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Yorodumi- PDB-2a9k: Crystal structure of the C3bot-NAD-RalA complex reveals a novel t... -
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-Basic information
Entry | Database: PDB / ID: 2a9k | ||||||
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Title | Crystal structure of the C3bot-NAD-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 / positive regulation of mitochondrial fission / myosin binding ...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 / positive regulation of mitochondrial fission / myosin binding / exocytosis / NAD+-protein ADP-ribosyltransferase activity / cleavage furrow / Transferases; Glycosyltransferases; Pentosyltransferases / p38MAPK events / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / nucleotidyltransferase activity / small monomeric GTPase / G protein activity / synaptic membrane / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / Schaffer collateral - CA1 synapse / cytoplasmic vesicle membrane / receptor internalization / GDP binding / chemotaxis / ATPase binding / Ras protein signal transduction / cell cycle / 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: 1.73 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 | 2a9k.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a9k.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 2a9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a9k_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2a9k_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2a9k_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2a9k_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/2a9k ftp://data.pdbj.org/pub/pdb/validation_reports/a9/2a9k | HTTPS FTP |
-Related structure data
Related structure data | 2a78C 1g24S 1uadS C: citing same article (ref.) S: Starting model for refinement |
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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: 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 |
-Non-polymers , 4 types, 213 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-GDP / |
#5: Chemical | ChemComp-NAD / |
#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: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M ammonium citrate pH 7.0, 25% PEG 3350, 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 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 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: 1.73→20 Å / Num. all: 40078 / Num. obs: 40078 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rsym value: 0.049 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.73→1.83 Å / Mean I/σ(I) obs: 3.6 / Rsym value: 0.239 / % possible all: 62.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G24, 1UAD Resolution: 1.73→19.03 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.808 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.116 / 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: 21.023 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→19.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 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 |
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