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- PDB-2wm9: Structure of the complex between DOCK9 and Cdc42. -

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Basic information

Entry
Database: PDB / ID: 2wm9
TitleStructure of the complex between DOCK9 and Cdc42.
Components
  • CELL DIVISION CONTROL PROTEIN 42 HOMOLOG
  • DEDICATOR OF CYTOKINESIS PROTEIN 9
KeywordsCELL CYCLE / POLYMORPHISM / CELL MEMBRANE / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING / ALTERNATIVE SPLICING / GUANINE-NUCLEOTIDE RELEASING FACTOR / METHYLATION / LIPOPROTEIN / COILED COIL / GTP-BINDING / GEFS / DOCK9 / CDC42 / PRENYLATION
Function / homology
Function and homology information


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 ...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 / 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 / endomembrane system / positive regulation of DNA replication / negative regulation of protein-containing complex assembly / phagocytic vesicle / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / 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 / 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 / positive regulation of GTPase activity / VEGFA-VEGFR2 Pathway
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 / Armadillo-type fold / 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 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsYang, J. / Roe, S.M. / Barford, D.
CitationJournal: Science / Year: 2009
Title: Activation of Rho Gtpases by Dock Exchange Factors is Mediated by a Nucleotide Sensor.
Authors: Yang, J. / Zhang, Z. / Roe, S.M. / Marshall, C.J. / Barford, D.
History
DepositionJun 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEDICATOR OF CYTOKINESIS PROTEIN 9
B: CELL DIVISION CONTROL PROTEIN 42 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4805
Polymers71,2042
Non-polymers2763
Water3,387188
1
A: DEDICATOR OF CYTOKINESIS PROTEIN 9
B: CELL DIVISION CONTROL PROTEIN 42 HOMOLOG
hetero molecules

A: DEDICATOR OF CYTOKINESIS PROTEIN 9
B: CELL DIVISION CONTROL PROTEIN 42 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,96010
Polymers142,4074
Non-polymers5536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area12430 Å2
ΔGint-67.51 kcal/mol
Surface area49680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.410, 93.980, 88.200
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 9 / CDC42 GUANINE NUCLEOTIDE EXCHANGE FACTOR ZIZIMIN-1 / DOCK9


Mass: 50020.320 Da / Num. of mol.: 1 / Fragment: DHR2 DOMAIN, RESIDUES 1605-1652,1676-2053
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9BZ29
#2: Protein CELL DIVISION CONTROL PROTEIN 42 HOMOLOG / G25K GTP-BINDING PROTEIN / CDC42


Mass: 21183.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P60953
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsISOFORM 2

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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: 2.33 Å3/Da / Density % sol: 47.2 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: THE PROTEIN WAS CONCENTRATED TO 6 MG/ML. CRYSTALS WERE GROWN USING HANGING DROP VAPOUR DIFFUSION. 1 UL OF COMPLEX WITH 200 MM NDSB-201 ADDED TO PROTEIN PRIOR TO CRYSTALLIZATION WAS MIXED ...Details: THE PROTEIN WAS CONCENTRATED TO 6 MG/ML. CRYSTALS WERE GROWN USING HANGING DROP VAPOUR DIFFUSION. 1 UL OF COMPLEX WITH 200 MM NDSB-201 ADDED TO PROTEIN PRIOR TO CRYSTALLIZATION WAS MIXED WITH EQUAL VOLUME OF CRYSTALLIZATION BUFFER: 14% (W/V) PEG3350,100 MM MES (PH 6.0), 200 MM AMMONIUM ACETATE, 12% GLYCEROL. CRYSTALS WERE GROWN AT 20C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 37540 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 28.28 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.8 / % possible all: 96.2

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Processing

Software
NameClassification
iMOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.2→39.463 Å / SU ML: 0.34 / σ(F): 1.17 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 3409 5 %
Rwork0.2092 --
obs0.2114 68510 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.553 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.2469 Å20 Å20 Å2
2--0.8127 Å2-0 Å2
3---5.4343 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4585 0 18 188 4791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124691
X-RAY DIFFRACTIONf_angle_d1.3256354
X-RAY DIFFRACTIONf_dihedral_angle_d17.71688
X-RAY DIFFRACTIONf_chiral_restr0.086722
X-RAY DIFFRACTIONf_plane_restr0.005819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23150.37871120.32832334X-RAY DIFFRACTION81
2.2315-2.26480.27761240.29692521X-RAY DIFFRACTION88
2.2648-2.30010.30481500.25292674X-RAY DIFFRACTION95
2.3001-2.33790.27751400.24912697X-RAY DIFFRACTION95
2.3379-2.37820.30961290.2532729X-RAY DIFFRACTION95
2.3782-2.42140.26661390.24462665X-RAY DIFFRACTION95
2.4214-2.4680.35551660.25432732X-RAY DIFFRACTION95
2.468-2.51830.29911490.23612708X-RAY DIFFRACTION95
2.5183-2.57310.33351350.22872744X-RAY DIFFRACTION96
2.5731-2.63290.25141400.22212750X-RAY DIFFRACTION96
2.6329-2.69880.26781500.20372727X-RAY DIFFRACTION96
2.6988-2.77170.2621440.20912719X-RAY DIFFRACTION96
2.7717-2.85320.27691370.2142732X-RAY DIFFRACTION96
2.8532-2.94530.31051360.22352764X-RAY DIFFRACTION96
2.9453-3.05050.26261600.20622722X-RAY DIFFRACTION96
3.0505-3.17260.25291390.20072754X-RAY DIFFRACTION96
3.1726-3.31690.24161260.19412769X-RAY DIFFRACTION97
3.3169-3.49170.21631570.18412742X-RAY DIFFRACTION97
3.4917-3.71030.21041550.1772762X-RAY DIFFRACTION97
3.7103-3.99660.20211500.18662775X-RAY DIFFRACTION97
3.9966-4.39830.25921520.16782752X-RAY DIFFRACTION97
4.3983-5.03360.21051540.17442761X-RAY DIFFRACTION97
5.0336-6.33760.22371390.1982783X-RAY DIFFRACTION97
6.3376-39.46930.15571260.18112785X-RAY DIFFRACTION97

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