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Open data
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Basic information
Entry | Database: PDB / ID: 5uf7 | ||||||
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Title | CRYSTAL STRUCTURE OF MUNC13-1 MUN DOMAIN | ||||||
![]() | Protein unc-13 homolog A | ||||||
![]() | EXOCYTOSIS / ALPHA HELICAL / NEUROTRANSMITTER RELEASE / SNARE MOTIF | ||||||
Function / homology | ![]() dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / regulation of synaptic vesicle priming / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / positive regulation of glutamate receptor signaling pathway / synaptic vesicle maturation / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity ...dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / regulation of synaptic vesicle priming / presynaptic dense core vesicle exocytosis / synaptic vesicle docking / positive regulation of glutamate receptor signaling pathway / synaptic vesicle maturation / presynaptic active zone cytoplasmic component / positive regulation of synaptic plasticity / innervation / positive regulation of dendrite extension / neurotransmitter secretion / regulation of short-term neuronal synaptic plasticity / regulation of amyloid precursor protein catabolic process / syntaxin-1 binding / positive regulation of neurotransmitter secretion / syntaxin binding / synaptic vesicle priming / Golgi-associated vesicle / neuromuscular junction development / spectrin binding / presynaptic active zone / synaptic vesicle exocytosis / calyx of Held / excitatory synapse / amyloid-beta metabolic process / SNARE binding / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / neuromuscular junction / terminal bouton / phospholipid binding / synaptic vesicle membrane / presynapse / presynaptic membrane / cell differentiation / calmodulin binding / protein domain specific binding / axon / glutamatergic synapse / synapse / calcium ion binding / protein-containing complex binding / protein-containing complex / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | Alternatively spliced loop between residues 1407 and 1453 has been removed, addition of two ...Alternatively spliced loop between residues 1407 and 1453 has been removed, addition of two residues (EF) as cloning artifact. | ||||||
![]() | Tomchick, D.R. / Rizo, J. / Xu, J. | ||||||
![]() | ![]() Title: Syntaxin opening by the MUN domain underlies the function of Munc13 in synaptic-vesicle priming. Authors: Yang, X. / Wang, S. / Sheng, Y. / Zhang, M. / Zou, W. / Wu, L. / Kang, L. / Rizo, J. / Zhang, R. / Xu, T. / Ma, C. #1: Journal: Elife / Year: 2016 Title: Functional synergy between the Munc13 C-terminal C1 and C2 domains. Authors: Liu, X. / Seven, A.B. / Camacho, M. / Esser, V. / Xu, J. / Trimbuch, T. / Quade, B. / Su, L. / Ma, C. / Rosenmund, C. / Rizo, J. #2: ![]() Title: The Crystal Structure of a Munc13 C-terminal Module Exhibits a Remarkable Similarity to Vesicle Tethering Factors Authors: Li, W. / Ma, C. / Guan, R. / Xu, Y. / Tomchick, D.R. / Rizo, J. | ||||||
History |
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Remark 0 | This entry reflects an alternative modeling of the original data in 4Y21, determined by: Yang, X.Y. ...This entry reflects an alternative modeling of the original data in 4Y21, determined by: Yang, X.Y., Wang, S., Sheng, Y., Zhang, M., Zou, W.J., Wu, L.J., Kang, L.J., Rizo, J., Zhang, R.G., Xu, T., Ma, C. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 323.6 KB | Display | ![]() |
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PDB format | ![]() | 270 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.4 KB | Display | ![]() |
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Full document | ![]() | 436.3 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ue8C ![]() 3swhS C: citing same article ( S: Starting model for refinement |
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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: 62849.934 Da / Num. of mol.: 1 / Fragment: MUN DOMAIN (UNP residues 942-1407 and 1453-1531) Mutation: Removal of alternatively spliced loop between residues 1407 and 1453, addition of two residues (EF) as cloning artifact. Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.95 Å3/Da / Density % sol: 79.33 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 4Y21. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.2 M Mg(NO3)2, 0.1 M MES pH 5.8 - 6.3, 0.15 M NaCl, 18-25% PEG 3350, 10% glycerol, 5 mM DTT, 30% ethylene glycol PH range: 5.8-6.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2011 / Details: MONOCHROMATOR |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.896→39.018 Å / Num. obs: 34107 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 85.4 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 2.896→2.95 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 1.95 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SWH Resolution: 2.896→39.018 Å / SU ML: 0.38 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 293.18 Å2 / Biso mean: 112.1631 Å2 / Biso min: 45.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.896→39.018 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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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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