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Yorodumi- PDB-2yqm: Solution structure of the FYVE domain in zinc finger FYVE domain-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yqm | ||||||
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Title | Solution structure of the FYVE domain in zinc finger FYVE domain-containing protein 12 | ||||||
Components | RUN and FYVE domain-containing protein 1 | ||||||
Keywords | PROTEIN TRANSPORT / FYVE domain / zinc finger FYVE domain-containing protein 12 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information small GTPase-mediated signal transduction / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / SH2 domain binding / SH3 domain binding / endocytosis / protein transport / early endosome membrane / endosome / nuclear speck ...small GTPase-mediated signal transduction / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / SH2 domain binding / SH3 domain binding / endocytosis / protein transport / early endosome membrane / endosome / nuclear speck / intracellular membrane-bounded organelle / lipid binding / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | He, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the FYVE domain in zinc finger FYVE domain-containing protein 12 Authors: He, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yqm.cif.gz | 526 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yqm.ent.gz | 438.3 KB | Display | PDB format |
PDBx/mmJSON format | 2yqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yqm_validation.pdf.gz | 344.8 KB | Display | wwPDB validaton report |
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Full document | 2yqm_full_validation.pdf.gz | 463.8 KB | Display | |
Data in XML | 2yqm_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 2yqm_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/2yqm ftp://data.pdbj.org/pub/pdb/validation_reports/yq/2yqm | 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: 9866.173 Da / Num. of mol.: 1 / Fragment: FYVE domain, UNP residues 627-708 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: RUFY1 / Plasmid: P060327-08 / References: UniProt: Q96T51 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.0mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH 7.0); 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: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |