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- PDB-8i5f: Crystal structure of the DHR-2 domain of DOCK10 in complex with C... -

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Basic information

Entry
Database: PDB / ID: 8i5f
TitleCrystal structure of the DHR-2 domain of DOCK10 in complex with Cdc42 (T17N mutant)
Components
  • Cell division control protein 42 homolog
  • Dedicator of cytokinesis protein 10
KeywordsSIGNALING PROTEIN / GEF / GTPase / Rho / Cdc42 / Rac
Function / homology
Function and homology information


RAC3 GTPase cycle / CDC42 GTPase cycle / RAC2 GTPase cycle / marginal zone B cell differentiation / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / RAC1 GTPase cycle / dendritic cell migration / endothelin receptor signaling pathway involved in heart process ...RAC3 GTPase cycle / CDC42 GTPase cycle / RAC2 GTPase cycle / marginal zone B cell differentiation / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / RAC1 GTPase cycle / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / Factors involved in megakaryocyte development and platelet production / cardiac conduction system development / host-mediated perturbation of viral process / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / establishment of Golgi localization / GTP-dependent protein binding / adherens junction organization / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / regulation of lamellipodium assembly / thioesterase binding / regulation of stress fiber assembly / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / phagocytosis, engulfment / RHOV GTPase cycle / nuclear migration / small GTPase-mediated signal transduction / regulation of mitotic nuclear division / Myogenesis / heart contraction / positive regulation of cytokinesis / spindle midzone / RHOJ GTPase cycle / establishment of cell polarity / Golgi organization / RHOQ GTPase cycle / establishment or maintenance of cell polarity / RHO GTPases activate PAKs / RHOU GTPase cycle / B cell homeostasis / CDC42 GTPase cycle / macrophage differentiation / regulation of postsynapse assembly / positive regulation of GTPase activity / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of stress fiber assembly / RAC1 GTPase cycle / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / regulation of cell migration / guanyl-nucleotide exchange factor activity / actin filament organization / small monomeric GTPase / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / filopodium / EGFR downregulation / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / small GTPase binding / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / endocytosis / apical part of cell / G beta:gamma signalling through CDC42 / mitotic spindle / ubiquitin protein ligase activity / cell-cell junction
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. / Cdc42 / 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
Cell division control protein 42 homolog / Dedicator of cytokinesis protein 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKukimoto-Niino, M. / Mishima-Tsumagari, C. / Fukui, Y. / Yokoyama, S. / Shirouzu, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
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 25, 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

Downloads & links

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Assembly

Deposited unit
A: Dedicator of cytokinesis protein 10
C: Cell division control protein 42 homolog
B: Dedicator of cytokinesis protein 10
D: Cell division control protein 42 homolog


Theoretical massNumber of molelcules
Total (without water)156,9294
Polymers156,9294
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-56 kcal/mol
Surface area55140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.718, 95.347, 171.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 56989.859 Da / Num. of mol.: 2
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 BL21 (bacteria) / References: UniProt: Q8BZN6
#2: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 21474.535 Da / Num. of mol.: 2 / Mutation: T17N, C188S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Cell (production host): Cell-free protein synthesis / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P60953, small monomeric GTPase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 8000, sodium chloride

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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: Oct 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 35850 / % possible obs: 91.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 55.34 Å2 / Rrim(I) all: 0.104 / Net I/σ(I): 15
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 3500 / Rrim(I) all: 0.614

