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

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Basic information

Entry
Database: PDB / ID: 6tkz
TitleCrystal structure of the DHR2 domain of DOCK10 in complex with CDC42
Components
  • Cell division control protein 42 homolog
  • Dedicator of cytokinesis protein 10
KeywordsSIGNALING PROTEIN / guanine nucleotide exchange factor / cytoskeleton / actin / cryoEM
Function / homology
Function and homology information


marginal zone B cell differentiation / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / 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 ...marginal zone B cell differentiation / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / 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 / host-mediated perturbation of viral process / cardiac conduction system development / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / establishment of Golgi localization / GTP-dependent protein binding / adherens junction organization / regulation of Rho protein signal transduction / 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 / positive regulation of filopodium assembly / Wnt signaling pathway, planar cell polarity pathway / phagocytosis, engulfment / RHOV GTPase cycle / nuclear migration / regulation of mitotic nuclear division / small GTPase-mediated signal transduction / Myogenesis / heart contraction / establishment of cell polarity / positive regulation of cytokinesis / spindle midzone / establishment or maintenance of cell polarity / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / RHO GTPases activate PAKs / B cell homeostasis / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / regulation of postsynapse assembly / RHOG GTPase cycle / positive regulation of GTPase activity / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / RAC1 GTPase cycle / 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 / actin filament organization / guanyl-nucleotide exchange factor activity / EGFR downregulation / small monomeric GTPase / integrin-mediated signaling pathway / FCGR3A-mediated phagocytosis / regulation of actin cytoskeleton organization / MAPK6/MAPK4 signaling / filopodium / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / small GTPase binding / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / endocytosis / G beta:gamma signalling through CDC42 / apical part of cell / mitotic spindle / cell-cell junction / ubiquitin protein ligase activity / intracellular protein localization / Factors involved in megakaryocyte development and platelet production / G protein activity / actin cytoskeleton organization
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / 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: 2.64 Å
AuthorsBarford, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/6 United Kingdom
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Sep 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: atom_site / citation_author ...atom_site / citation_author / entity_src_gen / pdbx_database_status / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _citation_author.identifier_ORCID / _entity_src_gen.gene_src_common_name / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.version / _struct_mon_prot_cis.pdbx_omega_angle
Description: Atomic clashes
Details: Replaced Lys16 of Chain C with a stub. Density for the Lys 16 side chain is ambiguous leading to refinement problems.
Provider: author / Type: Coordinate replacement
Revision 2.1Jan 31, 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)149,0627
Polymers148,0834
Non-polymers9783
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-31 kcal/mol
Surface area26390 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-30 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.170, 97.170, 312.000
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: 53083.465 Da / Num. of mol.: 2
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
#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: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
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: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2009
RadiationMonochromator: single bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.6→82.48 Å / Num. obs: 45143 / % possible obs: 99.9 % / Redundancy: 7.76 % / Biso Wilson estimate: 48.63 Å2 / Rsym value: 0.114 / Net I/av σ(I): 6.47 / Net I/σ(I): 6.47
Reflection shellResolution: 2.6→2.74 Å / Num. unique obs: 6562 / Rsym value: 0.35

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Processing

Software
NameVersionClassification
PHENIXdev_4620refinement
PHENIXdev_4620refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WM9

2wm9


Resolution: 2.64→82.48 Å / SU ML: 0.3341 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2778
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2744 2277 5.04 %
Rwork0.2121 42866 -
obs0.2153 45143 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.75 Å2
Refinement stepCycle: LAST / Resolution: 2.64→82.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9284 0 62 238 9584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00859543
X-RAY DIFFRACTIONf_angle_d1.001312961
X-RAY DIFFRACTIONf_chiral_restr0.05371470
X-RAY DIFFRACTIONf_plane_restr0.00871653
X-RAY DIFFRACTIONf_dihedral_angle_d8.5411313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.690.33971470.26962622X-RAY DIFFRACTION99.93
2.69-2.760.35821420.23962602X-RAY DIFFRACTION100
2.76-2.830.32521400.22712608X-RAY DIFFRACTION99.96
2.83-2.90.311430.23122630X-RAY DIFFRACTION100
2.9-2.990.33991330.24422659X-RAY DIFFRACTION99.96
2.99-3.080.31761530.26012597X-RAY DIFFRACTION99.96
3.08-3.190.35441390.25912690X-RAY DIFFRACTION99.86
3.19-3.320.33091390.23572609X-RAY DIFFRACTION99.93
3.32-3.470.25081400.21792681X-RAY DIFFRACTION100
3.47-3.660.29041240.20382652X-RAY DIFFRACTION99.96
3.66-3.890.25211440.21292704X-RAY DIFFRACTION100
3.89-4.190.26371410.19192679X-RAY DIFFRACTION100
4.19-4.610.25441580.17572698X-RAY DIFFRACTION100
4.61-5.270.23621460.18532712X-RAY DIFFRACTION99.83
5.27-6.640.26771420.22692759X-RAY DIFFRACTION99.97
6.65-82.480.23281460.22964X-RAY DIFFRACTION99.68

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