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- PDB-6tm1: Crystal structure of the DHR2 domain of DOCK10 in complex with RAC3 -

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Basic information

Entry
Database: PDB / ID: 6tm1
TitleCrystal structure of the DHR2 domain of DOCK10 in complex with RAC3
Components
  • (Dedicator of cytokinesis protein 10) x 2
  • Ras-related C3 botulinum toxin substrate 3
KeywordsSIGNALING PROTEIN / DOCK10 GEF RAC3 GTPase
Function / homology
Function and homology information


cerebral cortex GABAergic interneuron development / marginal zone B cell differentiation / regulation of neuron maturation / regulation of neutrophil migration / postsynaptic actin cytoskeleton organization / NADPH oxidase complex / engulfment of apoptotic cell / cortical cytoskeleton organization / respiratory burst / dendritic spine morphogenesis ...cerebral cortex GABAergic interneuron development / marginal zone B cell differentiation / regulation of neuron maturation / regulation of neutrophil migration / postsynaptic actin cytoskeleton organization / NADPH oxidase complex / engulfment of apoptotic cell / cortical cytoskeleton organization / respiratory burst / dendritic spine morphogenesis / cell projection assembly / PCP/CE pathway / synaptic transmission, GABAergic / motor neuron axon guidance / positive regulation of cell adhesion mediated by integrin / establishment or maintenance of cell polarity / small GTPase-mediated signal transduction / Rac protein signal transduction / filamentous actin / neuromuscular process controlling balance / B cell homeostasis / CDC42 GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / endomembrane system / positive regulation of substrate adhesion-dependent cell spreading / homeostasis of number of cells within a tissue / regulation of cell migration / RAC1 GTPase cycle / cell chemotaxis / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / actin filament organization / cell periphery / regulation of actin cytoskeleton organization / small GTPase binding / Wnt signaling pathway / positive regulation of GTPase activity / calcium-dependent protein binding / lamellipodium / Factors involved in megakaryocyte development and platelet production / regulation of cell shape / growth cone / cytoplasmic vesicle / actin cytoskeleton organization / dendritic spine / cytoskeleton / neuron projection / intracellular signal transduction / GTPase activity / neuronal cell body / glutamatergic synapse / GTP binding / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DOCK DHR2 domain, lobe A / DOCK DHR2 domain, lobe C / Dedicator of cytokinesis D, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe C / DHR-2, Lobe B ...DOCK DHR2 domain, lobe A / DOCK DHR2 domain, lobe C / Dedicator of cytokinesis D, C2 domain / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe C / DHR-2, Lobe B / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / C2 DOCK-type domain profile. / DOCKER domain profile. / Small GTPase Rho / small GTPase Rho family profile. / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ras-related C3 botulinum toxin substrate 3 / Dedicator of cytokinesis protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.71 Å
AuthorsBarford, D. / Fan, D. / Cronin, N. / Yang, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: Biorxiv / Year: 2022
Title: Structural basis for CDC42 and RAC activation by the dual specificity GEF DOCK10
Authors: Fan, D. / Yang, J. / Cronin, N. / Barford, D.
History
DepositionDec 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Dedicator of cytokinesis protein 10
A: Ras-related C3 botulinum toxin substrate 3
C: Dedicator of cytokinesis protein 10


Theoretical massNumber of molelcules
Total (without water)127,5163
Polymers127,5163
Non-polymers00
Water0
1
B: Dedicator of cytokinesis protein 10
A: Ras-related C3 botulinum toxin substrate 3

C: Dedicator of cytokinesis protein 10


Theoretical massNumber of molelcules
Total (without water)127,5163
Polymers127,5163
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area5280 Å2
ΔGint-39 kcal/mol
Surface area49250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.079, 128.455, 215.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 53026.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ...Details: STPELRRTWLESMAKIHARNGDLSEAAMCYIHIAALIAEYLKRKGYWKVEKICTASLLSEDTHPCDSNSLLTTPSGGSMFSMGWPAFLSITPNIKEEGAMKEDSGMQDTPYNENILVEQLYMCVEFLWKSERYELIADVNKPIIAVFEKQRDFKKLSDLYYDIHRSYLKVAEVVNSEKRLFGRYYRVAFYGQGFFEE EEGKEYIYKEPKLTGLSEISQRLLKLYADKFGADNVKIIQDSNKVNPKDLDPKYAYIQVTYVTPFFEEKEIEDRKTDFEMHHNINRFVFETPFTLSGKKH GGVAEQCKRRTILTTSHLFPYVKKRIQVISQSSTELNPIEVAIDEMSKKVSELNQLCTMEEVDMIRLQLKLQGSVSVKVNAGPMAYARAFLEETNAKKYP DNQVKLLKEIFRQFADACGQ ALDVNERLIK EDQLEYQEEL RSHYKDMLSE LSTVMNEQIT
Source: (gene. exp.) Homo sapiens (human) / Gene: DOCK10, KIAA0694, ZIZ3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q96BY6
#2: Protein Ras-related C3 botulinum toxin substrate 3 / p21-Rac3


Mass: 21405.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P60763
#3: Protein Dedicator of cytokinesis protein 10 / Zizimin-3


Mass: 53083.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOCK10, KIAA0694, ZIZ3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q96BY6

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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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 25% (w/v) PEG 1500, 100 mM MMT. MMT buffer is produced by mixing DL-malic acid, MES and Tris base in the molar ratios of 1:2:2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.71→29.6 Å / Num. obs: 29674 / % possible obs: 95.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 151.85 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.61
Reflection shellResolution: 3.71→3.85 Å / Rmerge(I) obs: 0.3 / Num. unique obs: 1515

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WM9,2C2H

2wm9

2c2h


Resolution: 3.71→29.6 Å / SU ML: 0.6511 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 38.1002
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3211 1484 5 %
Rwork0.2595 28190 -
obs0.2624 29674 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 148.82 Å2
Refinement stepCycle: LAST / Resolution: 3.71→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6775 0 0 0 6775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046907
X-RAY DIFFRACTIONf_angle_d0.82299474
X-RAY DIFFRACTIONf_chiral_restr0.04831134
X-RAY DIFFRACTIONf_plane_restr0.00681245
X-RAY DIFFRACTIONf_dihedral_angle_d14.11991037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.71-3.830.43721230.392178X-RAY DIFFRACTION81.39
3.83-3.970.39921330.35552574X-RAY DIFFRACTION96.44
3.97-4.130.37461290.34112663X-RAY DIFFRACTION98.03
4.13-4.310.37891310.34012642X-RAY DIFFRACTION98.47
4.32-4.540.36231470.30092582X-RAY DIFFRACTION97.01
4.54-4.820.40781550.292575X-RAY DIFFRACTION96.23
4.83-5.20.36611460.29262580X-RAY DIFFRACTION97.01
5.2-5.720.36721590.30622630X-RAY DIFFRACTION98.17
5.72-6.540.35581150.29482637X-RAY DIFFRACTION97.31
6.54-8.20.30641130.23822543X-RAY DIFFRACTION94.69
8.21-29.60.21171330.16972586X-RAY DIFFRACTION95.87

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