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- PDB-1ioj: HUMAN APOLIPOPROTEIN C-I, NMR, 18 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1ioj
TitleHUMAN APOLIPOPROTEIN C-I, NMR, 18 STRUCTURES
ComponentsAPOC-I
KeywordsAPOLIPOPROTEIN / AMPHIPATHIC HELIX / LIPID ASSOCIATION / LCAT ACTIVATION
Function / homology
Function and homology information


negative regulation of phosphatidylcholine catabolic process / VLDL clearance / VLDL assembly / lipase inhibitor activity / negative regulation of cholesterol transport / phospholipase inhibitor activity / negative regulation of very-low-density lipoprotein particle clearance / negative regulation of lipoprotein lipase activity / plasma lipoprotein particle remodeling / regulation of cholesterol transport ...negative regulation of phosphatidylcholine catabolic process / VLDL clearance / VLDL assembly / lipase inhibitor activity / negative regulation of cholesterol transport / phospholipase inhibitor activity / negative regulation of very-low-density lipoprotein particle clearance / negative regulation of lipoprotein lipase activity / plasma lipoprotein particle remodeling / regulation of cholesterol transport / very-low-density lipoprotein particle assembly / negative regulation of lipid metabolic process / chylomicron remnant clearance / negative regulation of receptor-mediated endocytosis / very-low-density lipoprotein particle clearance / negative regulation of fatty acid biosynthetic process / phosphatidylcholine-sterol O-acyltransferase activator activity / lipoprotein metabolic process / chylomicron / phosphatidylcholine binding / high-density lipoprotein particle remodeling / phospholipid efflux / very-low-density lipoprotein particle / high-density lipoprotein particle / cholesterol efflux / triglyceride metabolic process / negative regulation of lipid catabolic process / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cholesterol metabolic process / fatty acid binding / lipid metabolic process / endoplasmic reticulum / extracellular region
Similarity search - Function
Apolipoprotein C-I / Apolipoprotein C-I / Apolipoprotein C-I domain superfamily / Apolipoprotein C-I (ApoC-1) / G Protein Gi Gamma 2 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsRozek, A. / Sparrow, J.T. / Weisgraber, K.H. / Cushley, R.J.
CitationJournal: Biochemistry / Year: 1999
Title: Conformation of human apolipoprotein C-I in a lipid-mimetic environment determined by CD and NMR spectroscopy.
Authors: Rozek, A. / Sparrow, J.T. / Weisgraber, K.H. / Cushley, R.J.
History
DepositionMay 12, 1998Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 4, 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 / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity.src_method / _pdbx_database_status.process_site ..._entity.src_method / _pdbx_database_status.process_site / _pdbx_nmr_refine.details / _pdbx_nmr_spectrometer.field_strength
Revision 1.4May 1, 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

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Assembly

Deposited unit
A: APOC-I


Theoretical massNumber of molelcules
Total (without water)6,6431
Polymers6,6431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5620 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 50SELECTED STRUCTURES HAVE NO HELIX-HELIX CONTACTS <5 ANGSTROMS
RepresentativeModel #15

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Components

#1: Protein APOC-I


Mass: 6642.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02654

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-NOESY
1222D-TOCSY
132DQF-COSY
1422D-15N-FILTERED NOESY
1522D-15N-FILTERED TOCSY
1622D 1H-15N HSQC
1723D-NOESY-HSQC
1823D-TOCSY-HSQC
1922D-NOESY
NMR detailsText: USING WATERGATE FOR WATER SUPPRESSION, 2D-TOCSY USING MLEV-17 FOR MIXING, 3D-TOCSY USING DIPSY-2RC FOR MIXING. 15N-FILTERED NOESY AND TOCSY INCLUDE DIFFERENCE (SHOWING ONLY 15N LABELED RESIDUES) ...Text: USING WATERGATE FOR WATER SUPPRESSION, 2D-TOCSY USING MLEV-17 FOR MIXING, 3D-TOCSY USING DIPSY-2RC FOR MIXING. 15N-FILTERED NOESY AND TOCSY INCLUDE DIFFERENCE (SHOWING ONLY 15N LABELED RESIDUES) AND SUM SPECTRA (SHOWING ONLY UNLABELED RESIDUES).

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution15.8 mM native apoC-I, 90%H2O/10%D2O, 232 mM SDS-D25native apoC-I was isolated from blood plasmasample_190% H2O/10% D2O
solution25 mM selectively 15N-labeled synthetic apoC-I, 90%H2O/10%D2O, 200 mM SDS-D25sample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5.8 mMnative apoC-Inatural abundance1
5 mMsynthetic apoC-I[U-15N]2
232 mMSDS-D25natural abundance1
200 mMSDS-D25natural abundance2
Sample conditionspH: 4.8 / Temperature: 323 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
NameVersionDeveloperClassification
DGII, DISCOVERDISCOVERMOLECULAR SIMULATIONS INC, SAN DIEGOrefinement
DGII, DISCOVERDISCOVERMOLECULAR SIMULATIONS INC, SAN DIEGOstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURE OF APOC-I(1-38) IN THE PRESENCE OF SODIUM DODECYL SULFATE WAS REFINED USING 685 NOE-BASED DISTANCE RESTRAINTS. NO DIHEDRAL RESTRAINTS AND NO H-BOND RESTRAINTS WERE USED. THIS ...Details: THE STRUCTURE OF APOC-I(1-38) IN THE PRESENCE OF SODIUM DODECYL SULFATE WAS REFINED USING 685 NOE-BASED DISTANCE RESTRAINTS. NO DIHEDRAL RESTRAINTS AND NO H-BOND RESTRAINTS WERE USED. THIS ENTRY CONTAINS 18 ACCEPTED OUT OF 50 CALCULATED STRUCTURES. STRUCTURE CALCULATIONS WERE PERFORMED WITH THE PROGRAMS DGII AND DISCOVER INCLUDING DISTANCE GEOMETRY CALCULATIONS, SIMULATED ANNEALING AND ENERGY MINIMIZATION WITH A CONJUGATED GRADIENT. THE CVFF FORCEFIELD WAS USED. ALL FORMAL CHARGES WERE SWITCHED OFF. THE DIELECTRIC CONSTANT WAS SET TO 1. THE LENNARD-JONES POTENTIAL WAS USED FOR NON-BOND INTERACTIONS (CUTOFF 12A). FOR DETAILS ON STRUCTURE CALCULATION, RMSDS AND FINAL ENERGIES PLEASE SEE REFERENCE CITED UNDER "JRNL".
NMR ensembleConformer selection criteria: SELECTED STRUCTURES HAVE NO HELIX-HELIX CONTACTS <5 ANGSTROMS
Conformers calculated total number: 50 / Conformers submitted total number: 18

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