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- PDB-1opp: PEPTIDE OF HUMAN APOLIPOPROTEIN C-I RESIDUES 1-38, NMR, 28 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1opp
TitlePEPTIDE OF HUMAN APOLIPOPROTEIN C-I RESIDUES 1-38, NMR, 28 STRUCTURES
ComponentsAPOLIPOPROTEIN C-I
KeywordsAPOLIPOPROTEIN / AMPHIPATHIC HELIX / LIPID ASSOCIATION / LCAT ACTIVATION
Function / homology
Function and homology information


negative regulation of phosphatidylcholine catabolic process / VLDL clearance / negative regulation of very-low-density lipoprotein particle clearance / VLDL assembly / lipase inhibitor activity / negative regulation of cholesterol transport / negative regulation of lipoprotein lipase activity / phospholipase inhibitor activity / plasma lipoprotein particle remodeling / regulation of cholesterol transport ...negative regulation of phosphatidylcholine catabolic process / VLDL clearance / negative regulation of very-low-density lipoprotein particle clearance / VLDL assembly / lipase inhibitor activity / negative regulation of cholesterol transport / negative regulation of lipoprotein lipase activity / phospholipase inhibitor activity / plasma lipoprotein particle remodeling / regulation of cholesterol transport / very-low-density lipoprotein particle assembly / negative regulation of lipid metabolic process / negative regulation of receptor-mediated endocytosis / chylomicron remnant clearance / very-low-density lipoprotein particle clearance / negative regulation of fatty acid biosynthetic process / phosphatidylcholine-sterol O-acyltransferase activator activity / chylomicron / lipoprotein metabolic process / high-density lipoprotein particle remodeling / phosphatidylcholine binding / 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 domain superfamily / Apolipoprotein C-I (ApoC-1)
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsRozek, A. / Buchko, G.W. / Kanda, P. / Cushley, R.J.
CitationJournal: Protein Sci. / Year: 1997
Title: Conformational studies of the N-terminal lipid-associating domain of human apolipoprotein C-I by CD and 1H NMR spectroscopy.
Authors: Rozek, A. / Buchko, G.W. / Kanda, P. / Cushley, R.J.
History
DepositionMay 8, 1997Processing site: BNL
Revision 1.0May 13, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_ensemble / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_DOI / _entity.src_method ..._citation.pdbx_database_id_DOI / _entity.src_method / _pdbx_database_status.process_site / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_ensemble.conformers_calculated_total_number / _pdbx_nmr_software.authors / _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

Downloads & links

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Assembly

Deposited unit
A: APOLIPOPROTEIN C-I


Theoretical massNumber of molelcules
Total (without water)4,2571
Polymers4,2571
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4070 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)28 / 30structures with the least restraint violations
Representative

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Components

#1: Protein/peptide APOLIPOPROTEIN C-I / / APO-CI


Mass: 4256.853 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 38 / Source method: obtained synthetically
Details: synthesized using standard Fmoc-based solid-phase protocols
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
1212D-TOCSY
132DQF-COSY
1422D-NOESY
1532D-NOESY
1632D-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution15 mM apoC, 300 mM SDS-d2ssample_190% H2O/10% D2O
solution25 mM apoC, 300 mM SDS-d2ssample_299.9% D2O
solution35 mM apoC, 50 mM potassium chloride, 20 mM potassium phosphatesample_150% (v/v) TFE-d, 10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMapoC1
5 mMapoC2
300 mMSDS-d2snatural abundance1
300 mMSDS-d2snatural abundance2
5 mMapoC3
50 mMpotassium chloridenatural abundance3
20 mMpotassium phosphatenatural abundance3
Sample conditionspH: 4.8 / 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
DGIIHAVELrefinement
DGIIHAVELstructure 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 464 NOE-BASED DISTANCE RESTRAINTS. NO DIHEDRAL RESTRAINTS WERE USED. THIS ENTRY CONTAINS ALL 28 ...Details: THE STRUCTURE OF APOC-I(1-38) IN THE PRESENCE OF SODIUM DODECYL SULFATE WAS REFINED USING 464 NOE-BASED DISTANCE RESTRAINTS. NO DIHEDRAL RESTRAINTS WERE USED. THIS ENTRY CONTAINS ALL 28 ACCEPTED STRUCTURES. STRUCTURE CALCULATIONS WERE PERFORMED WITH THE PROGRAM DGII (BIOSYM/MSI, SAN DIEGO, CA) INCLUDING DISTANCE GEOMETRY CALCULATIONS, SIMULATED ANNEALING AND ENERGY MINIMIZATION WITH A CONJUGATED GRADIENT. THE CVFF FORCE FIELD WAS USED. FOR DETAILS ON STRUCTURE CALCULATION AND RMSDS PLEASE SEE REFERENCE CITED ON JRNL RECORDS ABOVE.
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 28

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