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- PDB-8i5w: Crystal structure of the DHR-2 domain of DOCK10 in complex with Rac1 -

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Basic information

Entry
Database: PDB / ID: 8i5w
TitleCrystal structure of the DHR-2 domain of DOCK10 in complex with Rac1
Components
  • Dedicator of cytokinesis protein 10
  • Ras-related C3 botulinum toxin substrate 1
KeywordsSIGNALING PROTEIN / DOCK / GEF / DHR-2 / GTPase / RHO / RAC / CDC42
Function / homology
Function and homology information


RAC3 GTPase cycle / CDC42 GTPase cycle / RAC2 GTPase cycle / marginal zone B cell differentiation / RAC1 GTPase cycle / embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development ...RAC3 GTPase cycle / CDC42 GTPase cycle / RAC2 GTPase cycle / marginal zone B cell differentiation / RAC1 GTPase cycle / embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / regulation of hydrogen peroxide metabolic process / kinocilium / regulation of cell adhesion involved in heart morphogenesis / interneuron migration / ruffle assembly / engulfment of apoptotic cell / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / cochlea morphogenesis / Factors involved in megakaryocyte development and platelet production / regulation of neuron maturation / respiratory burst / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / positive regulation of skeletal muscle acetylcholine-gated channel clustering / GTP-dependent protein binding / dendritic spine morphogenesis / midbrain dopaminergic neuron differentiation / epithelial cell morphogenesis / regulation of neuron migration / cell projection assembly / positive regulation of bicellular tight junction assembly / ruffle organization / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / cell-cell junction organization / motor neuron axon guidance / hepatocyte growth factor receptor signaling pathway / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / Activation of RAC1 / RHO GTPases activate KTN1 / MET activates RAP1 and RAC1 / regulation of nitric oxide biosynthetic process / DCC mediated attractive signaling / Sema4D mediated inhibition of cell attachment and migration / Azathioprine ADME / hyperosmotic response / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of neutrophil chemotaxis / positive regulation of ruffle assembly / positive regulation of cell-substrate adhesion / superoxide anion generation / Wnt signaling pathway, planar cell polarity pathway / regulation of receptor signaling pathway via JAK-STAT / lamellipodium assembly / NRAGE signals death through JNK / small GTPase-mediated signal transduction / dendrite morphogenesis / Activation of RAC1 downstream of NMDARs / Rho GDP-dissociation inhibitor binding / regulation of cell size / synaptic transmission, GABAergic / positive regulation of Rho protein signal transduction / positive regulation of dendritic spine development / pericentriolar material / establishment or maintenance of cell polarity / Rac protein signal transduction / positive regulation of actin filament polymerization / B cell homeostasis / semaphorin-plexin signaling pathway / RHO GTPases activate PAKs / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / positive regulation of GTPase activity / EPH-ephrin mediated repulsion of cells / regulation of postsynapse assembly / positive regulation of focal adhesion assembly / regulation of neuronal synaptic plasticity / RHO GTPases Activate NADPH Oxidases / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus
Similarity search - Function
Dedicator of cytokinesis D, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DOCKER, Lobe A / DOCKER, Lobe B ...Dedicator of cytokinesis D, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / DHR-2, Lobe C / DHR-2, Lobe B / C2 DOCK-type domain profile. / DOCKER domain profile. / Small GTPase Rho / Small GTPase Rho domain profile. / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ras-related C3 botulinum toxin substrate 1 / Dedicator of cytokinesis protein 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.432 Å
AuthorsKukimoto-Niino, M. / Mishima-Tsumagari, C. / Ihara, K. / Fukui, Y. / Yokoyama, S. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Structural basis for the dual GTPase specificity of the DOCK10 guanine nucleotide exchange factor.
Authors: Kukimoto-Niino, M. / Ihara, K. / Mishima-Tsumagari, C. / Inoue, M. / Fukui, Y. / Yokoyama, S. / Shirouzu, M.
History
DepositionJan 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dedicator of cytokinesis protein 10
B: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9303
Polymers52,8342
Non-polymers961
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-39 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.280, 106.860, 187.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2257-