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WM9

2wm9


Resolution: 2.8→49.07 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2964 3575 10 %
Rwork0.2257 --
obs0.2329 35761 91.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9889 0 0 32 9921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01510095
X-RAY DIFFRACTIONf_angle_d2.02113636
X-RAY DIFFRACTIONf_dihedral_angle_d12.0721331
X-RAY DIFFRACTIONf_chiral_restr0.1661509
X-RAY DIFFRACTIONf_plane_restr0.0131742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.3981150.33091178X-RAY DIFFRACTION89
2.84-2.870.37241590.29991225X-RAY DIFFRACTION92
2.87-2.910.30591250.27111226X-RAY DIFFRACTION92
2.91-2.960.35721410.2751223X-RAY DIFFRACTION92
2.96-30.37691460.26831200X-RAY DIFFRACTION92
3-3.050.32661300.24621238X-RAY DIFFRACTION92
3.05-3.110.31931410.25621218X-RAY DIFFRACTION92
3.11-3.160.31691380.25481220X-RAY DIFFRACTION90
3.16-3.220.29911320.25581214X-RAY DIFFRACTION91
3.22-3.290.36411360.26251196X-RAY DIFFRACTION89
3.29-3.360.35321300.26681222X-RAY DIFFRACTION91
3.36-3.440.34941050.26251228X-RAY DIFFRACTION90
3.44-3.530.32131410.23261173X-RAY DIFFRACTION89
3.53-3.620.30211290.22171208X-RAY DIFFRACTION90
3.62-3.730.24961390.21711181X-RAY DIFFRACTION88
3.73-3.850.30971290.20441204X-RAY DIFFRACTION88
3.85-3.980.30041360.21071171X-RAY DIFFRACTION88
3.98-4.140.25181130.19831212X-RAY DIFFRACTION88
4.14-4.330.31261350.20521198X-RAY DIFFRACTION88
4.33-4.560.25491480.18871189X-RAY DIFFRACTION89
4.56-4.850.2841400.19041207X-RAY DIFFRACTION90
4.85-5.220.25361420.18791277X-RAY DIFFRACTION93
5.22-5.740.30611510.21361321X-RAY DIFFRACTION96
5.75-6.570.28451370.23921395X-RAY DIFFRACTION100
6.58-8.270.26661600.21161404X-RAY DIFFRACTION100
8.28-49.070.27911770.2311458X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.66570.2243-0.03152.8895-0.9074.03070.2710.4708-0.275-0.68590.10941.0421-0.1927-0.813-0.35320.47280.2134-0.02480.56940.06040.8114-30.400518.632538.7485
22.4633-0.8095-0.90033.9558-2.08571.8692-0.0501-0.60520.5240.7041-0.1847-0.0091-1.3256-0.3897-0.01160.5693-0.00780.14070.470.05740.3703-12.05625.04140.8796
30.7354-1.7441-0.78674.13891.35388.27480.6721-0.2113-0.4565-0.0513-0.2852-0.51160.35871.2849-0.34951.1735-0.1601-0.09680.7173-0.08830.528854.772680.078533.9716
41.7046-0.43010.93010.61081.42515.59620.274-1.1178-0.13731.0976-0.5026-0.9488-0.54430.14420.29341.2101-0.4023-0.10211.0678-0.05341.154155.823582.84635.6332
52.7411.04761.46913.394-0.2541.68740.5686-1.05710.73852.6087-0.3043-1.1829-0.92130.8035-0.09222.2808-0.3056-0.38270.9887-0.01751.186569.662480.483941.6702
63.6939-0.92631.81670.99761.04054.36150.01640.48040.63431.2144-0.08860.1059-0.23050.89410.1672.1186-0.5313-0.35430.79540.04991.000160.497372.104140.4316
72.60840.41810.9043.392-0.15563.36510.04570.18010.8821-0.09070.11380.2474-0.20970.059-0.15140.2076-0.00240.01650.2230.01930.57042.262753.204714.2411
88.10122.81221.20792.80611.30310.31220.2143-0.2125-0.17-0.00320.06470.22640.10.05610.01080.1956-0.01450.10370.3757-0.05630.2829-6.112938.686621.1761
92.58450.5851-0.6684.04760.49812.8428-0.02740.5482-0.7365-0.14240.05580.11020.3993-0.2439-0.00060.303-0.0054-0.12520.2938-0.05580.4139-11.321926.013111.6607
102.0850.2497-0.51782.31550.11145.8392-0.0939-0.3386-0.6371-0.3329-0.0655-0.30520.74410.81710.08850.56880.15780.12950.57240.23761.06470.93521.982924.8521
116.78360.4544-1.06625.25552.79695.74210.3846-0.1353-0.73390.10120.1623-1.24130.03670.4764-0.45420.33280.05270.05880.43330.05620.719153.384942.706514.7786
121.21930.90690.27736.44151.85842.8201-0.2297-0.1570.0405-0.6377-0.13870.9048-0.2239-0.33640.10560.20870.0694-0.00480.4025-0.01480.547538.328341.51298.1838
133.2507-0.2375-0.94130.6432-0.58560.9270.0837-0.3312-0.45030.0898-0.01180.3441-0.06640.1143-0.10680.31370.00740.09140.2908-0.01580.381731.86942.872819.6592
147.57413.22630.2612.2647-0.35560.13540.02830.30270.29310.04350.0104-0.2321-0.0148-0.0098-0.01960.31730.00490.06410.4443-0.03920.461349.099356.978420.753
151.58440.39370.25544.0697-0.16491.96120.37020.29360.7295-0.0404-0.2434-0.0827-0.3906-0.0267-0.13690.3261-0.02740.17720.35570.03550.572654.399769.380911.1406
161.8417-0.47890.98141.62880.01635.79340.0115-0.37380.17170.16490.47520.3349-0.7392-0.8042-0.36980.9976-0.08410.51210.7676-0.10941.304841.311493.579223.5181
172.61661.9677-3.06013.3201-2.83033.7096-0.0126-0.10890.7456-0.25170.00550.51210.26890.1199-0.20310.41850.11840.15290.56650.06510.6883-12.416515.389934.221
183.8940.14950.10790.6213-0.52162.92440.678-0.14060.54810.7056-0.38620.91370.22270.1458-0.09930.5402-0.03790.14850.5392-0.09590.7632-10.629515.352530.853
197.4527-1.14681.97362.6478-1.95485.0523-0.09560.0671-0.53130.1566-0.05790.00920.1982-0.03710.32780.25260.02110.06650.27870.08410.3985-17.04279.731145.0674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 116 through 164 )
2X-RAY DIFFRACTION2chain 'C' and (resid 165 through 178 )
3X-RAY DIFFRACTION3chain 'D' and (resid 1 through 24 )
4X-RAY DIFFRACTION4chain 'D' and (resid 25 through 95 )
5X-RAY DIFFRACTION5chain 'D' and (resid 96 through 146 )
6X-RAY DIFFRACTION6chain 'D' and (resid 147 through 177 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1678 through 1845 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1846 through 1921 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1922 through 2027 )
10X-RAY DIFFRACTION10chain 'A' and (resid 2028 through 2150 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1678 through 1715 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1716 through 1805 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1806 through 1845 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1846 through 1921 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1922 through 2027 )
16X-RAY DIFFRACTION16chain 'B' and (resid 2028 through 2150 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 25 )
18X-RAY DIFFRACTION18chain 'C' and (resid 26 through 64 )
19X-RAY DIFFRACTION19chain 'C' and (resid 65 through 115 )

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