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- PDB-8i5v: DOCK10 mutant L1903Y complexed with Rac1 -

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Basic information

Entry
Database: PDB / ID: 8i5v
TitleDOCK10 mutant L1903Y complexed 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 / cerebral cortex GABAergic interneuron 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 / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / positive regulation of ovarian follicle development / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis / ruffle assembly / interneuron migration / NTRK2 activates RAC1 / Factors involved in megakaryocyte development and platelet production / NADPH oxidase complex / cochlea morphogenesis / Inactivation of CDC42 and RAC1 / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / regulation of neuron maturation / respiratory burst / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / positive regulation of skeletal muscle acetylcholine-gated channel clustering / ruffle organization / dendritic spine morphogenesis / epithelial cell morphogenesis / midbrain dopaminergic neuron differentiation / positive regulation of bicellular tight junction assembly / GTP-dependent protein binding / regulation of Rho protein signal transduction / cell projection assembly / thioesterase binding / regulation of lamellipodium assembly / negative regulation of fibroblast migration / regulation of neuron migration / RHO GTPases activate CIT / regulation of stress fiber assembly / cell-cell junction organization / Nef and signal transduction / motor neuron axon guidance / Activation of RAC1 / PCP/CE pathway / hepatocyte growth factor receptor signaling pathway / sphingosine-1-phosphate receptor signaling pathway / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / quinolinate biosynthetic process / DCC mediated attractive signaling / MET activates RAP1 and RAC1 / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / hyperosmotic response / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of neutrophil chemotaxis / Wnt signaling pathway, planar cell polarity pathway / superoxide anion generation / regulation of receptor signaling pathway via JAK-STAT / lamellipodium assembly / NRAGE signals death through JNK / positive regulation of ruffle assembly / dendrite morphogenesis / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / Activation of RAC1 downstream of NMDARs / positive regulation of Rho protein signal transduction / positive regulation of dendritic spine development / pericentriolar material / synaptic transmission, GABAergic / B cell homeostasis / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / semaphorin-plexin signaling pathway / RHO GTPases activate PAKs / Rac protein signal transduction / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / EPH-ephrin mediated repulsion of cells / positive regulation of GTPase activity / positive regulation of focal adhesion assembly / regulation of postsynapse assembly / RHO GTPases Activate NADPH Oxidases / anatomical structure morphogenesis / regulation of synaptic vesicle endocytosis / regulation of neuronal synaptic plasticity / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs
Similarity search - Function
DOCK6-11, TPR domain / 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 ...DOCK6-11, TPR domain / 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 / PH domain profile. / C2 domain superfamily / 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: 1.726 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)52,9803
Polymers52,8842
Non-polymers961
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-38 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.420, 107.420, 187.380
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-2500-

HOH

21A-2501-

HOH

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Components

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


Mass: 32653.939 Da / Num. of mol.: 1 / Mutation: L1903Y
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: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.87 Å3/Da / Density % sol: 57.21 %
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: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.726→46.845 Å / Num. obs: 64336 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rrim(I) all: 0.101 / Net I/σ(I): 14.6
Reflection shellResolution: 1.73→1.83 Å / Rmerge(I) obs: 0.994 / Num. unique obs: 10207

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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: 1.726→46.845 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 3819 3.09 %
Rwork0.1785 --
obs0.1794 64289 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.726→46.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 5 516 4169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063724
X-RAY DIFFRACTIONf_angle_d0.745033
X-RAY DIFFRACTIONf_dihedral_angle_d12.5522277
X-RAY DIFFRACTIONf_chiral_restr0.049558
X-RAY DIFFRACTIONf_plane_restr0.005650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.726-1.74740.33971300.33094222X-RAY DIFFRACTION97
1.7474-1.77040.35011490.32044460X-RAY DIFFRACTION100
1.7704-1.79470.28891370.29724417X-RAY DIFFRACTION100
1.7947-1.82030.29231490.27364513X-RAY DIFFRACTION100
1.8203-1.84750.32361310.26744390X-RAY DIFFRACTION100
1.8475-1.87630.36181450.26444466X-RAY DIFFRACTION100
1.8763-1.90710.28381310.24894421X-RAY DIFFRACTION100
1.9071-1.940.25841510.23164428X-RAY DIFFRACTION100
1.94-1.97530.29411450.21524481X-RAY DIFFRACTION100
1.9753-2.01330.25331460.20794409X-RAY DIFFRACTION100
2.0133-2.05440.24171540.20544506X-RAY DIFFRACTION100
2.0544-2.0990.25241300.18794431X-RAY DIFFRACTION100
2.099-2.14790.22091460.18274465X-RAY DIFFRACTION100
2.1479-2.20160.18421480.1734405X-RAY DIFFRACTION100
2.2016-2.26110.17481530.16684415X-RAY DIFFRACTION100
2.2611-2.32760.25441290.16764455X-RAY DIFFRACTION100
2.3276-2.40280.20281580.17034442X-RAY DIFFRACTION100
2.4028-2.48860.19621500.16974423X-RAY DIFFRACTION100
2.4886-2.58830.25421370.16784449X-RAY DIFFRACTION100
2.5883-2.7060.1941480.17634453X-RAY DIFFRACTION100
2.706-2.84870.21241360.17434449X-RAY DIFFRACTION100
2.8487-3.02710.20441350.16594484X-RAY DIFFRACTION100
3.0271-3.26080.19211450.15794418X-RAY DIFFRACTION100
3.2608-3.58890.16321320.15054464X-RAY DIFFRACTION100
3.5889-4.10790.16111510.14594452X-RAY DIFFRACTION100
4.1079-5.17450.15891180.13794465X-RAY DIFFRACTION100
5.1745-46.80.18971350.19494446X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.3903 Å / Origin y: 28.6735 Å / Origin z: -23.1065 Å
111213212223313233
T0.1831 Å2-0.0031 Å20.0035 Å2-0.1816 Å2-0.0088 Å2--0.1876 Å2
L0.1229 °2-0.0137 °2-0.06 °2-0.0631 °2-0.0028 °2--0.4134 °2
S-0.0365 Å °0.0408 Å °0.009 Å °0.0111 Å °0.0116 Å °-0.0036 Å °0.0056 Å °-0.002 Å °-0 Å °
Refinement TLS groupSelection details: all

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