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- PDB-4qe8: FXR with DM175 and NCoA-2 peptide -

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Basic information

Entry
Database: PDB / ID: 4qe8
TitleFXR with DM175 and NCoA-2 peptide
Components
  • Bile acid receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Receptor / bile acid receptor dna
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 / : / cellular response to bile acid / intracellular triglyceride homeostasis / urea metabolic process / negative regulation of interleukin-1 production / negative regulation of very-low-density lipoprotein particle remodeling ...chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of ammonia assimilation cycle / regulation of low-density lipoprotein particle clearance / : / cellular response to bile acid / intracellular triglyceride homeostasis / urea metabolic process / negative regulation of interleukin-1 production / negative regulation of very-low-density lipoprotein particle remodeling / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of bile acid biosynthetic process / negative regulation of monocyte chemotactic protein-1 production / toll-like receptor 9 signaling pathway / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / bile acid binding / cellular response to fatty acid / cell-cell junction assembly / regulation of cholesterol metabolic process / positive regulation of interleukin-17 production / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / negative regulation of interleukin-2 production / negative regulation of interleukin-6 production / locomotor rhythm / negative regulation of type II interferon production / aryl hydrocarbon receptor binding / 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 / fatty acid homeostasis / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of insulin receptor signaling pathway / negative regulation of tumor necrosis factor-mediated signaling pathway / nuclear retinoid X receptor binding / Recycling of bile acids and salts / transcription regulator inhibitor activity / cellular response to hormone stimulus / intracellular receptor signaling pathway / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / positive regulation of adipose tissue development / bile acid and bile salt transport / cholesterol homeostasis / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of cellular response to insulin stimulus / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / negative regulation of smoothened signaling pathway / intracellular glucose homeostasis / nuclear receptor binding / negative regulation of canonical NF-kappaB signal transduction / transcription coregulator binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / circadian regulation of gene expression / RNA polymerase II transcription regulator complex / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / negative regulation of inflammatory response / euchromatin / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / mRNA transcription by RNA polymerase II / nuclear receptor activity / transcription coregulator activity / cellular response to lipopolysaccharide / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / sequence-specific DNA binding / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / signaling receptor complex / transcription coactivator activity / defense response to bacterium / nuclear speck / protein dimerization activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / DNA-binding transcription factor activity / protein domain specific binding / innate immune response / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription
Similarity search - Function
Bile acid receptor, ligand binding domain / Thyroid hormone receptor / 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 ...Bile acid receptor, ligand binding domain / Thyroid hormone receptor / 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-31D / Nuclear receptor coactivator 2 / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsKudlinzki, D. / Merk, D. / Linhard, V.L. / Saxena, K. / Sreeramulu, S. / Nilsson, E. / Dekker, N. / Wissler, L. / Bamberg, K. / Schubert-Zsilavecz, M. / Schwalbe, H.
CitationJournal: To be Published
Title: FXR with DM175 and NCoA-2 peptide
Authors: Kudlinzki, D. / Merk, D. / Linhard, V.L. / Saxena, K. / Sreeramulu, S. / Nilsson, E. / Dekker, N. / Wissler, L. / Bamberg, K. / Schubert-Zsilavecz, M. / Schwalbe, H.
History
DepositionMay 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _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
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,00614
Polymers57,6204
Non-polymers1,38610
Water2,072115
1
A: Bile acid receptor
C: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4757
Polymers28,8102
Non-polymers6655
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint2 kcal/mol
Surface area12380 Å2
MethodPISA
2
B: Bile acid receptor
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5317
Polymers28,8102
Non-polymers7215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-0 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.483, 48.683, 82.201
Angle α, β, γ (deg.)88.89, 78.10, 85.07
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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: 27216.264 Da / Num. of mol.: 2 / Fragment: unp residues 258-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H4, BAR, FXR, HRR1, RIP14 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q96RI1
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1593.844 Da / Num. of mol.: 2 / Fragment: unp residues 740-752 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596

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Non-polymers , 4 types, 125 molecules

#3: Chemical ChemComp-31D / 4-({2-[(4-tert-butylbenzoyl)amino]benzoyl}amino)benzoic acid


Mass: 416.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H24N2O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 300 mM MgCl2, 100 mM Bis-Tris, 15-20% PEG 3350, pH 7, VAPOR DIFFUSION, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.98
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.62→80.44 Å / Num. obs: 15585

