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Yorodumi- PDB-8bav: Secretagogin (human) in complex with its target peptide from SNAP-25 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bav | ||||||
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Title | Secretagogin (human) in complex with its target peptide from SNAP-25 | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / Protein complex | ||||||
Function / homology | Function and homology information Toxicity of botulinum toxin type C (botC) / 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 ...Toxicity of botulinum toxin type C (botC) / 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 / ribbon synapse / synaptic vesicle docking / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / regulation of presynaptic cytosolic calcium ion concentration / SNARE complex / SNAP receptor activity / Glutamate Neurotransmitter Release Cycle / neurotransmitter receptor internalization / Sensory processing of sound by inner hair cells of the cochlea / regulation of long-term synaptic potentiation / syntaxin-1 binding / SNARE complex assembly / synaptic vesicle priming / transport vesicle membrane / 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 / photoreceptor inner segment / bioluminescence / axonogenesis / filopodium / generation of precursor metabolites and energy / locomotory behavior / Regulation of insulin secretion / long-term synaptic potentiation / trans-Golgi network / positive regulation of insulin secretion / terminal bouton / calcium-dependent protein binding / actin cytoskeleton / synaptic vesicle / lamellipodium / presynaptic membrane / cell cortex / growth cone / postsynapse / chemical synaptic transmission / transmembrane transporter binding / cytoskeleton / endosome / neuron projection / protein domain specific binding / neuronal cell body / glutamatergic synapse / lipid binding / synapse / calcium ion binding / dendrite / Neutrophil degranulation / perinuclear region of cytoplasm / extracellular region / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Aequorea victoria (jellyfish) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Schnell, R. / Szodorai, E. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: A hydrophobic groove in secretagogin allows for alternate interactions with SNAP-25 and syntaxin-4 in endocrine tissues. Authors: Szodorai, E. / Hevesi, Z. / Wagner, L. / Hokfelt, T.G.M. / Harkany, T. / Schnell, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bav.cif.gz | 225 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bav.ent.gz | 177.2 KB | Display | PDB format |
PDBx/mmJSON format | 8bav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bav_validation.pdf.gz | 478 KB | Display | wwPDB validaton report |
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Full document | 8bav_full_validation.pdf.gz | 484.7 KB | Display | |
Data in XML | 8bav_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 8bav_validation.cif.gz | 58.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/8bav ftp://data.pdbj.org/pub/pdb/validation_reports/ba/8bav | HTTPS FTP |
-Related structure data
Related structure data | 8banSC 8bbjC 1emaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 28980.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GFP was engineered to carry the target peptide for the binding interaction. GFP-fusion protein carrying a short peptide from human SNAP25 (sequence: GIIGNLRHMALDMGNEIDTQNRQID) on its C- ...Details: GFP was engineered to carry the target peptide for the binding interaction. GFP-fusion protein carrying a short peptide from human SNAP25 (sequence: GIIGNLRHMALDMGNEIDTQNRQID) on its C-terminus. The Chromophore of GFP is formed from residues Ser65-Tyr66-Gly67, and represented as non-peptide residue CRO (Chromophore / Fluorophore). This alteration results in an apparent mismatch when comparing the encoded polypeptide sequence (present in datbases) and the residues present in the PDB file. Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human) Gene: GFP, SNAP25, SNAP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212, UniProt: P60880 #2: Protein | Mass: 32085.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCGN, SECRET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76038 |
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-Non-polymers , 4 types, 433 molecules
#3: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-144 / | #6: 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: 2.15 Å3/Da / Density % sol: 42.91 % / Description: rod |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M Na-acetate 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97996 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2020 / Details: Toroidal Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97996 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→41.36 Å / Num. obs: 47592 / % possible obs: 99.8 % / Observed criterion σ(I): 1.9 / Redundancy: 4.5 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.079 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.702 / Num. unique obs: 4599 / CC1/2: 0.601 / Rpim(I) all: 0.545 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EMA, 8BAN Resolution: 2.3→41.36 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.713 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→41.36 Å
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