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Solution NMR structure of the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate
Authors
Horvath, G., Egyed, O., Bencsura, A., Simon, A., Tochtrop, G.P., DeKoster, G.T., Covey, D.F., Cistola, D.P., Toke, O.
Assembly
ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate
Entity
1. ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate, entity 1 (polymer, Thiol state: not present), 127 monomers, 14239.88 Da Detail

AFTGKFEMES EKNYDEFMKL LGISSDVIEK ARNFKIVTEV QQDGQDFTWS QHYSGGHTMT NKFTVGKESN IQTMGGKTFK ATVQMEGGKL VVNFPNYHQT SEIVGDKLVE VSTIGGVTYE RVSKRLA


2. ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate, entity GCH (non-polymer), 465.623 Da
3. ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate, entity CHO (non-polymer), 449.623 Da
Total weight
15155.126 Da
Max. entity weight
14239.88 Da
Source organism
Homo sapiens
Exptl. method
solution NMR
Refine. method
simulated annealing, torsion angle dynamics
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 100.0 %, Completeness: 96.4 %, Completeness (bb): 99.5 % Detail

Polymer type: polypeptide(L)

Total1H13C15N
All96.4 % (1434 of 1487)97.7 % (753 of 771)93.9 % (541 of 576)100.0 % (140 of 140)
Backbone99.5 % (756 of 760)100.0 % (266 of 266)98.9 % (364 of 368)100.0 % (126 of 126)
Sidechain94.2 % (792 of 841)96.4 % (487 of 505)90.4 % (291 of 322)100.0 % (14 of 14)
Aromatic75.0 % (102 of 136)91.2 % (62 of 68)58.2 % (39 of 67)100.0 % (1 of 1)
Methyl97.6 % (121 of 124)98.4 % (61 of 62)96.8 % (60 of 62)

1. entity 1

AFTGKFEMES EKNYDEFMKL LGISSDVIEK ARNFKIVTEV QQDGQDFTWS QHYSGGHTMT NKFTVGKESN IQTMGGKTFK ATVQMEGGKL VVNFPNYHQT SEIVGDKLVE VSTIGGVTYE RVSKRLA

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3


#NameIsotope labelingTypeConcentration
1human ileal bile acid-binding protein[U-13C; U-15N]1.0 mM
2GLYCOCHOLIC ACIDnatural abundance1.5 mM
3GLYCOCHENODEOXYCHOLIC ACIDnatural abundance1.5 mM
4potassium phosphatenatural abundance20 mM
5potassium chloridenatural abundance50 mM
6sodium azidenatural abundance0.05 %
Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3


#NameIsotope labelingTypeConcentration
7human ileal bile acid-binding proteinnatural abundance1.0 mM
8GLYCOCHOLIC ACID[U-15N]1.5 mM
9GLYCOCHENODEOXYCHOLIC ACID[U-15N]1.5 mM
10potassium phosphatenatural abundance20 mM
11potassium chloridenatural abundance50 mM
12sodium azidenatural abundance0.05 %
Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3


#NameIsotope labelingTypeConcentration
13human ileal bile acid-binding proteinnatural abundance1.0 mM
14GLYCOCHOLIC ACID[1',2'-13C]1.5 mM
15GLYCOCHENODEOXYCHOLIC ACID[1',2'-13C]1.5 mM
16potassium phosphatenatural abundance20 mM
17potassium chloridenatural abundance50 mM
18sodium azidenatural abundance0.05 %
Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3


#NameIsotope labelingTypeConcentration
19human ileal bile acid-binding proteinnatural abundance1.0 mM
20GLYCOCHOLIC ACID[3,4-13C]1.5 mM
21GLYCOCHENODEOXYCHOLIC ACID[3,4-13C]1.5 mM
22potassium phosphatenatural abundance20 mM
23potassium chloridenatural abundance50 mM
24sodium azidenatural abundance0.05 %
Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3


#NameIsotope labelingTypeConcentration
25human ileal bile acid-binding proteinnatural abundance1.0 mM
26GLYCOCHOLIC ACID[23,24-13C]1.5 mM
27GLYCOCHENODEOXYCHOLIC ACID[23,24-13C]1.5 mM
28potassium phosphatenatural abundance20 mM
29potassium chloridenatural abundance50 mM
30sodium azidenatural abundance0.05 %

LACS Plot; CA
Referencing offset: -0.36 ppm, Outliers: 1 Detail
LACS Plot; CB
Referencing offset: -0.36 ppm, Outliers: 1 Detail
LACS Plot; HA
Referencing offset: -0.16 ppm, Outliers: 1 Detail
LACS Plot; CO
Referencing offset: 0.53 ppm, Outliers: 3 Detail
Protein Blocks Logo
Calculated from 10 models in PDB: 2MM3, Strand ID: A Detail


Release date
2014-05-04
Citation 1
Structural determinants of ligand binding in the ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR
Horvath, G., Egyed, O., Bencsura, A., Simon, A., Tochtrop, G.P., DeKoster, G.T., Covey, D.F., Cistola, D.P., Toke, O.
FEBS J. (2015), PubMed 26613247 , DOI 10.1111/febs.13610 ,
Citation 2
Determinants of cooperativity and site selectivity in human ileal bile acid binding protein
Toke, O., Monsey, J.D., DeKoster, G.T., Tochtrop, G.P., Tang, C., Cistola, D.P.
Biochemistry (2006), 45, 727-737, PubMed 16411748 , DOI 10.1021/bi051781p ,
Citation 3
A single hydroxyl group governs ligand site selectivity in human ileal bile acid binding protein
Tochtrop, G.P., DeKoster, G.T., Covey, D.F., Cistola, D.P.
J. Am. Chem. Soc. (2004), 126, 11024-11029, PubMed 15339188 , DOI 10.1021/ja047589c ,
Citation 4
Kinetic mechanism of ligand binding in human ileal bile acid binding protein as determined by stopped-flow fluorescence analysis
Toke, O., Monsey, J., Cistola, D.P.
Biochemistry (2007), 46, 5427-5436, PubMed 17432832 , DOI 10.1021/bi700030r ,
Citation 5
Internal motions and exchange processes in human ileal bile acid binding protein as studied by backbone (15)N nuclear magnetic resonance spectroscopy
Horvath, G., Kiraly, P., Tarkanyi, G., Toke, O.
Biochemistry (2012), 51, 1848-1861, PubMed 22329738 , DOI 10.1021/bi201588q ,
Related entities 1. ternary complex of human ileal bile acid-binding protein with glycocholate and glycochenodeoxycholate, entity 1, : 1 : 7 : 189 entities Detail
Experiments performed 27 experiments Detail
NMR combined restraints 5 contents Detail
Keywords lipid-binding proteins, orthogonal beta sheets