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
autoPROCdata scaling
ABSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→80.44 Å / σ(F): 1.96 / Phase error: 32.68 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.273 730 4.68 %
Rwork0.249 --
obs0.252 15585 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.62→80.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 98 115 4101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074055
X-RAY DIFFRACTIONf_angle_d1.1625454
X-RAY DIFFRACTIONf_dihedral_angle_d21.9841554
X-RAY DIFFRACTIONf_chiral_restr0.049603
X-RAY DIFFRACTIONf_plane_restr0.015690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.615-2.81330.31621300.30362927X-RAY DIFFRACTION94
2.8133-3.08980.32521540.28552912X-RAY DIFFRACTION94
3.0898-3.52210.31161660.26452901X-RAY DIFFRACTION94
3.5221-4.38320.2361260.22382969X-RAY DIFFRACTION95
4.3832-10.50770.23891510.22972916X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.6939-0.9028-0.52218.2782-1.06245.08750.033-0.0310.27510.1246-0.24060.1387-0.9108-1.3568-0.22360.46910.1103-0.13820.4767-0.06580.2859-24.820520.173529.5276
24.9877-2.49462.72281.8891-2.62094.26640.0553-0.66940.3296-0.69990.2255-0.0596-0.0059-0.4978-0.37850.3768-0.0853-0.08190.50520.01550.6353-22.329-5.581212.8481
32.2521.01640.79772.60194.27563.3827-0.1427-0.020.0060.13940.09310.45690.1043-0.14680.12320.2842-0.0035-0.04650.28250.05970.2769-12.22687.438817.2199
47.13886.2439-0.01625.67721.02836.7889-0.0017-0.5252-1.2590.7791-0.1502-0.60020.2455-0.76940.09660.679-0.1034-0.11560.36970.03950.4449-17.3092-10.708821.4195
57.1795-3.0076-3.22347.22142.45486.1684-0.6149-0.7318-1.20920.99350.18690.39770.93650.10270.58680.4855-0.016-0.05910.42090.12440.4118-14.30960.899130.1681
64.52540.8999-2.43831.1625-0.45573.76320.1606-0.6874-0.080.4352-0.1542-0.1955-0.12980.2823-0.0070.3432-0.0437-0.09420.38230.01150.2289-12.167217.004132.9297
74.8869-0.7376-2.12122.02411.32785.0296-0.3234-0.2525-0.67310.17780.2181-0.13630.6551.34240.24080.32350.0155-0.050.40730.0510.3878-4.73421.655621.7107
88.41682.91970.33917.6636-0.55284.6787-0.3217-0.2952-0.34620.218-0.43930.85030.8271-1.25570.33690.3683-0.119-0.02990.5707-0.03780.3065-24.8883.7182-21.7282
96.2972.8471-0.09552.058-4.85718.583-0.03190.81910.18960.19850.468-0.3489-0.42610.44860.40020.37120.055-0.01960.62410.1070.688-21.665530.4346-5.5325
104.2528-0.6223-1.2392.73862.77832.54860.0505-0.08080.08420.0848-0.2410.2267-0.27250.03150.19140.3718-0.0178-0.04290.36850.03870.2068-12.451515.821-10.7197
112.0317-4.0292-5.29134.8001-2.03897.5334-0.54270.88170.8731-0.1616-0.1348-0.5546-0.5132-0.04880.56110.8242-0.0822-0.08540.54510.22910.5788-16.026735.0676-14.254
122.9084-0.06921.32173.1955-0.60564.5496-0.03460.51620.5867-0.2622-0.2244-0.2306-0.63990.08430.18780.3868-0.0433-0.03260.39670.11310.3198-10.918117.7064-21.8985
133.6215-0.02152.92241.536-0.62776.00640.36330.61690.208-0.6586-0.4253-0.31750.5346-0.4093-0.17040.2908-0.0504-0.0240.47340.02640.2122-15.88856.0245-29.5065
142.94761.81632.65762.23361.91495.1909-0.39541.07740.7213-0.15590.09530.1216-1.21580.71910.23020.5136-0.108-0.00560.37720.08420.3892-6.195519.662-23.6157
152.4077-1.897-0.17494.10945.43922.0191-0.1671-0.92370.91681.2017-0.5196-2.634-0.24421.92380.26990.69950.0015-0.07490.4205-0.439-0.0398-2.417722.2102-3.804
161.99714.1647.24572.1091-0.34472.0539-0.34031.21481.2228-0.01990.3592-0.0254-0.81741.078-0.13180.61580.0664-0.08680.5567-0.01840.2873-9.051916.26717.1678
177.3371-0.5612-8.16746.91830.96149.202-0.6277-1.4956-1.1251-0.4128-0.0770.32821.7020.44180.52890.59610.0527-0.03630.5906-0.00130.2771-9.55887.0884-0.7386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 243 through 260 )
2X-RAY DIFFRACTION2chain 'A' and (resid 261 through 279 )
3X-RAY DIFFRACTION3chain 'A' and (resid 280 through 336 )
4X-RAY DIFFRACTION4chain 'A' and (resid 337 through 358 )
5X-RAY DIFFRACTION5chain 'A' and (resid 359 through 390 )
6X-RAY DIFFRACTION6chain 'A' and (resid 391 through 428 )
7X-RAY DIFFRACTION7chain 'A' and (resid 429 through 472 )
8X-RAY DIFFRACTION8chain 'B' and (resid 243 through 262 )
9X-RAY DIFFRACTION9chain 'B' and (resid 263 through 279 )
10X-RAY DIFFRACTION10chain 'B' and (resid 280 through 338 )
11X-RAY DIFFRACTION11chain 'B' and (resid 339 through 358 )
12X-RAY DIFFRACTION12chain 'B' and (resid 359 through 400 )
13X-RAY DIFFRACTION13chain 'B' and (resid 401 through 428 )
14X-RAY DIFFRACTION14chain 'B' and (resid 429 through 451 )
15X-RAY DIFFRACTION15chain 'B' and (resid 452 through 472 )
16X-RAY DIFFRACTION16chain 'C' and (resid 740 through 752 )
17X-RAY DIFFRACTION17chain 'D' and (resid 741 through 752 )

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