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

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Basic information

Entry
Database: PDB / ID: 2wmn
TitleStructure of the complex between DOCK9 and Cdc42-GDP.
Components
  • CELL DIVISION CONTROL PROTEIN 42 HOMOLOG
  • DEDICATOR OF CYTOKINESIS PROTEIN 9
KeywordsCELL CYCLE / ALTERNATIVE SPLICING / METHYLATION / PRENYLATION / LIPOPROTEIN / COILED COIL / GEFS / DOCK9 / CDC42 / MEMBRANE / NUCLEOTIDE / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING / GTP-BINDING / POLYMORPHISM / CELL MEMBRANE / GUANINE-NUCLEOTIDE RELEASING FACTOR
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
GUANOSINE-5'-DIPHOSPHATE / Cell division control protein 42 homolog / Dedicator of cytokinesis protein 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.391 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
DepositionJul 2, 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

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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)71,6473
Polymers71,2042
Non-polymers4431
Water3,189177
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)143,2946
Polymers142,4074
Non-polymers8862
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area11830 Å2
ΔGint-74.34 kcal/mol
Surface area49490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.050, 88.472, 90.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2020-

HOH

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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-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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 growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.2822
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 2.4→47 Å / Num. obs: 28789 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.5 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WM9

2wm9


Resolution: 2.391→37.454 Å / SU ML: 0.56 / σ(F): 1.35 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2762 1448 5 %
Rwork0.2197 --
obs0.2225 28748 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.178 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.4571 Å2-0 Å20 Å2
2---13.4304 Å2-0 Å2
3---10.9734 Å2
Refinement stepCycle: LAST / Resolution: 2.391→37.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 28 177 4751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094667
X-RAY DIFFRACTIONf_angle_d1.126335
X-RAY DIFFRACTIONf_dihedral_angle_d17.2711678
X-RAY DIFFRACTIONf_chiral_restr0.073722
X-RAY DIFFRACTIONf_plane_restr0.004812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3912-2.47670.32531270.26612524X-RAY DIFFRACTION90
2.4767-2.57580.29541420.23432631X-RAY DIFFRACTION93
2.5758-2.6930.32471590.23292591X-RAY DIFFRACTION93
2.693-2.83490.24971260.2342592X-RAY DIFFRACTION92
2.8349-3.01250.28571370.23032627X-RAY DIFFRACTION92
3.0125-3.24490.29521430.22382832X-RAY DIFFRACTION100
3.2449-3.57130.26791550.21182851X-RAY DIFFRACTION100
3.5713-4.08750.29641570.20642845X-RAY DIFFRACTION100
4.0875-5.14770.23181550.19192874X-RAY DIFFRACTION99
5.1477-37.45830.24771470.20132933X-RAY DIFFRACTION96

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