium assembly / semaphorin-plexin signaling pathway / regulation of stress fiber assembly / regulation of cell size / small GTPase mediated signal transduction / establishment or maintenance of cell polarity / anatomical structure morphogenesis / ficolin-1-rich granule membrane / positive regulation of microtubule polymerization / positive regulation of focal adhesion assembly / Rho protein signal transduction / Wnt signaling pathway, planar cell polarity pathway / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of small GTPase mediated signal transduction / bone resorption / positive regulation of substrate adhesion-dependent cell spreading / cell motility / Rab GTPase binding / positive regulation of stress fiber assembly / regulation of cell migration / substrate adhesion-dependent cell spreading / regulation of actin cytoskeleton organization / positive regulation of phagocytosis / actin filament polymerization / cell-matrix adhesion / positive regulation of DNA replication / GTPase activator activity / cell projection / T cell receptor binding / secretory granule membrane / actin filament organization / phagocytosis, engulfment / T cell costimulation / ruffle membrane / cytoplasmic ribonucleoprotein granule / neuron migration / ephrin receptor signaling pathway / trans-Golgi network / actin cytoskeleton organization / regulation of defense response to virus by virus / response to wounding / SH3 domain binding / recycling endosome membrane / cell population proliferation / postsynapse / cell cortex / melanosome / histone deacetylase binding / vascular endothelial growth factor receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / specific granule lumen / cellular response to mechanical stimulus / chemotaxis / Fc-epsilon receptor signaling pathway / lamellipodium / cell migration / cytoplasmic vesicle / ATPase binding / regulation of cell shape / dendritic spine / blood coagulation / cytoskeleton / intracellular signal transduction / GTPase activity / cell adhesion / inflammatory response
Small GTP-binding protein domain / DHR-2 domain / Small GTPase Rho / Pleckstrin homology domain / Dedicator of cytokinesis, C-terminal / Small GTPase / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold / SH3 domain ...Small GTP-binding protein domain / DHR-2 domain / Small GTPase Rho / Pleckstrin homology domain / Dedicator of cytokinesis, C-terminal / Small GTPase / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold / SH3 domain / Domain of unknown function DUF3361 / Dedicator of cytokinesis / Dedicator of cytokinesis protein 2 / DHR-1 domain / P-loop containing nucleoside triphosphate hydrolase / ELMO domain / Engulfment and cell motility protein 1 / Dedicator of cytokinesis, N-terminal domain / C2 domain superfamily / SH3-like domain superfamily / Dedicator of cytokinesis, N-terminal, subdomain 1 / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C
Ras-related C3 botulinum toxin substrate 1 / Engulfment and cell motility protein 1 / Dedicator of cytokinesis protein 2
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsChang L / Yang J / Chang JH / Zhang Z / Boland A / McLaughlin SH / Abu-Thuraia A / Killoran RC / Smith MJ / Cote JF / Barford D
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/6 United Kingdom
Marie Sklodowska-Curie Actions, FragNET ITN657725 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
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.
Validation ReportPDB-ID: 6tgc

SummaryFull reportAbout validation report
History
DepositionNov 15, 2019-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-6tgc
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tgc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10498.map.gz / Format: CCP4 / Size: 85.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 282 pix.
= 403.26 Å
1.43 Å/pix.
x 282 pix.
= 403.26 Å
1.43 Å/pix.
x 282 pix.
= 403.26 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.07212933 - 0.17415883
Average (Standard dev.)-0.000120875775 (±0.003674054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions282282282
Spacing282282282
CellA=B=C: 403.25998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z282282282
origin x/y/z0.0000.0000.000
length x/y/z403.260403.260403.260
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS282282282
D min/max/mean-0.0720.174-0.000

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Supplemental data

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Additional map: #1

Fileemd_10498_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Ternary complex of DOCK2-ELMO1-RAC1

EntireName: Ternary complex of DOCK2-ELMO1-RAC1 / Number of components: 4

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Component #1: protein, Ternary complex of DOCK2-ELMO1-RAC1

ProteinName: Ternary complex of DOCK2-ELMO1-RAC1 / Recombinant expression: No
MassTheoretical: 600 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #2: protein, Dedicator of cytokinesis protein 2

ProteinName: Dedicator of cytokinesis protein 2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 195.902516 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: protein, Engulfment and cell motility protein 1

ProteinName: Engulfment and cell motility protein 1ELMO1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 83.891328 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #4: protein, Ras-related C3 botulinum toxin substrate 1

ProteinName: Ras-related C3 botulinum toxin substrate 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.478113 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL / pH: 8
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Energy filter: GIF Quantum ER
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 245763
3D reconstructionSoftware: RELION / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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