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- PDB-5z12: A structure of FXR/RXR -

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Basic information

Entry
Database: PDB / ID: 5z12
TitleA structure of FXR/RXR
Components
  • (Peptide from Nuclear receptor coactivator ...) x 2
  • Bile acid receptor
  • Retinoic acid receptor RXR-alpha
KeywordsNUCLEAR PROTEIN / complex
Function / homology
Function and homology information


: / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic 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 interleukin-1 production / retinoic acid-responsive element binding ...: / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic 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 interleukin-1 production / retinoic acid-responsive element binding / negative regulation of very-low-density lipoprotein particle remodeling / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / positive regulation of thyroid hormone receptor signaling pathway / regulation of bile acid biosynthetic process / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of monocyte chemotactic protein-1 production / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / toll-like receptor 9 signaling pathway / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / Carnitine shuttle / retinoic acid binding / bile acid metabolic process / bile acid binding / cellular response to fatty acid / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway / cell-cell junction assembly / nuclear vitamin D receptor binding / regulation of cholesterol metabolic process / Signaling by Retinoic Acid / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / DNA binding domain binding / negative regulation of interleukin-2 production / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of lipid metabolic process / bile acid and bile salt transport / LBD domain binding / locomotor rhythm / positive regulation of lipoprotein transport / nuclear steroid receptor activity / positive regulation of interleukin-17 production / intracellular glucose homeostasis / aryl hydrocarbon receptor binding / negative regulation of type II interferon production / cellular response to Thyroglobulin triiodothyronine / negative regulation of interleukin-6 production / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / regulation of lipid metabolic process / negative regulation of tumor necrosis factor production / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of cholesterol efflux / monocyte differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / fatty acid homeostasis / cellular response to low-density lipoprotein particle stimulus / positive regulation of insulin receptor signaling pathway / response to retinoic acid / positive regulation of bone mineralization / negative regulation of tumor necrosis factor-mediated signaling pathway / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Recycling of bile acids and salts / transcription regulator inhibitor activity / retinoic acid receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to hormone stimulus / intracellular receptor signaling pathway / Notch signaling pathway / Regulation of lipid metabolism by PPARalpha / cell maturation / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / peptide binding / ciliary tip / positive regulation of adipose tissue development / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / response to progesterone / Activation of gene expression by SREBF (SREBP) / cholesterol homeostasis / nuclear receptor binding / transcription coregulator binding / negative regulation of canonical NF-kappaB signal transduction / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of smoothened signaling pathway / SUMOylation of intracellular receptors / circadian regulation of gene expression / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / euchromatin
Similarity search - Function
Bile acid receptor, ligand binding domain / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Thyroid hormone receptor / Retinoid X receptor/HNF4 / : / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 ...Bile acid receptor, ligand binding domain / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Thyroid hormone receptor / Retinoid X receptor/HNF4 / : / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / : / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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-33Y / (9cis)-retinoic acid / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 2 / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLu, Y. / Li, Y.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural insights into the heterodimeric complex of the nuclear receptors FXR and RXR
Authors: Zheng, W. / Lu, Y. / Tian, S. / Ma, F. / Wei, Y. / Xu, S. / Li, Y.
History
DepositionDec 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 25, 2019Group: Derived calculations / Refinement description / Category: pdbx_struct_assembly_gen / refine_hist
Item: _pdbx_struct_assembly_gen.asym_id_list / _refine_hist.d_res_low
Revision 1.4Mar 27, 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: Bile acid receptor
C: Retinoic acid receptor RXR-alpha
F: Peptide from Nuclear receptor coactivator 2
J: Peptide from Nuclear receptor coactivator 2
D: Bile acid receptor
H: Peptide from Nuclear receptor coactivator 2
B: Retinoic acid receptor RXR-alpha
I: Peptide from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,55612
Polymers109,0788
Non-polymers1,4784
Water1,24369
1
A: Bile acid receptor
J: Peptide from Nuclear receptor coactivator 2
B: Retinoic acid receptor RXR-alpha
I: Peptide from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2786
Polymers54,5394
Non-polymers7392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Retinoic acid receptor RXR-alpha
F: Peptide from Nuclear receptor coactivator 2
D: Bile acid receptor
H: Peptide from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2786
Polymers54,5394
Non-polymers7392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.873, 95.484, 116.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ADCB

