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Yorodumi- PDB-2ngr: TRANSITION STATE COMPLEX FOR GTP HYDROLYSIS BY CDC42: COMPARISONS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ngr | ||||||
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Title | TRANSITION STATE COMPLEX FOR GTP HYDROLYSIS BY CDC42: COMPARISONS OF THE HIGH RESOLUTION STRUCTURES FOR CDC42 BOUND TO THE ACTIVE AND CATALYTICALLY COMPROMISED FORMS OF THE CDC42-GAP. | ||||||
Components |
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Keywords | HYDROLASE / TRANSITION STATE / G-PROTEIN / GAP / CDC42 / ALF3. | ||||||
Function / homology | Function and homology information negative regulation of endocytic recycling / 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 ...negative regulation of endocytic recycling / 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 / transferrin transport / 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 / cardiac conduction system development / Inactivation of CDC42 and RAC1 / establishment of Golgi localization / leading edge membrane / regulation of filopodium assembly / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / mitogen-activated protein kinase kinase kinase binding / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / embryonic heart tube development / thioesterase binding / RHOF GTPase cycle / regulation of stress fiber assembly / RHOD GTPase cycle / RHO GTPases activate KTN1 / nuclear migration / regulation of lamellipodium assembly / adherens junction organization / sprouting angiogenesis / DCC mediated attractive signaling / regulation of small GTPase mediated signal transduction / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / RND2 GTPase cycle / positive regulation of filopodium assembly / regulation of postsynapse organization / endosomal transport / regulation of mitotic nuclear division / RHOV GTPase cycle / establishment or maintenance of cell polarity / RHOB GTPase cycle / small GTPase-mediated signal transduction / phagocytosis, engulfment / heart contraction / positive regulation of DNA replication / Myogenesis / RHOC GTPase cycle / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / Rho protein signal transduction / macrophage differentiation / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / 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 / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / EGFR downregulation / small monomeric GTPase / G protein activity / secretory granule / filopodium / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / positive regulation of JNK cascade Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Nassar, N. / Hoffman, G. / Clardy, J. / Cerione, R. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Structures of Cdc42 bound to the active and catalytically compromised forms of Cdc42GAP. Authors: Nassar, N. / Hoffman, G.R. / Manor, D. / Clardy, J.C. / Cerione, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ngr.cif.gz | 95 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ngr.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ngr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ngr_validation.pdf.gz | 462.5 KB | Display | wwPDB validaton report |
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Full document | 2ngr_full_validation.pdf.gz | 466.5 KB | Display | |
Data in XML | 2ngr_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 2ngr_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/2ngr ftp://data.pdbj.org/pub/pdb/validation_reports/ng/2ngr | HTTPS FTP |
-Related structure data
Related structure data | 1grnSC 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 21283.582 Da / Num. of mol.: 1 Fragment: FULL-LENGTH CDC42 IN COMPLEX WITH A C-TERMINAL ACTIVE DOMAIN OF CDC42GAP(R305A) MUTANT. Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: HIS-TAG FUSION PROTEIN; / Cellular location: CYTOPLASM / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P60953 |
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#2: Protein | Mass: 26451.281 Da / Num. of mol.: 1 Fragment: FULL-LENGTH CDC42 IN COMPLEX WITH A C-TERMINAL ACTIVE DOMAIN OF CDC42GAP(R305A) MUTANT. Mutation: R305A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: HIS-TAG FUSION PROTEIN / Cellular location: CYTOPLASM / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q07960 |
-Non-polymers , 4 types, 104 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-GDP / |
#5: Chemical | ChemComp-AF3 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Type: ADSC / Detector: CCD / Date: Mar 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 394559 / % possible obs: 99.4 % / Redundancy: 9.7 % / Rsym value: 0.098 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.9→2 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.32 / % possible all: 99.6 |
Reflection | *PLUS Num. obs: 40680 / Num. measured all: 394559 / Rmerge(I) obs: 0.098 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GRN Resolution: 1.9→22 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THE ALF3 MOLECULE WAS RESTRAINED TO BE PLANAR
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 22 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.414 |