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- PDB-5w7i: X-ray structure of ankyrin repeat domain of DHHC17 in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w7i | ||||||
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Title | X-ray structure of ankyrin repeat domain of DHHC17 in complex with Snap25b peptide | ||||||
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![]() | PROTEIN BINDING / Palmitoyltransferases / Snap25 / ankyrin repeat domain | ||||||
Function / homology | ![]() regulation of neurotrophin TRK receptor signaling pathway / protein-cysteine S-myristoyltransferase activity / protein-cysteine S-stearoyltransferase activity / Toxicity of botulinum toxin type C (botC) / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / neurotransmitter uptake / Toxicity of botulinum toxin type E (botE) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane ...regulation of neurotrophin TRK receptor signaling pathway / protein-cysteine S-myristoyltransferase activity / protein-cysteine S-stearoyltransferase activity / Toxicity of botulinum toxin type C (botC) / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / neurotransmitter uptake / Toxicity of botulinum toxin type E (botE) / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / extrinsic component of presynaptic membrane / Acetylcholine Neurotransmitter Release Cycle / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / Toxicity of botulinum toxin type A (botA) / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptic vesicle fusion to presynaptic active zone membrane / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / palmitoyltransferase activity / ribbon synapse / synaptic vesicle docking / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / regulation of programmed cell death / SNARE complex / SNAP receptor activity / Glutamate Neurotransmitter Release Cycle / Golgi-associated vesicle membrane / neurotransmitter receptor internalization / Sensory processing of sound by inner hair cells of the cochlea / syntaxin-1 binding / SNARE complex assembly / lipoprotein transport / synaptic vesicle priming / regulation of synapse assembly / regulation of neuron projection development / endosomal transport / Other interleukin signaling / myosin binding / exocytosis / voltage-gated potassium channel activity / synaptic vesicle exocytosis / associative learning / regulation of insulin secretion / tertiary granule membrane / long-term memory / specific granule membrane / axonal growth cone / presynaptic active zone membrane / voltage-gated potassium channel complex / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / photoreceptor inner segment / axonogenesis / regulation of ERK1 and ERK2 cascade / filopodium / locomotory behavior / cell projection / Regulation of insulin secretion / long-term synaptic potentiation / trans-Golgi network / positive regulation of insulin secretion / calcium-dependent protein binding / actin cytoskeleton / synaptic vesicle / lamellipodium / presynaptic membrane / cell cortex / growth cone / postsynapse / chemical synaptic transmission / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / cytoskeleton / endosome / neuron projection / protein domain specific binding / Golgi membrane / intracellular membrane-bounded organelle / signaling receptor binding / neuronal cell body / glutamatergic synapse / lipid binding / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Verardi, R. / Kim, J.-S. / Ghirlando, R. / Banerjee, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Substrate Recognition by the Ankyrin Repeat Domain of Human DHHC17 Palmitoyltransferase. Authors: Verardi, R. / Kim, J.S. / Ghirlando, R. / Banerjee, A. #1: ![]() Title: Structural Basis for Substrate Recognition by the Ankyrin Repeat Domain of Human DHHC17 Palmitoyltransferase Authors: Verardi, R. / Kim, J.-S. / Ghirlando, R. / Banerjee, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108 KB | Display | ![]() |
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PDB format | ![]() | 81.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.9 KB | Display | ![]() |
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Full document | ![]() | 439.8 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w7jC ![]() 3eu9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26703.416 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 984.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris-HCl pH 7.5, 12.5% PEG-6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 29948 / % possible obs: 91.8 % / Redundancy: 3.2 % / Net I/σ(I): 17.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EU9 Resolution: 2.105→19.92 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 23.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.105→19.92 Å
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Refine LS restraints |
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LS refinement shell |
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