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- PDB-2lem: Monomeric Mouse ApoAI(1-216) -

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Basic information

Entry
Database: PDB / ID: 2lem
TitleMonomeric Mouse ApoAI(1-216)
ComponentsApolipoprotein A-I
KeywordsLIPID TRANSPORT
Function / homology
Function and homology information


ABC transporters in lipid homeostasis / Chylomicron assembly / Chylomicron remodeling / HDL remodeling / Scavenging by Class B Receptors / HDL clearance / Scavenging of heme from plasma / Scavenging by Class A Receptors / Heme signaling / lipase inhibitor activity ...ABC transporters in lipid homeostasis / Chylomicron assembly / Chylomicron remodeling / HDL remodeling / Scavenging by Class B Receptors / HDL clearance / Scavenging of heme from plasma / Scavenging by Class A Receptors / Heme signaling / lipase inhibitor activity / Retinoid metabolism and transport / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / regulation of intestinal cholesterol absorption / protein oxidation / vitamin transport / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / cholesterol import / HDL assembly / high-density lipoprotein particle binding / blood vessel endothelial cell migration / negative regulation of heterotypic cell-cell adhesion / apolipoprotein A-I receptor binding / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion molecule production / negative regulation of very-low-density lipoprotein particle remodeling / Platelet degranulation / peptidyl-methionine modification / discoidal high-density lipoprotein particle / intermediate-density lipoprotein particle / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / lipid transporter activity / positive regulation of phospholipid efflux / positive regulation of cholesterol metabolic process / lipid storage / phospholipid homeostasis / chylomicron / high-density lipoprotein particle remodeling / phospholipid efflux / phospholipid transport / chemorepellent activity / very-low-density lipoprotein particle / reverse cholesterol transport / cholesterol transfer activity / high-density lipoprotein particle assembly / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transport / high-density lipoprotein particle / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / endothelial cell proliferation / negative regulation of interleukin-1 beta production / cholesterol efflux / adrenal gland development / positive regulation of Rho protein signal transduction / cholesterol binding / cholesterol biosynthetic process / lipoprotein particle binding / endocytic vesicle / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of cholesterol efflux / animal organ regeneration / phospholipid metabolic process / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / positive regulation of stress fiber assembly / heat shock protein binding / cholesterol metabolic process / integrin-mediated signaling pathway / cholesterol homeostasis / regulation of protein phosphorylation / phospholipid binding / negative regulation of inflammatory response / extracellular vesicle / amyloid-beta binding / protein stabilization / G protein-coupled receptor signaling pathway / lipid binding / enzyme binding / cell surface / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / cytosol
Similarity search - Function
Apolipoprotein A/E / Apolipoprotein A1/A4/E domain
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsChen, J. / Wang, J. / Yang, Y.
CitationJournal: To be Published
Title: NMR Structure of Mouse ApoAI(1-216)
Authors: Chen, J. / Yang, Y. / Wang, J.
History
DepositionJun 17, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / 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 A-I


Theoretical massNumber of molelcules
Total (without water)25,2641
Polymers25,2641
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)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Apolipoprotein A-I / Apo-AI / ApoA-I / Apolipoprotein A1


Mass: 25264.043 Da / Num. of mol.: 1 / Fragment: sequence database residues 25-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apoa1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00623

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCA
1323D HN(CO)CA
1423D HN(CA)CB
1523D HN(COCA)CB
1613D 1H-15N NOESY
1713D (H)CCH-TOCSY
1813D CCC-TOCSY-NNH
1914D 13C15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1~1.0 mM [U-100% 13C; U-100% 15N] protein, 0.03 mM DSS, 0.01 mM sodium azide, 10 mM [U-100% 2H] EDTA, 25 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
2~1.0 mM [U-13C; U-15N; U-2H] protein, 0.03 mM DSS, 0.01 mM sodium azide, 10 mM [U-100% 2H] EDTA, 25 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMprotein-1[U-100% 13C; U-100% 15N]1
0.03 mMDSS-21
0.01 mMsodium azide-31
10 mMEDTA-4[U-100% 2H]1
25 mMsodium phosphate-51
1.0 mMprotein-6[U-13C; U-15N; U-2H]2
0.03 mMDSS-72
0.01 mMsodium azide-82
10 mMEDTA-9[U-100% 2H]2
25 mMsodium phosphate-102
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
ProcheckNMRLaskowski and MacArthurrefinement
NMRViewJohnson, One Moon Scientificchemical shift assignment
PIPPGarrettchemical shift assignment
VNMRVariancollection
TALOSCornilescu, Delaglio and Baxchemical shift calculation
Insight IIAccelrys Software Inc.refinement
CSIJohnson, One Moon Scientificchemical shift calculation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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