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- PDB-1soh: The structure of human apolipoprotein C-II in dodecyl phosphocholine -

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Basic information

Entry
Database: PDB / ID: 1soh
TitleThe structure of human apolipoprotein C-II in dodecyl phosphocholine
ComponentsApolipoprotein C-II
KeywordsLIPID TRANSPORT
Function / homology
Function and homology information


positive regulation of very-low-density lipoprotein particle remodeling / triglyceride-rich lipoprotein particle remodeling / positive regulation of phospholipid catabolic process / positive regulation of triglyceride catabolic process / chylomicron remodeling / lipase inhibitor activity / lipoprotein lipase activator 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 / triglyceride-rich lipoprotein particle remodeling / positive regulation of phospholipid catabolic process / positive regulation of triglyceride catabolic process / chylomicron remodeling / lipase inhibitor activity / lipoprotein lipase activator 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
Apolipoprotein Cii; Chain: A; / Apolipoprotein C-II / Apolipoprotein C-II / ApoC-II domain superfamily / Apolipoprotein C-II / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Torsion angle simulated annealing with final Cartesian refinement stage
AuthorsMacRaild, C.A. / Howlett, G.J. / Gooley, P.R.
CitationJournal: Biochemistry / Year: 2004
Title: The structure and interactions of human apolipoprotein C-II in dodecyl phosphocholine
Authors: MacRaild, C.A. / Howlett, G.J. / Gooley, P.R.
History
DepositionMar 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein C-II


Theoretical massNumber of molelcules
Total (without water)8,9221
Polymers8,9221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 100Structures with minimal restraint violations and favourable non-bond energy
Representative

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Components

#1: Protein Apolipoprotein C-II / Apo-CII / ApoC-II / APC2


Mass: 8921.864 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02655

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 15N-separated TOCSY
131HNHA
141HNHB

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Sample preparation

DetailsContents: 1.8 mM U-15N apoC-II,85 mM DPC, 20 mM sodium acetate, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, F.processing
XEASY1.2Bartels, C.data analysis
CNS1Brunger, A.structure solution
CNS1Brunger, A.refinement
RefinementMethod: Torsion angle simulated annealing with final Cartesian refinement stage
Software ordinal: 1
NMR ensembleConformer selection criteria: Structures with minimal restraint violations and favourable non-bond energy
Conformers calculated total number: 100 / Conformers submitted total number: 18

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