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- PDB-6ajl: DOCK7 mutant I1836Y complexed with Cdc42 -

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Basic information

Entry
Database: PDB / ID: 6ajl
TitleDOCK7 mutant I1836Y complexed with Cdc42
Components
  • Cell division control protein 42 homolog
  • Dedicator of cytokinesis protein 7
KeywordsSIGNALING PROTEIN / DOCK / GEF / DHR-2 / GTPase / Rho / Rac / Cdc42 / mutant
Function / homology
Function and homology information


establishment of neuroblast polarity / interkinetic nuclear migration / 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 / apolipoprotein A-I receptor binding ...establishment of neuroblast polarity / interkinetic nuclear migration / 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 / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / 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 / cardiac conduction system development / host-mediated perturbation of viral process / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / basal part of cell / 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 / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / embryonic heart tube development / positive regulation of vascular associated smooth muscle cell migration / RHO GTPases activate KTN1 / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / positive regulation of filopodium assembly / Wnt signaling pathway, planar cell polarity pathway / negative regulation of cold-induced thermogenesis / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / nuclear migration / small GTPase-mediated signal transduction / Myogenesis / heart contraction / positive regulation of cytokinesis / establishment of cell polarity / spindle midzone / establishment or maintenance of cell polarity / RHOJ GTPase cycle / Golgi organization / Rac protein signal transduction / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of neurogenesis / 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 / substantia nigra development / positive regulation of substrate adhesion-dependent cell spreading / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / axonogenesis / GTPase activator activity / actin filament organization / guanyl-nucleotide exchange factor activity / EGFR downregulation / small monomeric GTPase / integrin-mediated signaling pathway / MAPK6/MAPK4 signaling / FCGR3A-mediated phagocytosis / regulation of actin cytoskeleton organization / 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 / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / endocytosis / G beta:gamma signalling through CDC42 / neuron projection development / apical part of cell
Similarity search - Function
Dedicator of cytokinesis C, C2 domain / DOCK DHR2 domain, lobe C / 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 ...Dedicator of cytokinesis C, C2 domain / DOCK DHR2 domain, lobe C / 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. / C2 domain superfamily / 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 / Small GTP-binding protein domain / 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
Cell division control protein 42 homolog / Dedicator of cytokinesis protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsKukimoto-Niino, M. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K06987 Japan
CitationJournal: Structure / Year: 2019
Title: Structural Basis for the Dual Substrate Specificity of DOCK7 Guanine Nucleotide Exchange Factor.
Authors: Kukimoto-Niino, M. / Tsuda, K. / Ihara, K. / Mishima-Tsumagari, C. / Honda, K. / Ohsawa, N. / Shirouzu, M.
History
DepositionAug 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dedicator of cytokinesis protein 7
B: Cell division control protein 42 homolog
C: Dedicator of cytokinesis protein 7
D: Cell division control protein 42 homolog
E: Dedicator of cytokinesis protein 7
F: Cell division control protein 42 homolog
G: Dedicator of cytokinesis protein 7
H: Cell division control protein 42 homolog


Theoretical massNumber of molelcules
Total (without water)221,5578
Polymers221,5578
Non-polymers00
Water00
1
A: Dedicator of cytokinesis protein 7
B: Cell division control protein 42 homolog


Theoretical massNumber of molelcules
Total (without water)55,3892
Polymers55,3892
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-24 kcal/mol
Surface area22180 Å2
MethodPISA
2
C: Dedicator of cytokinesis protein 7
D: Cell division control protein 42 homolog


Theoretical massNumber of molelcules
Total (without water)55,3892
Polymers55,3892
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-24 kcal/mol
Surface area22250 Å2
MethodPISA
3
E: Dedicator of cytokinesis protein 7
F: Cell division control protein 42 homolog


Theoretical massNumber of molelcules
Total (without water)55,3892
Polymers55,3892
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-24 kcal/mol
Surface area22360 Å2
MethodPISA
4
G: Dedicator of cytokinesis protein 7
H: Cell division control protein 42 homolog


