+Open data
-Basic information
Entry | Database: PDB / ID: 1by6 | ||||||
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Title | Peptide of human apolipoprotein C-II | ||||||
Components | APOLIPOPROTEIN C-II | ||||||
Keywords | SIGNALING PROTEIN / APOLIPOPROTEIN / AMPHIPATHIC HELIX / LIPID ASSOCIATION / LPL ACTIVATION | ||||||
Function / homology | Function and homology information positive regulation of very-low-density lipoprotein particle remodeling / positive regulation of phospholipid catabolic process / triglyceride-rich lipoprotein particle remodeling / positive regulation of triglyceride catabolic process / chylomicron remodeling / lipoprotein lipase activator activity / lipase inhibitor activity / negative regulation of cholesterol transport / negative regulation of very-low-density lipoprotein particle clearance / spherical high-density lipoprotein particle ...positive regulation of very-low-density lipoprotein particle remodeling / positive regulation of phospholipid catabolic process / triglyceride-rich lipoprotein particle remodeling / positive regulation of triglyceride catabolic process / chylomicron remodeling / lipoprotein lipase activator activity / lipase inhibitor activity / negative regulation of cholesterol transport / negative regulation of very-low-density lipoprotein particle clearance / spherical high-density lipoprotein particle / Assembly of active LPL and LIPC lipase complexes / negative regulation of lipid metabolic process / positive regulation of lipoprotein lipase activity / intermediate-density lipoprotein particle / chylomicron remnant clearance / negative regulation of receptor-mediated endocytosis / very-low-density lipoprotein particle remodeling / Chylomicron remodeling / Chylomicron assembly / positive regulation of fatty acid biosynthetic process / high-density lipoprotein particle clearance / chylomicron / phospholipid efflux / positive regulation of phospholipase activity / reverse cholesterol transport / very-low-density lipoprotein particle / low-density lipoprotein particle / triglyceride homeostasis / HDL remodeling / cholesterol efflux / phospholipase activator activity / phospholipase binding / lipid catabolic process / Retinoid metabolism and transport / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cholesterol homeostasis / molecular function activator activity / early endosome / lipid binding / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RELAXATION MATRIX REFINEMENT | ||||||
Authors | Storjohann, R. / Rozek, A. / Sparrow, J.T. / Cushley, R.J. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2000 Title: Structure of a biologically active fragment of human serum apolipoprotein C-II in the presence of sodium dodecyl sulfate and dodecylphosphocholine. Authors: Storjohann, R. / Rozek, A. / Sparrow, J.T. / Cushley, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1by6.cif.gz | 212.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1by6.ent.gz | 172.9 KB | Display | PDB format |
PDBx/mmJSON format | 1by6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1by6_validation.pdf.gz | 341.7 KB | Display | wwPDB validaton report |
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Full document | 1by6_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 1by6_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1by6_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/1by6 ftp://data.pdbj.org/pub/pdb/validation_reports/by/1by6 | 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/peptide | Mass: 3971.444 Da / Num. of mol.: 1 / Fragment: RESIDUES 44-79 / Source method: obtained synthetically Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED ON AN ABI 430A SYNTHESIZER (PE APPLIED BIOSYSTEMS, FOSTER CITY, CA, USA) BY THE SOLID PHASE METHOD USING T-BOC/BENZYL PROTECTING GROUPS AND A PHENYL- ...Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED ON AN ABI 430A SYNTHESIZER (PE APPLIED BIOSYSTEMS, FOSTER CITY, CA, USA) BY THE SOLID PHASE METHOD USING T-BOC/BENZYL PROTECTING GROUPS AND A PHENYL-ACETAMIDOMETHYL-POLYSTYRENE SUPPORT WITH FAST HBTU/HOBT COUPLING. AFTER SYNTHESIS THE PEPTIDE WAS DEPROTECTED AND CLEAVED FROM THE RESIN WITH TMSBR. Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P02655 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: USING WATERGATE FOR WATER SUPPRESSION |
-Sample preparation
Details | Contents: PERDEUTERATED SODIUM DODECYL SULFATE (SDS) IN 160 FOLD MOLAR EXCESS RELATIVE TO PEPTIDE CONCENTRATION Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 5 mM / Component: apoC-II / Isotopic labeling: natural abundance |
Sample conditions | pH: 4.1 / Temperature: 310 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX 600 / Manufacturer: Bruker / Model: AMX 600 / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING, RELAXATION MATRIX REFINEMENT Software ordinal: 1 Details: THE STRUCTURE OF APOC-II(44-79) IN THE PRESENCE OF SODIUM DODECYL SULFATE WAS REFINED USING A RELAXATION MATRIX REFINEMENT PROTOCOL BASED ON 241 NOESY CROSS- PEAK INTENSITIES MEASURED AT ...Details: THE STRUCTURE OF APOC-II(44-79) IN THE PRESENCE OF SODIUM DODECYL SULFATE WAS REFINED USING A RELAXATION MATRIX REFINEMENT PROTOCOL BASED ON 241 NOESY CROSS- PEAK INTENSITIES MEASURED AT SEVEN DIFFERENT NOESY MIXING TIMES BETWEEN 75 MS AND 300 MS. NO DIHEDRAL RESTRAINTS WERE USED. THIS ENTRY CONTAINS 19 ACCEPTED STRUCTURES. ONE CALCULATED STRUCTURE WAS REJECTED BECAUSE OF HIGH COVALENT ENERGY. STRUCTURE CALCULATIONS WERE PERFORMED WITH THE PROGRAM X-PLOR (AXEL BRUNGER) INCLUDING DISTANCE GEOMETRY CALCULATIONS, SIMULATED ANNEALING (BOTH UNDER THE ISOLATED SPIN PAIR APPROXIMATION AND COMPLETE RELAXATION MATRIX CALCULATIONS) AS WELL AS ENERGY MINIMIZATION WITH A CONJUGATED GRADIENT. THE CHARMM FORCEFIELD WAS USED. FOR DETAILS ON STRUCTURE CALCULATION PLEASE SEE REFERENCE CITED UNDER "JRNL". | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry Conformers calculated total number: 20 / Conformers submitted total number: 19 |