#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: 26673.674 Da / Num. of mol.: 2 / Fragment: UNP residues 259-486 / Mutation: C480Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H4, BAR, FXR, HRR1, RIP14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RI1
#2: Protein Retinoic acid receptor RXR-alpha / Nuclear receptor subfamily 2 group B member 1 / Retinoid X receptor alpha


Mass: 25897.021 Da / Num. of mol.: 2 / Fragment: UNP residues 228-458
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19793

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Peptide from Nuclear receptor coactivator ... , 2 types, 4 molecules FIJH

#3: Protein/peptide Peptide from Nuclear receptor coactivator 2


Mass: 1161.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS
#4: Protein/peptide Peptide from Nuclear receptor coactivator 2


Mass: 806.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS

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Non-polymers , 3 types, 73 molecules

#5: Chemical ChemComp-33Y / 1-methylethyl 3-[(3,4-difluorophenyl)carbonyl]-1,1-dimethyl-1,2,3,6-tetrahydroazepino[4,5-b]indole-5-carboxylate


Mass: 438.466 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C25H24F2N2O3
#6: Chemical ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4% v/v Tacsimate pH 8.0, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 25979 / % possible obs: 97.2 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.043 / Rrim(I) all: 0.138 / Χ2: 0.981 / Net I/σ(I): 3.5 / Num. measured all: 320129
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.89.20.94510210.9360.3030.9961.00877.7
2.8-2.859.70.92910930.920.2980.9790.97983.9
2.85-2.910.411960.9490.3120.96689.7
2.9-2.9611.312230.9020.3520.97894.7
2.96-3.0311.612810.9420.3120.95998.1
3.03-3.1120.87213210.950.2580.9110.95899.4
3.1-3.1712.50.66113120.990.1930.690.988100
3.17-3.2612.90.66513190.9810.1910.6920.997100
3.26-3.36130.55613280.9850.160.5790.993100
3.36-3.4613.10.38313090.9920.110.3991.006100
3.46-3.5912.30.31113440.9930.0920.3241.026100
3.59-3.7312.40.24113130.9930.0710.2511.042100
3.73-3.913.50.19813310.9980.0560.2051.047100
3.9-4.1113.90.15613340.9980.0430.1621.029100
4.11-4.3613.70.1313360.9980.0360.1351.032100
4.36-4.713.40.10813480.9980.0310.1131.006100
4.7-5.1712.60.10213400.9980.030.1071.004100
5.17-5.9212.20.09213680.9980.0270.0960.928100
5.92-7.4613.40.07913860.9990.0220.0820.915100
7.46-5011.80.03914760.9990.0120.0410.769100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.858 / SU B: 20.894 / SU ML: 0.409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.586 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2901 968 5.1 %RANDOM
Rwork0.2297 ---
obs0.2329 17944 70.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.06 Å2 / Biso mean: 43.757 Å2 / Biso min: 8.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å20 Å2
2---0.45 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7228 0 108 69 7405
Biso mean--27.84 25.93 -
Num. residues----896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197487
X-RAY DIFFRACTIONr_bond_other_d0.0060.027172
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.99110116
X-RAY DIFFRACTIONr_angle_other_deg1.065316633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.90524.26338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.401151381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9141543
X-RAY DIFFRACTIONr_chiral_restr0.0760.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218081
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021472
LS refinement shellResolution: 2.753→2.824 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 26 -
Rwork0.302 435 -
all-461 -
obs--23.75 %

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