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Yorodumi- PDB-2dnx: Solution structure of RSGI RUH-063, an N-terminal domain of Synta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dnx | ||||||
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Title | Solution structure of RSGI RUH-063, an N-terminal domain of Syntaxin 12 from human cDNA | ||||||
Components | Syntaxin-12 | ||||||
Keywords | TRANSPORT PROTEIN / syntaxin / SNARE / Habc domain / up and down three helix bundle / left-handed twist / membrane fusion / vesicle transport / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information : / postsynaptic recycling endosome / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / phagophore assembly site / cholesterol efflux / autophagosome assembly / endomembrane system ...: / postsynaptic recycling endosome / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / phagophore assembly site / cholesterol efflux / autophagosome assembly / endomembrane system / phagocytic vesicle / SNARE binding / intracellular protein transport / recycling endosome membrane / synaptic vesicle / early endosome membrane / vesicle / membrane => GO:0016020 / protein stabilization / membrane raft / Golgi membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Abe, T. / Hirota, H. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of RSGI RUH-063, an N-terminal domain of Syntaxin 12 from human cDNA Authors: Abe, T. / Hirota, H. / Muto, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dnx.cif.gz | 781.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dnx.ent.gz | 656.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dnx_validation.pdf.gz | 350.4 KB | Display | wwPDB validaton report |
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Full document | 2dnx_full_validation.pdf.gz | 510.9 KB | Display | |
Data in XML | 2dnx_validation.xml.gz | 56.8 KB | Display | |
Data in CIF | 2dnx_validation.cif.gz | 70.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/2dnx ftp://data.pdbj.org/pub/pdb/validation_reports/dn/2dnx | 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: 14348.924 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 8-124 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: STX12 / Plasmid: P050302-94 / Production host: Cell free synthesis / References: UniProt: Q86Y82 |
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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: 1.35mM RSGI RUH-063 U-15N, 13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O 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: JEOL AVANCE / Manufacturer: JEOL / 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, target function | ||||||||||||||||||||||||
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 |