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- PDB-6tky: Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42 -

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Basic information

Entry
Database: PDB / ID: 6tky
TitleCrystal structure of the DHR2 domain of DOCK10 in complex with CDC42
Components
  • (Dedicator of cytokinesis protein 10) x 2
  • Cell division control protein 42 homolog
KeywordsSIGNALING PROTEIN / DOCK10 GEF CDC42 GTPase
Function / homology
Function and homology information


marginal zone B cell differentiation / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis ...marginal zone B cell differentiation / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / neuron fate determination / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / GTP-dependent protein binding / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / DCC mediated attractive signaling / adherens junction organization / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / regulation of mitotic nuclear division / establishment or maintenance of cell polarity / phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / B cell homeostasis / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / negative regulation of protein-containing complex assembly / phagocytic vesicle / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / filopodium / positive regulation of DNA replication / secretory granule / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / EGFR downregulation / positive regulation of JNK cascade / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / protein localization / G beta:gamma signalling through CDC42 / cytoplasmic ribonucleoprotein granule / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation
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. / Cdc42 / 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
Cell division control protein 42 homolog / Dedicator of cytokinesis protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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
DepositionNov 29, 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
C: Cell division control protein 42 homolog
D: Cell division control protein 42 homolog
A: Dedicator of cytokinesis protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3027
Polymers148,0264
Non-polymers2763
Water4,161231
1
B: Dedicator of cytokinesis protein 10
D: Cell division control protein 42 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0773
Polymers73,9852
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-26 kcal/mol
Surface area26310 Å2
MethodPISA
2
C: Cell division control protein 42 homolog
A: Dedicator of cytokinesis protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2264
Polymers74,0422
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-23 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.898, 96.898, 310.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-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: NA / Source: (gene. exp.) Homo sapiens (human) / Tissue: NA / Cell: NA / Cell line: NA / Gene: DOCK10, KIAA0694, ZIZ3 / Organ: NA / Variant: NA / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q96BY6
#2: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 20958.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P60953, small monomeric GTPase
#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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 25% (w/v) PEG 3350, 200 mM potassium acetate, 8% (v/v) 1,1,1,3,3,3-Hexafluoro-2-propanol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→29.83 Å / Num. obs: 49296 / % possible obs: 99.9 % / Redundancy: 7.23 % / Biso Wilson estimate: 42.35 Å2 / Rsym value: 0.126 / Net I/σ(I): 5.52
Reflection shellResolution: 2.55→2.64 Å / Num. unique obs: 5918 / Rsym value: 0.34

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Processing

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

2wm9


Resolution: 2.55→29.83 Å / SU ML: 0.3249 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.18
RfactorNum. reflection% reflection
Rfree0.2464 2495 5.06 %
Rwork0.1884 --
obs0.1913 49296 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.26 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9295 0 18 231 9544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00849505
X-RAY DIFFRACTIONf_angle_d0.928612893
X-RAY DIFFRACTIONf_chiral_restr0.05011462
X-RAY DIFFRACTIONf_plane_restr0.00561653
X-RAY DIFFRACTIONf_dihedral_angle_d14.56661296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.60.3231490.23092497X-RAY DIFFRACTION100
2.6-2.650.30191210.22972569X-RAY DIFFRACTION100
2.65-2.710.32341570.22392545X-RAY DIFFRACTION99.96
2.71-2.770.26921340.20762558X-RAY DIFFRACTION99.96
2.77-2.840.31051340.2162556X-RAY DIFFRACTION100
2.84-2.920.29781570.2072549X-RAY DIFFRACTION100
2.92-30.30461260.21012577X-RAY DIFFRACTION99.96
3-3.10.28911290.20772574X-RAY DIFFRACTION100
3.1-3.210.26421490.20282544X-RAY DIFFRACTION99.45
3.21-3.340.31641340.20112593X-RAY DIFFRACTION99.74
3.34-3.490.25161440.19562568X-RAY DIFFRACTION100
3.49-3.680.24081380.18432588X-RAY DIFFRACTION99.96
3.68-3.910.23311300.18182621X-RAY DIFFRACTION99.93
3.91-4.210.22091290.1762631X-RAY DIFFRACTION99.96
4.21-4.630.20581440.16132623X-RAY DIFFRACTION99.96
4.63-5.30.20481470.1692635X-RAY DIFFRACTION99.61
5.3-6.660.22921210.20412724X-RAY DIFFRACTION99.96
6.66-29.830.20691520.1662849X-RAY DIFFRACTION99.54

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