Theoretical massNumber of molelcules
Total (without water)55,3892
Polymers55,3892
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-24 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.550, 105.290, 117.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Dedicator of cytokinesis protein 7


Mass: 33927.590 Da / Num. of mol.: 4 / Mutation: I1836Y
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: DOCK7, KIAA1771 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q96N67
#2: Protein
Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 21461.537 Da / Num. of mol.: 4 / Mutation: C188S
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P60953

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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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG3350, tri-potassium citrate monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.23→50 Å / Num. obs: 74614 / % possible obs: 99.4 % / Redundancy: 3.6 % / CC1/2: 0.991 / Rrim(I) all: 0.18 / Net I/σ(I): 7.5
Reflection shellResolution: 3.23→3.43 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 11786 / CC1/2: 0.635 / Rrim(I) all: 0.94 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AJ4

6aj4


Resolution: 3.23→48.638 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 27.5
RfactorNum. reflection% reflection
Rfree0.2587 3778 5.07 %
Rwork0.1845 --
obs0.1883 74567 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.23→48.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14700 0 0 0 14700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115040
X-RAY DIFFRACTIONf_angle_d1.24220348
X-RAY DIFFRACTIONf_dihedral_angle_d5.0649156
X-RAY DIFFRACTIONf_chiral_restr0.062244
X-RAY DIFFRACTIONf_plane_restr0.0072628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2304-3.27130.40291290.32712353X-RAY DIFFRACTION90
3.2713-3.31430.43781380.32042635X-RAY DIFFRACTION100
3.3143-3.35970.35021440.30272671X-RAY DIFFRACTION100
3.3597-3.40770.34881350.27432643X-RAY DIFFRACTION100
3.4077-3.45850.34021430.27072616X-RAY DIFFRACTION100
3.4585-3.51260.32291410.24642650X-RAY DIFFRACTION100
3.5126-3.57010.31121430.22972630X-RAY DIFFRACTION100
3.5701-3.63170.32441410.22792636X-RAY DIFFRACTION100
3.6317-3.69770.27591390.21962612X-RAY DIFFRACTION100
3.6977-3.76880.26781450.20892646X-RAY DIFFRACTION100
3.7688-3.84570.31811390.21452604X-RAY DIFFRACTION100
3.8457-3.92930.26811410.1962661X-RAY DIFFRACTION100
3.9293-4.02060.25861390.18732609X-RAY DIFFRACTION100
4.0206-4.12110.26171370.17842613X-RAY DIFFRACTION100
4.1211-4.23250.25531420.1642664X-RAY DIFFRACTION100
4.2325-4.3570.25721410.15782615X-RAY DIFFRACTION100
4.357-4.49750.20961440.14372645X-RAY DIFFRACTION100
4.4975-4.65810.20521360.14952593X-RAY DIFFRACTION100
4.6581-4.84450.23951400.14682667X-RAY DIFFRACTION100
4.8445-5.06470.25631390.15382626X-RAY DIFFRACTION100
5.0647-5.33150.2181430.14832613X-RAY DIFFRACTION100
5.3315-5.6650.26051380.16212623X-RAY DIFFRACTION99
5.665-6.10170.29311450.17652646X-RAY DIFFRACTION100
6.1017-6.71430.23241390.17322606X-RAY DIFFRACTION100
6.7143-7.68260.27671370.17052633X-RAY DIFFRACTION100
7.6826-9.66670.1561370.13342662X-RAY DIFFRACTION100
9.6667-48.6430.23951430.18622617X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 20.1907 Å / Origin y: 3.1934 Å / Origin z: 44.1978 Å
111213212223313233
T0.3153 Å2-0.0347 Å20.0121 Å2-0.4729 Å20.0074 Å2--0.4405 Å2
L0.1822 °2-0.0866 °20.1184 °2-0.2746 °20.1086 °2--0.8277 °2
S0.0591 Å °0.0571 Å °0.0069 Å °-0.052 Å °-0.0056 Å °-0.1004 Å °-0.0032 Å °0.2053 Å °-0.0608 Å °
Refinement TLS groupSelection details: all

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