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Open data
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Basic information
Entry | Database: PDB / ID: 7xsj | |||||||||
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Title | The structure of the Mint1/Munc18-1/syntaxin-1 complex | |||||||||
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![]() | PROTEIN BINDING / Munc18-1 / Mint1-MID / Syntaxin-1 / the Mint1-MID-Munc18-1-syntaxin-1 complex | |||||||||
Function / homology | ![]() positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / positive regulation of glutamate secretion, neurotransmission / negative regulation of SNARE complex assembly / regulation of vesicle fusion / developmental process involved in reproduction / axon target recognition / myosin head/neck binding / Other interleukin signaling / gamma-aminobutyric acid secretion ...positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / positive regulation of glutamate secretion, neurotransmission / negative regulation of SNARE complex assembly / regulation of vesicle fusion / developmental process involved in reproduction / axon target recognition / myosin head/neck binding / Other interleukin signaling / gamma-aminobutyric acid secretion / extrinsic component of presynaptic membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / synaptic vesicle fusion to presynaptic active zone membrane / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / positive regulation of norepinephrine secretion / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / positive regulation of catecholamine secretion / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / regulated exocytosis / presynaptic dense core vesicle exocytosis / negative regulation of synaptic transmission, GABAergic / synaptic vesicle docking / response to gravity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / neuromuscular synaptic transmission / platelet degranulation / synaptic vesicle maturation / vesicle docking / positive regulation of calcium ion-dependent exocytosis / chloride channel inhibitor activity / secretion by cell / SNARE complex / SNAP receptor activity / presynaptic active zone cytoplasmic component / LGI-ADAM interactions / hormone secretion / calcium-ion regulated exocytosis / actomyosin / positive regulation of mast cell degranulation / platelet alpha granule / regulation of exocytosis / neurotransmitter secretion / protein localization to membrane / ATP-dependent protein binding / presynaptic cytosol / glutamate secretion / vesicle docking involved in exocytosis / neurotransmitter transport / parallel fiber to Purkinje cell synapse / insulin secretion / long-term synaptic depression / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / syntaxin binding / synaptic vesicle priming / myosin binding / exocytosis / synaptic vesicle exocytosis / positive regulation of exocytosis / modulation of excitatory postsynaptic potential / positive regulation of excitatory postsynaptic potential / phospholipase binding / protein sumoylation / synaptic vesicle endocytosis / calcium channel inhibitor activity / endomembrane system / negative regulation of protein-containing complex assembly / presynaptic active zone membrane / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / presynaptic modulation of chemical synaptic transmission / phagocytic vesicle / SNARE binding / acrosomal vesicle / secretory granule / locomotory behavior / establishment of localization in cell / protein localization to plasma membrane / PDZ domain binding / postsynaptic density membrane / intracellular protein transport / Schaffer collateral - CA1 synapse / multicellular organism growth / terminal bouton / synaptic vesicle membrane / kinase binding / platelet aggregation / cellular response to type II interferon / calcium-dependent protein binding / synaptic vesicle / presynapse / response to estradiol / protein-macromolecule adaptor activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Feng, W. / Li, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A non-canonical target-binding site in Munc18-1 domain 3b for assembling the Mint1-Munc18-1-syntaxin-1 complex. Authors: Li, W. / Xing, Y. / Wang, Y. / Xu, T. / Song, E. / Feng, W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337.9 KB | Display | ![]() |
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PDB format | ![]() | 274.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446 KB | Display | ![]() |
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Full document | ![]() | 450.8 KB | Display | |
Data in XML | ![]() | 27.3 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jehS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 68240.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P61765 |
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#2: Protein | Mass: 28880.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P32851 |
#3: Protein | Mass: 9493.023 Da / Num. of mol.: 1 / Fragment: MID Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: O35430 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium Malonate, pH 7.0, 20% (v/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. obs: 16652 / % possible obs: 100 % / Redundancy: 25.4 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.022 / Rrim(I) all: 0.111 / Χ2: 1.352 / Net I/σ(I): 9.2 / Num. measured all: 422820 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JEH Resolution: 3.2→41.87 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.84 Å2 / Biso mean: 64.314 Å2 / Biso min: 18.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→41.87 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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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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