+Open data
-Basic information
Entry | Database: PDB / ID: 2h80 | ||||||
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Title | NMR structures of SAM domain of Deleted in Liver Cancer 2 (DLC2) | ||||||
Components | StAR-related lipid transfer protein 13 | ||||||
Keywords | LIPID BINDING PROTEIN / Helical bundle | ||||||
Function / homology | Function and homology information endothelial tube lumen extension / regulation of Rho protein signal transduction / negative regulation of cell migration involved in sprouting angiogenesis / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / endothelial cell migration / lipid droplet ...endothelial tube lumen extension / regulation of Rho protein signal transduction / negative regulation of cell migration involved in sprouting angiogenesis / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / endothelial cell migration / lipid droplet / GTPase activator activity / mitochondrial membrane / actin cytoskeleton organization / lipid binding / signal transduction / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics | ||||||
Authors | Li, H.Y. / Fung, K.L. / Jin, D.Y. / Chung, S.S. / Ko, B.C. / Sun, H.Z. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: Solution structures, dynamics, and lipid-binding of the sterile alpha-motif domain of the deleted in liver cancer 2 Authors: Li, H. / Fung, K.L. / Jin, D.Y. / Chung, S.S. / Ching, Y.P. / Ng, I.O. / Sze, K.H. / Ko, B.C. / Sun, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h80.cif.gz | 498.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h80.ent.gz | 419 KB | Display | PDB format |
PDBx/mmJSON format | 2h80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h80_validation.pdf.gz | 343.7 KB | Display | wwPDB validaton report |
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Full document | 2h80_full_validation.pdf.gz | 431.3 KB | Display | |
Data in XML | 2h80_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 2h80_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/2h80 ftp://data.pdbj.org/pub/pdb/validation_reports/h8/2h80 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9339.574 Da / Num. of mol.: 1 / Fragment: SAM domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q9Y3M8 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 1mM 15N, 13C labelled, 20mM phosphate buffer, pH 7.1, 0.05% NaN3, 4mM DTT; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 20mM phosphate / pH: 7.1 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics, torsion angle dynamics Software ordinal: 1 Details: The structure was based on 1098 NOE-derived distance constraints and 104 angel constraints from Talos | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |