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Yorodumi- PDB-2dmw: Solution structure of the LONGIN domain of Synaptobrevin-like pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dmw | ||||||
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Title | Solution structure of the LONGIN domain of Synaptobrevin-like protein 1 | ||||||
Components | synaptobrevin-like 1 variant | ||||||
Keywords | MEMBRANE PROTEIN / LONGIN domain / beta(2)-alpha-beta(3)-alpha(2) / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of protein targeting to vacuolar membrane / positive regulation of histamine secretion by mast cell / : / triglyceride transport / natural killer cell degranulation / vesicle fusion with Golgi apparatus / trans-Golgi Network Vesicle Budding / post-Golgi vesicle-mediated transport / neutrophil degranulation / eosinophil degranulation ...regulation of protein targeting to vacuolar membrane / positive regulation of histamine secretion by mast cell / : / triglyceride transport / natural killer cell degranulation / vesicle fusion with Golgi apparatus / trans-Golgi Network Vesicle Budding / post-Golgi vesicle-mediated transport / neutrophil degranulation / eosinophil degranulation / vesicle fusion / vesicle transport along microtubule / SNARE complex / SNAP receptor activity / clathrin-coated vesicle membrane / calcium-ion regulated exocytosis / Golgi to plasma membrane protein transport / platelet alpha granule / membrane organization / Interleukin-12 signaling / positive regulation of dendrite morphogenesis / SNARE complex assembly / syntaxin binding / azurophil granule membrane / Lysosome Vesicle Biogenesis / phagocytosis, engulfment / Golgi Associated Vesicle Biogenesis / endosome to lysosome transport / exocytosis / pseudopodium / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / phagocytic vesicle / hippocampal mossy fiber to CA3 synapse / SNARE binding / secretory granule membrane / secretory granule / filopodium / trans-Golgi network / phagocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / lamellipodium / apical part of cell / Clathrin-mediated endocytosis / late endosome membrane / neuron projection / lysosomal membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / cell surface / extracellular exosome / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Ohnishi, S. / Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the LONGIN domain of Synaptobrevin-like protein 1 Authors: Ohnishi, S. / Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dmw.cif.gz | 776.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dmw.ent.gz | 651.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dmw_validation.pdf.gz | 341.8 KB | Display | wwPDB validaton report |
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Full document | 2dmw_full_validation.pdf.gz | 480.3 KB | Display | |
Data in XML | 2dmw_validation.xml.gz | 49.8 KB | Display | |
Data in CIF | 2dmw_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/2dmw ftp://data.pdbj.org/pub/pdb/validation_reports/dm/2dmw | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14475.255 Da / Num. of mol.: 1 / Fragment: LONGIN domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: SYBL1 / Plasmid: P050829-06 / Production host: Cell free synthesis / References: UniProt: Q0JU02, UniProt: P51809*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.0mM protein U-15N, 13C; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |