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- PDB-2mm3: Solution NMR structure of the ternary complex of human ileal bile... -

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Basic information

Entry
Database: PDB / ID: 2mm3
TitleSolution NMR structure of the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate
ComponentsGastrotropin
KeywordsLIPID BINDING PROTEIN / lipid-binding protein / orthogonal beta sheets / positive binding cooperativity / site-selectivity / enterohepatic circulation
Function / homology
Function and homology information


NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Triglyceride catabolism / fatty acid transport / Recycling of bile acids and salts / fatty acid binding / lipid metabolic process / negative regulation of cell population proliferation / lipid binding / membrane / nucleus ...NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Triglyceride catabolism / fatty acid transport / Recycling of bile acids and salts / fatty acid binding / lipid metabolic process / negative regulation of cell population proliferation / lipid binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
GLYCOCHOLIC ACID / Gastrotropin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsclosest to the average, model9
AuthorsHorvath, G. / Egyed, O. / Bencsura, A. / Simon, A. / Tochtrop, G.P. / DeKoster, G.T. / Covey, D.F. / Cistola, D.P. / Toke, O.
Citation
Journal: FEBS J. / Year: 2016
Title: Structural determinants of ligand binding in the ternary complex of human ileal bile acid binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR
Authors: Horvath, G. / Bencsura, A. / Simon, A. / Tochtrop, G.P. / DeKoster, G.T. / Covey, D.F. / Cistola, D.P. / Toke, O.
#1: Journal: Biochemistry / Year: 2006
Title: Determinants of cooperativity and site selectivity in human ileal bile acid binding protein.
Authors: Toke, O. / Monsey, J.D. / DeKoster, G.T. / Tochtrop, G.P. / Tang, C. / Cistola, D.P.
#2: Journal: J.Am.Chem.Soc. / Year: 2004
Title: A single hydroxyl group governs ligand site selectivity in human ileal bile acid binding protein.
Authors: Tochtrop, G.P. / DeKoster, G.T. / Covey, D.F. / Cistola, D.P.
#3: Journal: Biochemistry / Year: 2007
Title: Kinetic mechanism of ligand binding in human ileal bile acid binding protein as determined by stopped-flow fluorescence analysis.
Authors: Toke, O. / Monsey, J.D. / Cistola, D.P.
#4: Journal: Biochemistry / Year: 2012
Title: Internal motions and exchange processes in human ileal bile acid binding protein as studied by backbone (15)N nuclear magnetic resonance spectroscopy.
Authors: Horvath, G. / Kiraly, P. / Tarkanyi, G. / Toke, O.
#5: Journal: Biochemistry / Year: 2012
Title: Internal motions and exchange processes in human ileal bile acid binding protein as studied by backbone (15)N nuclear magnetic resonance spectroscopy
Authors: Horvath, G. / Kiraly, P. / Tarkanyi, G. / Toke, O.
History
DepositionMar 7, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Jun 14, 2023Group: 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 / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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: Gastrotropin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1733
Polymers14,2581
Non-polymers9152
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Gastrotropin / Ileal lipid-binding protein


Mass: 14258.038 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP6 / Production host: Escherichia coli (E. coli) / References: UniProt: P51161
#2: Chemical ChemComp-GCH / GLYCOCHOLIC ACID / N-CHOLYLGLYCINE


Mass: 465.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H43NO6
#3: Chemical ChemComp-CHO / GLYCOCHENODEOXYCHOLIC ACID


Mass: 449.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H43NO5 / Comment: detergent*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
151CBCACOCAHA
161HN(CO)CA
1713D CC-TOCSY-NNH
1813D HCC-TOCSY
1913D (H)CCH-TOCSY
11012D CG(CB)HB
11112D CG(CD)HD
11212D CG(CDCE)HE
11312D 1H-13C HSQC aliphatic
11412D 1H-13C HSQC aromatic
11513D 1H-15N NOESY
11613D 1H-13C NOESY aliphatic
11713D 1H-13C NOESY aromatic
11813D NH-NH NOESY
11913D MET-MET NOESY
12022D 1H-15N HSQC
12122D 15N-edited NOESY
12232D 1H-13C HSQC
12332D 13C-edited NOESY
12442D 1H-13C HSQC
12542D 13C-edited NOESY
12652D 1H-13C HSQC
12752D 13C-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-13C; U-15N] human ileal bile acid-binding protein-1, 1.5 mM GLYCOCHOLIC ACID-2, 1.5 mM GLYCOCHENODEOXYCHOLIC ACID-3, 20 mM potassium phosphate-4, 50 mM potassium chloride-5, 0.05 % sodium azide-6, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM human ileal bile acid-binding protein-7, 1.5 mM [U-15N] GLYCOCHOLIC ACID-8, 1.5 mM [U-15N] GLYCOCHENODEOXYCHOLIC ACID-9, 20 mM potassium phosphate-10, 50 mM potassium chloride-11, 0.05 % sodium azide-12, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM human ileal bile acid-binding protein-13, 1.5 mM 1',2'-13C GLYCOCHOLIC ACID-14, 1.5 mM 1',2'-13C GLYCOCHENODEOXYCHOLIC ACID-15, 20 mM potassium phosphate-16, 50 mM potassium chloride-17, 0.05 % sodium azide-18, 90% H2O/10% D2O90% H2O/10% D2O
41.0 mM human ileal bile acid-binding protein-19, 1.5 mM 3,4-13C GLYCOCHOLIC ACID-20, 1.5 mM 3,4-13C GLYCOCHENODEOXYCHOLIC ACID-21, 20 mM potassium phosphate-22, 50 mM potassium chloride-23, 0.05 % sodium azide-24, 90% H2O/10% D2O90% H2O/10% D2O
51.0 mM human ileal bile acid-binding protein-25, 1.5 mM 23,24-13C GLYCOCHOLIC ACID-26, 1.5 mM 23,24-13C GLYCOCHENODEOXYCHOLIC ACID-27, 20 mM potassium phosphate-28, 50 mM potassium chloride-29, 0.05 % sodium azide-30, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMhuman ileal bile acid-binding protein-1[U-13C; U-15N]1
1.5 mMGLYCOCHOLIC ACID-21
1.5 mMGLYCOCHENODEOXYCHOLIC ACID-31
20 mMpotassium phosphate-41
50 mMpotassium chloride-51
0.05 %sodium azide-61
1.0 mMhuman ileal bile acid-binding protein-72
1.5 mMGLYCOCHOLIC ACID-8[U-15N]2
1.5 mMGLYCOCHENODEOXYCHOLIC ACID-9[U-15N]2
20 mMpotassium phosphate-102
50 mMpotassium chloride-112
0.05 %sodium azide-122
1.0 mMhuman ileal bile acid-binding protein-133
1.5 mMGLYCOCHOLIC ACID-141',2'-13C3
1.5 mMGLYCOCHENODEOXYCHOLIC ACID-151',2'-13C3
20 mMpotassium phosphate-163
50 mMpotassium chloride-173
0.05 %sodium azide-183
1.0 mMhuman ileal bile acid-binding protein-194
1.5 mMGLYCOCHOLIC ACID-203,4-13C4
1.5 mMGLYCOCHENODEOXYCHOLIC ACID-213,4-13C4
20 mMpotassium phosphate-224
50 mMpotassium chloride-234
0.05 %sodium azide-244
1.0 mMhuman ileal bile acid-binding protein-255
1.5 mMGLYCOCHOLIC ACID-2623,24-13C5
1.5 mMGLYCOCHENODEOXYCHOLIC ACID-2723,24-13C5
20 mMpotassium phosphate-285
50 mMpotassium chloride-295
0.05 %sodium azide-305
Sample conditionsIonic strength: 70 / pH: 6.3 / Pressure: ambient / Temperature: 293 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariandata collection
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.peak picking
FelixAccelrys Software Inc.chemical shift assignment
ARIA2.1Linge, O'Donoghue and Nilgesstructure solution
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 9

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