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Yorodumi- PDB-2a78: Crystal structure of the C3bot-RalA complex reveals a novel type ... -
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-Basic information
Entry | Database: PDB / ID: 2a78 | ||||||
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Title | Crystal structure of the C3bot-RalA complex reveals a novel type of action of a bacterial exoenzyme | ||||||
Components |
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Keywords | PROTEIN BINDING/TRANSFERASE / exoenzyme C3 / Bacterial ADP-ribosyltransferase / Ral / Rho / GDP-binding / PROTEIN BINDING-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / Flemming body / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / myosin binding / positive regulation of mitochondrial fission ...membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / Flemming body / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / myosin binding / positive regulation of mitochondrial fission / exocytosis / NAD+-protein ADP-ribosyltransferase activity / cleavage furrow / Transferases; Glycosyltransferases; Pentosyltransferases / p38MAPK events / nucleotidyltransferase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / G protein activity / synaptic membrane / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / cytoplasmic vesicle membrane / Schaffer collateral - CA1 synapse / receptor internalization / GDP binding / chemotaxis / ATPase binding / Ras protein signal transduction / cell division / focal adhesion / GTPase activity / ubiquitin protein ligase binding / GTP binding / cell surface / signal transduction / mitochondrion / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Clostridium botulinum D phage (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Pautsch, A. / Vogelsgesang, M. / Trankle, J. / Herrmann, C. / Aktories, K. | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Crystal structure of the C3bot-RalA complex reveals a novel type of action of a bacterial exoenzyme. Authors: Pautsch, A. / Vogelsgesang, M. / Trankle, J. / Herrmann, C. / Aktories, K. #1: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Molecular recognition of an ADP-ribosylating Clostridium botulinum C3 exoenzyme by RalA GTPase. Authors: Holbourn, K.P. / Sutton, J.M. / Evans, H.R. / Shone, C.C. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a78.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a78.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 2a78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a78_validation.pdf.gz | 805.4 KB | Display | wwPDB validaton report |
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Full document | 2a78_full_validation.pdf.gz | 807.9 KB | Display | |
Data in XML | 2a78_validation.xml.gz | 19 KB | Display | |
Data in CIF | 2a78_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/2a78 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/2a78 | HTTPS FTP |
-Related structure data
Related structure data | 2a9kC 1g24S 1uadS 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
#1: Protein | Mass: 20895.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RALA, RAL / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P11233 |
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#2: Protein | Mass: 24462.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum D phage (virus) / Species: Clostridium phage c-st / Gene: C3 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P15879, Transferases; Glycosyltransferases; Pentosyltransferases |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GDP / |
#5: 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: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M ammonium sulfate, 0.1 M bis-Tris, 25% w/v polyethylene glycol 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 30, 2004 / Details: Osmic Blue |
Radiation | Monochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 39025 / Num. obs: 35816 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.059 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3978 / Rsym value: 0.345 / % possible all: 62.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G24, 1UAD Resolution: 1.81→19.57 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.338 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→19.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.806→1.852 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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