+Open data
-Basic information
Entry | Database: PDB / ID: 1am4 | ||||||
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Title | COMPLEX BETWEEN CDC42HS.GMPPNP AND P50 RHOGAP (H. SAPIENS) | ||||||
Components |
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Keywords | COMPLEX (GTPASE-ACTIVATING/GTP-BINDING) / COMPLEX (GTPASE-ACTIVATING-GTP-BINDING) / GTPASE ACTIVATION / COMPLEX (GTPASE-ACTIVATING-GTP-BINDING) complex | ||||||
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 / 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 / RHOF GTPase cycle / regulation of stress fiber assembly / RHOD GTPase cycle / 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 / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / regulation of postsynapse organization / RND2 GTPase cycle / positive regulation of filopodium assembly / endosomal transport / regulation of mitotic nuclear division / establishment or maintenance of cell polarity / phagocytosis, engulfment / RHOV GTPase cycle / RHOB GTPase cycle / small GTPase-mediated signal transduction / heart contraction / Myogenesis / RHOJ GTPase cycle / RHOC 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 / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / 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 / GTPase activator 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Rittinger, K. / Walker, P. / Gamblin, S.J. / Smerdon, S.J. | ||||||
Citation | Journal: Nature / Year: 1997 Title: Crystal structure of a small G protein in complex with the GTPase-activating protein rhoGAP. Authors: Rittinger, K. / Walker, P.A. / Eccleston, J.F. / Nurmahomed, K. / Owen, D. / Laue, E. / Gamblin, S.J. / Smerdon, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1am4.cif.gz | 235.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1am4.ent.gz | 187.9 KB | Display | PDB format |
PDBx/mmJSON format | 1am4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/1am4 ftp://data.pdbj.org/pub/pdb/validation_reports/am/1am4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 22741.998 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: Q07960 #2: Protein | Mass: 19639.521 Da / Num. of mol.: 3 / Mutation: M501P Source method: isolated from a genetically manipulated source Details: HETERODIMER / Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P60953 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.9 / Details: pH 5.9 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. obs: 49357 / % possible obs: 97.6 % / Redundancy: 5 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 26 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 5 / % possible all: 96.5 |
Reflection | *PLUS Num. measured all: 246060 |
Reflection shell | *PLUS % possible obs: 96.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1RGP, 1MH1 Resolution: 2.7→12 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→12 Å
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Refine LS restraints |
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Software | *PLUS Name: CCP4 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.231 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_deg / Dev ideal: 2.7 |