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- PDB-1by6: Peptide of human apolipoprotein C-II -

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Basic information

Entry
Database: PDB / ID: 1by6
TitlePeptide of human apolipoprotein C-II
ComponentsAPOLIPOPROTEIN C-II
KeywordsSIGNALING 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 / very-low-density lipoprotein particle / reverse cholesterol transport / 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 / molecular function activator activity / cholesterol homeostasis / early endosome / lipid binding / extracellular space / extracellular region
Similarity search - Function
Apolipoprotein C-II / ApoC-II domain superfamily / Apolipoprotein C-II
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RELAXATION MATRIX REFINEMENT
AuthorsStorjohann, R. / Rozek, A. / Sparrow, J.T. / Cushley, R.J.
CitationJournal: 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
DepositionDec 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_nmr_exptl_sample ...pdbx_entity_src_syn / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_spectrometer.field_strength
Revision 1.4Apr 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APOLIPOPROTEIN C-II


Theoretical massNumber of molelcules
Total (without water)3,9711
Polymers3,9711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4050 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 20structures with acceptable covalent geometry
RepresentativeModel #19lowest energy

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Components

#1: Protein/peptide APOLIPOPROTEIN C-II


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D-TOCSY
131DQF-COSY
NMR detailsText: USING WATERGATE FOR WATER SUPPRESSION

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Sample preparation

DetailsContents: PERDEUTERATED SODIUM DODECYL SULFATE (SDS) IN 160 FOLD MOLAR EXCESS RELATIVE TO PEPTIDE CONCENTRATION
Solvent system: 90% H2O/10% D2O
SampleConc.: 5 mM / Component: apoC-II / Isotopic labeling: natural abundance
Sample conditionspH: 4.1 / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX 600 / Manufacturer: Bruker / Model: AMX 600 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORBRUNGERstructure solution
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 20 / Conformers submitted total number: 19

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