[English] 日本語
Yorodumi
- PDB-6tm1: Crystal structure of the DHR2 domain of DOCK10 in complex with RAC3 -

+
Open data


ID or keywords:

Loading...

-
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


postsynaptic actin cytoskeleton organization / marginal zone B cell differentiation / cerebral cortex GABAergic interneuron development / regulation of neutrophil migration / NADPH oxidase complex / regulation of neuron maturation / respiratory burst / cortical cytoskeleton organization / regulation of Rho protein signal transduction / dendritic spine morphogenesis ...postsynaptic actin cytoskeleton organization / marginal zone B cell differentiation / cerebral cortex GABAergic interneuron development / regulation of neutrophil migration / NADPH oxidase complex / regulation of neuron maturation / respiratory burst / cortical cytoskeleton organization / regulation of Rho protein signal transduction / dendritic spine morphogenesis / cell projection assembly / motor neuron axon guidance / PCP/CE pathway / positive regulation of cell adhesion mediated by integrin / neuromuscular process controlling balance / small GTPase-mediated signal transduction / synaptic transmission, GABAergic / filamentous actin / establishment or maintenance of cell polarity / Rac protein signal transduction / B cell homeostasis / CDC42 GTPase cycle / regulation of postsynapse assembly / positive regulation of GTPase activity / RAC2 GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / endomembrane system / homeostasis of number of cells within a tissue / regulation of cell migration / actin filament organization / guanyl-nucleotide exchange factor activity / small monomeric GTPase / cell periphery / cell chemotaxis / regulation of actin cytoskeleton organization / small GTPase binding / Wnt signaling pathway / calcium-dependent protein binding / regulation of cell shape / lamellipodium / G protein activity / Factors involved in megakaryocyte development and platelet production / growth cone / actin cytoskeleton organization / cytoplasmic vesicle / dendritic spine / cytoskeleton / postsynapse / neuron projection / intracellular signal transduction / neuronal cell body / GTPase activity / endoplasmic reticulum membrane / protein kinase binding / GTP binding / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / membrane / plasma membrane / cytoplasm / cytosol
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 / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C ...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 / 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 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more