+Open data
-Basic information
Entry | Database: PDB / ID: 2wmn | ||||||
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Title | Structure of the complex between DOCK9 and Cdc42-GDP. | ||||||
Components |
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Keywords | CELL 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 / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / modulation by host of viral process / GTP-dependent protein binding / 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 / 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 / mitogen-activated protein kinase kinase kinase binding / dendritic spine morphogenesis / thioesterase binding / embryonic heart tube development / 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 / positive regulation of filopodium assembly / regulation of postsynapse organization / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / establishment or maintenance of cell polarity / small GTPase-mediated signal transduction / heart contraction / Myogenesis / RHOJ GTPase cycle / RHOQ GTPase cycle / Golgi organization / 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 / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / RAC3 GTPase cycle / spindle midzone / endomembrane system / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / phagocytic vesicle / 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 / secretory granule / positive regulation of DNA replication / filopodium / integrin-mediated signaling pathway / RHO GTPases Activate Formins / actin filament organization / 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 / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation / positive regulation of GTPase activity / VEGFA-VEGFR2 Pathway / cellular response to type II interferon Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.391 Å | ||||||
Authors | Yang, J. / Roe, S.M. / Barford, D. | ||||||
Citation | Journal: 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 |
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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wmn.cif.gz | 135.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wmn.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/2wmn ftp://data.pdbj.org/pub/pdb/validation_reports/wm/2wmn | HTTPS FTP |
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-Related structure data
Related structure data | 2wm9SC 2wmoC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 / |
#4: Water | ChemComp-HOH / |
Sequence details | ISOFORM 2 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.2 % / Description: NONE |
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Crystal grow | pH: 6 / Details: pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.2822 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2822 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.5 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WM9 Resolution: 2.391→37.454 Å / SU ML: 0.56 / σ(F): 1.35 / Phase error: 27.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage 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 |
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Refinement step | Cycle: LAST / Resolution: 2.391→37.454 Å
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Refine LS restraints |
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LS refinement shell |
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