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- PDB-2jq3: Structure and Dynamics of Human Apolipoprotein C-III -

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Basic information

Entry
Database: PDB / ID: 2jq3
TitleStructure and Dynamics of Human Apolipoprotein C-III
ComponentsApolipoprotein C-III
KeywordsLIPID BINDING PROTEIN / ApoCIII / dynamics / apolipoprotein / receptor
Function / homology
Function and homology information


negative regulation of high-density lipoprotein particle clearance / negative regulation of cholesterol import / chylomicron assembly / chylomicron remodeling / lipase inhibitor activity / negative regulation of very-low-density lipoprotein particle clearance / negative regulation of lipoprotein lipase activity / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / triglyceride catabolic process ...negative regulation of high-density lipoprotein particle clearance / negative regulation of cholesterol import / chylomicron assembly / chylomicron remodeling / lipase inhibitor activity / negative regulation of very-low-density lipoprotein particle clearance / negative regulation of lipoprotein lipase activity / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / triglyceride catabolic process / very-low-density lipoprotein particle assembly / negative regulation of lipid metabolic process / negative regulation of low-density lipoprotein particle clearance / negative regulation of triglyceride catabolic process / negative regulation of very-low-density lipoprotein particle remodeling / intermediate-density lipoprotein particle / negative regulation of receptor-mediated endocytosis / chylomicron remnant clearance / negative regulation of fatty acid biosynthetic process / Chylomicron remodeling / Chylomicron assembly / lipoprotein metabolic process / chylomicron / high-density lipoprotein particle remodeling / phospholipid efflux / very-low-density lipoprotein particle / reverse cholesterol transport / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / HDL remodeling / retinoid metabolic process / cholesterol efflux / triglyceride metabolic process / cholesterol binding / negative regulation of lipid catabolic process / enzyme regulator activity / Retinoid metabolism and transport / cholesterol homeostasis / phospholipid binding / collagen-containing extracellular matrix / early endosome / G protein-coupled receptor signaling pathway / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
NK-Lysin / Apolipoprotein CIII / Apolipoprotein CIII / Apolipoprotein CIII superfamily / Apolipoprotein CIII (Apo-CIII) / Helix non-globular / Special
Similarity search - Domain/homology
Apolipoprotein C-III
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsGangabadage, C.S. / Zdunek, J. / Tessari, M. / Nilsson, S. / Olivecrona, G. / Wijmenga, S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure and Dynamics of Human Apolipoprotein CIII
Authors: Gangabadage, C.S. / Zdunek, J. / Tessari, M. / Nilsson, S. / Olivecrona, G. / Wijmenga, S.S.
History
DepositionMay 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.deposit_site
Revision 1.4May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein C-III


Theoretical massNumber of molelcules
Total (without water)8,7741
Polymers8,7741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Apolipoprotein C-III / Apo-CIII / ApoC-III


Mass: 8773.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOC3 / Production host: Escherichia coli (E. coli) / References: UniProt: P02656

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CBCA(CO)NH
121HN(CA)CB
131HNCO
141HNHA
15115N NOESY HSQC
16115N HSQC NOESY HSQC

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] Apolipoprotein CIII, 180 mM [U-2H] SDS, 92% H2O/8% D2O
Solvent system: 92% H2O/8% D2O
SampleConc.: 0.5 mM / Component: Apolipoprotein CIII / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 0.3 / pH: 5.0 / Pressure: ambient / Temperature: 315.7 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.peak picking
TALOSCornilescu, Delaglio and Baxbackbone torsion angles from chemical shifts
X-PLOR NIH2.1Schwieters, Kuszewski, Tjandra and Clorerestr. md caclulations
Monte_Carlo_scriptS.Wijmenga (unpublished)monte carlo simulation to fit helical structures to experimental rdc's
Protein Constructorunder development)program for positioning helices on the micelle
Protein Constructorunder development)caclulations of hydropobic moment directions
Protein Constructorunder development)inverse kinematic for junction of helices, rdc simulation
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: Simulated annealing using IVM algorithm available within XPLOR-NIH (2.10) followed by energy minimization. IVM dynamics (XPLOR-NIH) with restraining terms: noe, cdih, jcoup, rdc and 7 ...Details: Simulated annealing using IVM algorithm available within XPLOR-NIH (2.10) followed by energy minimization. IVM dynamics (XPLOR-NIH) with restraining terms: noe, cdih, jcoup, rdc and 7 positional restraints (appr. one CA atom per helix near the middle of each helix).
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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