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Yorodumi- PDB-1gzs: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE GEF DOMAIN OF THE SA... -
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-Basic information
Entry | Database: PDB / ID: 1gzs | ||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE GEF DOMAIN OF THE SALMONELLA TYPHIMURIUM SOPE TOXIN AND HUMAN Cdc42 | ||||||
Components |
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Keywords | TOXIN/CELL CYCLE / COMPLEX (TOXIN-CELL CYCLE PROTEIN) / SOPE / CDC42 / SALMONELLA TYPHIMURIUM / GEF / TOXIN / GTP- BINDING / LIPOPROTEIN / PRENYLATION / TOXIN-CELL CYCLE complex | ||||||
Function / homology | Function and homology information GPVI-mediated activation cascade / EGFR downregulation / : / Regulation of actin dynamics for phagocytic cup formation / CD28 dependent Vav1 pathway / EPHB-mediated forward signaling / DCC mediated attractive signaling / VEGFA-VEGFR2 Pathway / Myogenesis / RHO GTPases activate KTN1 ...GPVI-mediated activation cascade / EGFR downregulation / : / Regulation of actin dynamics for phagocytic cup formation / CD28 dependent Vav1 pathway / EPHB-mediated forward signaling / DCC mediated attractive signaling / VEGFA-VEGFR2 Pathway / Myogenesis / RHO GTPases activate KTN1 / RHO GTPases activate IQGAPs / RHO GTPases activate PAKs / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / G beta:gamma signalling through CDC42 / : / Factors involved in megakaryocyte development and platelet production / : / 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 / 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 / mitogen-activated protein kinase kinase kinase binding / cell projection assembly / dendritic spine morphogenesis / thioesterase binding / embryonic heart tube development / regulation of stress fiber assembly / activation of GTPase activity / 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 / microtubule organizing center / positive regulation of filopodium assembly / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / establishment or maintenance of cell polarity / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / lamellipodium membrane / 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 / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) SALMONELLA TYPHIMURIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å | ||||||
Authors | Buchwald, G. / Friebel, A. / Galan, J.E. / Hardt, W.D. / Wittinghofer, A. / Scheffzek, K. | ||||||
Citation | Journal: Embo J. / Year: 2002 Title: Structural Basis for the Reversible Activation of a Rho Protein by the Bacterial Toxin Sope Authors: Buchwald, G. / Friebel, A. / Galan, J.E. / Hardt, W.D. / Wittinghofer, A. / Scheffzek, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gzs.cif.gz | 143.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gzs.ent.gz | 114.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/1gzs ftp://data.pdbj.org/pub/pdb/validation_reports/gz/1gzs | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.36758, -0.26308, 0.892), Vector: |
-Components
#1: Protein | Mass: 19918.832 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-178 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P25763, UniProt: P60953*PLUS #2: Protein | Mass: 18059.607 Da / Num. of mol.: 2 Fragment: GUANINE NUCTLEOTIDE EXCHANGE FACTOR (GEF-DOMAIN), RESIDUES 78-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O52623 #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 1.9 M (NH4)2SO4, 0.1 M SODIUM CITRATE PH 5.6, 2% PEG400, 0.05 M BETAINE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 40507 / % possible obs: 99.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.112 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.328 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.112 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 4737 / Rmerge(I) obs: 0.328 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.3→19.86 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 5242854.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.1614 Å2 / ksol: 0.381516 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.227 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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