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- PDB-3bej: Structure of human FXR in complex with MFA-1 and co-activator peptide -

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Basic information

Entry
Database: PDB / ID: 3bej
TitleStructure of human FXR in complex with MFA-1 and co-activator peptide
Components
  • Bile acid receptor
  • Nuclear receptor coactivator 1
KeywordsTRANSCRIPTION REGULATOR / FXR / BAR / NR1H4 / bile acid receptor / NHR / nuclear receptor / Activator / Alternative splicing / DNA-binding / Metal-binding / Nucleus / Repressor / Transcription / Transcription regulation / Zinc / Zinc-finger / Acyltransferase / Chromosomal rearrangement / Phosphoprotein / Polymorphism / Proto-oncogene / Transferase / Ubl conjugation / transcription-transferase COMPLEX
Function / homology
Function and homology information


regulation of urea metabolic process / nuclear receptor-mediated bile acid signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / : / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid ...regulation of urea metabolic process / nuclear receptor-mediated bile acid signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / : / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production / regulation of bile acid biosynthetic process / regulation of insulin secretion involved in cellular response to glucose stimulus / : / toll-like receptor 9 signaling pathway / intracellular receptor signaling pathway / negative regulation of monocyte chemotactic protein-1 production / bile acid metabolic process / nitrogen catabolite activation of transcription from RNA polymerase II promoter / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / bile acid binding / cell-cell junction assembly / positive regulation of female receptivity / bile acid signaling pathway / cellular response to fatty acid / negative regulation of interleukin-2 production / regulation of cholesterol metabolic process / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of interleukin-17 production / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / cellular response to Thyroglobulin triiodothyronine / negative regulation of tumor necrosis factor-mediated signaling pathway / estrous cycle / Synthesis of bile acids and bile salts / fatty acid homeostasis / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / positive regulation of insulin receptor signaling pathway / response to retinoic acid / negative regulation of canonical NF-kappaB signal transduction / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / Notch signaling pathway / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / transcription coregulator binding / response to progesterone / cholesterol homeostasis / hippocampus development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / Circadian Clock / response to estradiol / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity
Similarity search - Function
Bile acid receptor, ligand binding domain / Thyroid hormone receptor / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain ...Bile acid receptor, ligand binding domain / Thyroid hormone receptor / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MUF / YTTRIUM (III) ION / Nuclear receptor coactivator 1 / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsSoisson, S.M. / Parthasarathy, G. / Becker, J.W.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Identification of a potent synthetic FXR agonist with an unexpected mode of binding and activation.
Authors: Soisson, S.M. / Parthasarathy, G. / Adams, A.D. / Sahoo, S. / Sitlani, A. / Sparrow, C. / Cui, J. / Becker, J.W.
History
DepositionNov 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 31, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: entity / pdbx_distant_solvent_atoms ...entity / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct
Item: _entity.pdbx_ec / _struct.pdbx_descriptor
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bile acid receptor
B: Bile acid receptor
E: Nuclear receptor coactivator 1
F: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3138
Polymers61,2944
Non-polymers1,0194
Water6,521362
1
A: Bile acid receptor
E: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1574
Polymers30,6472
Non-polymers5092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-7 kcal/mol
Surface area11630 Å2
MethodPISA
2
B: Bile acid receptor
F: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1574
Polymers30,6472
Non-polymers5092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-10 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.642, 90.889, 129.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bile acid receptor / Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group H ...Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group H member 4 / Retinoid X receptor-interacting protein 14 / RXR-interacting protein 14


Mass: 27840.994 Da / Num. of mol.: 2 / Fragment: residues 249-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H4, BAR, FXR, HRR1, RIP14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q96RI1
#2: Protein/peptide Nuclear receptor coactivator 1 / NCoA-1 / Steroid receptor coactivator 1 / SRC-1 / RIP160 / Protein Hin-2 / Renal carcinoma antigen NY-REN-52


Mass: 2806.163 Da / Num. of mol.: 2 / Fragment: residues 676-700
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA1, SRC1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q15788
#3: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Y
#4: Chemical ChemComp-MUF / (8alpha,10alpha,13alpha,17beta)-17-[(4-hydroxyphenyl)carbonyl]androsta-3,5-diene-3-carboxylic acid


Mass: 420.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H32O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16-22% PEG3350, 0.1M Bis-Tris, 4 mM YCl(3), 0.2M Ammonium acetate, 1 mM DTT. Protein was carboxymethylated with iodoacetic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.98793, 0.97931, 0.97907, 0.96863
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 28, 2003
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.987931
20.979311
30.979071
40.968631
ReflectionResolution: 1.9→50 Å / Num. all: 41792 / Num. obs: 41792 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.065 / Χ2: 1.028 / Net I/σ(I): 10.7
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.577 / Num. unique all: 3895 / Χ2: 0.927 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
TNTrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER-TNT2.1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→39.65 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1997 5.02 %RANDOM
Rwork0.2 ---
all0.203 41792 --
obs0.203 41792 99.35 %-
Displacement parametersBiso mean: 34.81 Å2
Baniso -1Baniso -2Baniso -3
1--6.862 Å20 Å20 Å2
2--1.683 Å20 Å2
3---5.179 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 64 362 4370
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01140962
X-RAY DIFFRACTIONt_angle_deg1.27155222
X-RAY DIFFRACTIONt_dihedral_angle_d23.2048740
X-RAY DIFFRACTIONt_trig_c_planes0.0041298
X-RAY DIFFRACTIONt_gen_planes0.0126108
X-RAY DIFFRACTIONt_it1.828402620
X-RAY DIFFRACTIONt_nbd0.0681695
LS refinement shellResolution: 1.9→2.01 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.284 297 4.86 %
Rwork0.221 5809 -
all0.224 6106 -
obs--99.35 %

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