HOH

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Components

#1: Protein Dedicator of cytokinesis protein 10 / Zizimin-3


Mass: 32603.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dock10, Kiaa0694, Ziz3 / Cell (production host): Cell-free protein synthesis / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BZN6
#2: Protein Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 20230.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Cell (production host): Cell-free protein synthesis / Production host: Escherichia coli (E. coli) / References: UniProt: P63000, small monomeric GTPase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulfate, sodium cacodylate, PEG 8000, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→46.8 Å / Num. obs: 23123 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rrim(I) all: 0.331 / Net I/σ(I): 8.69
Reflection shellResolution: 2.43→2.58 Å / Rmerge(I) obs: 0.996 / Num. unique obs: 3630

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8i5f

8i5f


Resolution: 2.432→46.778 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.6 / Phase error: 31.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 3815 8.72 %
Rwork0.2195 --
obs0.2249 23116 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.432→46.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 5 144 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073719
X-RAY DIFFRACTIONf_angle_d0.8515026
X-RAY DIFFRACTIONf_dihedral_angle_d15.6722276
X-RAY DIFFRACTIONf_chiral_restr0.05559
X-RAY DIFFRACTIONf_plane_restr0.006649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.432-2.46250.33821320.30341415X-RAY DIFFRACTION97
2.4625-2.49490.37381310.2961496X-RAY DIFFRACTION100
2.4949-2.52910.37391380.27151485X-RAY DIFFRACTION100
2.5291-2.56520.29781530.25341475X-RAY DIFFRACTION100
2.5652-2.60350.30351340.24061449X-RAY DIFFRACTION100
2.6035-2.64410.3051390.2491497X-RAY DIFFRACTION100
2.6441-2.68750.31461420.26341507X-RAY DIFFRACTION100
2.6875-2.73380.361520.24651481X-RAY DIFFRACTION100
2.7338-2.78350.33031270.24911494X-RAY DIFFRACTION100
2.7835-2.83710.2971510.24461439X-RAY DIFFRACTION100
2.8371-2.8950.30311410.23251520X-RAY DIFFRACTION100
2.895-2.95790.3971380.23781455X-RAY DIFFRACTION100
2.9579-3.02670.31161430.21881499X-RAY DIFFRACTION100
3.0267-3.10240.24661380.21421454X-RAY DIFFRACTION100
3.1024-3.18620.311420.20031504X-RAY DIFFRACTION100
3.1862-3.280.28581340.21111488X-RAY DIFFRACTION100
3.28-3.38580.22311390.19661507X-RAY DIFFRACTION100
3.3858-3.50680.28721360.19441465X-RAY DIFFRACTION100
3.5068-3.64710.22961360.1921498X-RAY DIFFRACTION100
3.6471-3.81310.24851330.1941492X-RAY DIFFRACTION100
3.8131-4.0140.24731470.20551456X-RAY DIFFRACTION99
4.014-4.26530.22471360.17691481X-RAY DIFFRACTION100
4.2653-4.59440.28961610.17981468X-RAY DIFFRACTION100
4.5944-5.05620.17381430.16721498X-RAY DIFFRACTION100
5.0562-5.78670.27031420.1951459X-RAY DIFFRACTION100
5.7867-7.28620.23581490.2431480X-RAY DIFFRACTION100
7.2862-46.7780.3811580.33021474X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.351 Å / Origin y: 28.8533 Å / Origin z: -22.826 Å
111213212223313233
T0.1298 Å2-0.0076 Å20.0014 Å2-0.1206 Å2-0.0063 Å2--0.1317 Å2
L0.1701 °2-0.0974 °2-0.1837 °2-0.1301 °2-0.012 °2--0.1705 °2
S-0.0368 Å °0.0085 Å °0.0109 Å °0.0326 Å °-0.0193 Å °0.0023 Å °-0.0152 Å °-0.0064 Å °-0 Å °
Refinement TLS groupSelection details: all

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