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- PDB-1o8t: Global Structure and Dynamics of Human Apolipoprotein CII in Comp... -

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Basic information

Entry
Database: PDB / ID: 1o8t
TitleGlobal Structure and Dynamics of Human Apolipoprotein CII in Complex with Micelles: Evidence for increased mobility of the helix involved in the activation of lipoprotein lipase
ComponentsAPOLIPOPROTEIN C-II
KeywordsLIPID TRANSPORT / APOCII / LPL / ACTIVATION MECHANISM / DOMAIN MOTION / SDS / MICELLE / GLOBAL STRUCTURE / LOCAL STRUCTURE / DYNAMICS / HELIX / LIPID DEGRADATION / CHYLOMICRON
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 / RESTRAINT MOLECULAR DYNAMICS
AuthorsZdunek, J. / Martinez, G.V. / Schleucher, J. / Lycksell, P.O. / Yin, Y. / Nilsson, S. / Shen, Y. / Olivecrona, G. / Wijmenga, S.
CitationJournal: Biochemistry / Year: 2003
Title: Global Structure and Dynamics of Human Apolipoprotein Cii in Complex with Micelles: Evidence for Increased Mobility of the Helix Involved in the Activation of Lipoprotein Lipase
Authors: Zdunek, J. / Martinez, G.V. / Schleucher, J. / Lycksell, P.O. / Yin, Y. / Nilsson, S. / Shen, Y. / Olivecrona, G. / Wijmenga, S.
History
DepositionNov 29, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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)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)68 / 100LEAST ENERGY, LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein APOLIPOPROTEIN C-II / APO-CII


Mass: 8921.864 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Plasmid: PET29A-HAPOCII / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02655
Compound detailsAPOC-II IS A COMPONENT OF THE VERY LOW DENSITY LIPOPROTEIN (VLDL) FUNCTIONS AS AN ACTIVATOR OF ...APOC-II IS A COMPONENT OF THE VERY LOW DENSITY LIPOPROTEIN (VLDL) FUNCTIONS AS AN ACTIVATOR OF SEVERAL TRIACYLGLYCEROL LIPASES.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: CBCANHCBCA(CO)NHCBCACO(N) HHNCOSPIN-LOCK HCANHHCC(CO) NH1H-15N NOESY-HSQC2D NOESY1H-15N HNHA15N T115N T215N-{1H} NOE

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Sample preparation

Sample conditionsIonic strength: 10 MM ACETIC ACID 380 MM SDS / pH: 4.5 / Pressure: 1 atm / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AMXBrukerAMX5002
Bruker DRXBrukerDRX4003

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
XEASYstructure solution
SYBYLstructure solution
X-PLORstructure solution
CNSstructure solution
RefinementMethod: RESTRAINT MOLECULAR DYNAMICS / Software ordinal: 1
Details: IN ADDITION TO CLASSICAL NMR CONSTRAINTS THREE TYPES OF GLOBAL CONSTRAINTS WERE USED TO DEFINE THE GLOBAL STRUCTURE OF APO-CII IN THE APO-CII/SDS- MICELLE COMPLEX. SCRIPTS FOR THE GLOBAL ...Details: IN ADDITION TO CLASSICAL NMR CONSTRAINTS THREE TYPES OF GLOBAL CONSTRAINTS WERE USED TO DEFINE THE GLOBAL STRUCTURE OF APO-CII IN THE APO-CII/SDS- MICELLE COMPLEX. SCRIPTS FOR THE GLOBAL STRUCTURE DETERMINATION HAVE BEEN WRITTEN AND ARE AVAILABLE UPON REQUEST. FINALLY, CNS WAS USED FOR THE FINAL MINIMIZATION.
NMR ensembleConformer selection criteria: LEAST ENERGY, LEAST RESTRAINT VIOLATION
Conformers calculated total number: 100 / Conformers submitted total number: 68

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