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- PDB-6hl1: Crystal Structure of Farnesoid X receptor (FXR) with bound NCoA-2... -

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Basic information

Entry
Database: PDB / ID: 6hl1
TitleCrystal Structure of Farnesoid X receptor (FXR) with bound NCoA-2 peptide and CDCA
Components
  • Bile acid receptor
  • NCoA-2 peptide (Nuclear receptor coactivator 2), LYS-GLU-ASN-ALA-LEU-LEU-ARG-TYR-LEU-LEU-ASP-LYS-ASP
KeywordsNUCLEAR PROTEIN / Activator / DNA-binding / Receptor / Repressor / 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 / bile acid binding / cell-cell junction assembly / bile acid signaling pathway / cellular response to fatty acid / negative regulation of interleukin-2 production / regulation of cholesterol metabolic process / 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 / negative regulation of tumor necrosis factor-mediated signaling pathway / 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 / negative regulation of canonical NF-kappaB signal transduction / Recycling of bile acids and salts / Notch signaling pathway / positive regulation of adipose tissue development / transcription coregulator binding / cholesterol homeostasis / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / euchromatin / PPARA activates gene expression / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / nuclear receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm
Similarity search - Function
Bile acid receptor, ligand binding domain / Thyroid hormone receptor / 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 ...Bile acid receptor, ligand binding domain / Thyroid hormone receptor / 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
CHENODEOXYCHOLIC ACID / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsKudlinzki, D. / Merk, D. / Linhard, V.L. / Saxena, K. / Schubert-Zsilavecz, M. / Schwalbe, H.
CitationJournal: Nat Commun / Year: 2019
Title: Molecular tuning of farnesoid X receptor partial agonism.
Authors: Merk, D. / Sreeramulu, S. / Kudlinzki, D. / Saxena, K. / Linhard, V. / Gande, S.L. / Hiller, F. / Lamers, C. / Nilsson, E. / Aagaard, A. / Wissler, L. / Dekker, N. / Bamberg, K. / Schubert- ...Authors: Merk, D. / Sreeramulu, S. / Kudlinzki, D. / Saxena, K. / Linhard, V. / Gande, S.L. / Hiller, F. / Lamers, C. / Nilsson, E. / Aagaard, A. / Wissler, L. / Dekker, N. / Bamberg, K. / Schubert-Zsilavecz, M. / Schwalbe, H.
History
DepositionSep 10, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionMay 29, 2019ID: 4QE6
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: NCoA-2 peptide (Nuclear receptor coactivator 2), LYS-GLU-ASN-ALA-LEU-LEU-ARG-TYR-LEU-LEU-ASP-LYS-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1463
Polymers28,7532
Non-polymers3931
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein/Peptide Complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-3 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.444, 33.815, 83.040
Angle α, β, γ (deg.)90.00, 101.47, 90.00
Int Tables number5
Space group name H-MC121

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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: 27159.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Protein Domain with bound CDCA / Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H4, BAR, FXR, HRR1, RIP14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RI1
#2: Protein/peptide NCoA-2 peptide (Nuclear receptor coactivator 2), LYS-GLU-ASN-ALA-LEU-LEU-ARG-TYR-LEU-LEU-ASP-LYS-ASP


Mass: 1593.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-JN3 / CHENODEOXYCHOLIC ACID / (3ALPHA,5ALPHA,7BETA,8ALPHA,17ALPHA)-3,7-DIHYDROXYCHOLAN-24-OIC ACID


Mass: 392.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.23 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Ca(CH3COO)2, 10 mM DTT, 25-30% PEG 3350, 100 mM Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.98004 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98004 Å / Relative weight: 1
ReflectionResolution: 1.599→34.236 Å / Num. obs: 29422 / % possible obs: 95.4 % / Redundancy: 6.74 % / Biso Wilson estimate: 31.17 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.049 / Net I/σ(I): 24.06
Reflection shellResolution: 1.599→1.7 Å / Redundancy: 4.58 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3739 / CC1/2: 0.736 / Rrim(I) all: 0.846 / % possible all: 75.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3259: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QE6

4qe6
PDB Unreleased entry


Resolution: 1.599→34.236 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.05
RfactorNum. reflection% reflection
Rfree0.246 1471 5 %
Rwork0.1979 --
obs0.2 29411 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.599→34.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 28 183 2177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072020
X-RAY DIFFRACTIONf_angle_d0.7752727
X-RAY DIFFRACTIONf_dihedral_angle_d18.2181244
X-RAY DIFFRACTIONf_chiral_restr0.048306
X-RAY DIFFRACTIONf_plane_restr0.005351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.599-1.65060.3982950.29861801X-RAY DIFFRACTION69
1.6506-1.70960.32551190.27162249X-RAY DIFFRACTION85
1.7096-1.7780.32161340.25232548X-RAY DIFFRACTION96
1.778-1.85890.2971370.24052618X-RAY DIFFRACTION100
1.8589-1.95690.25821390.22172647X-RAY DIFFRACTION100
1.9569-2.07950.25841400.21362658X-RAY DIFFRACTION100
2.0795-2.240.27661400.19882654X-RAY DIFFRACTION100
2.24-2.46540.19951390.19042649X-RAY DIFFRACTION100
2.4654-2.8220.24681420.19272693X-RAY DIFFRACTION100
2.822-3.55490.25311410.19692669X-RAY DIFFRACTION100
3.5549-34.24380.22381450.17642754X-RAY DIFFRACTION99
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)
13.13481.628-2.09073.09441.14164.17380.0123-0.0828-0.04280.03970.03250.0480.23320.0998-0.0710.26520.0273-0.0050.13420.01530.2616-1.0266-26.751233.8082
22.8111-1.9327-0.53073.6064-0.60117.4748-0.24930.0494-0.5903-0.8590.34530.32861.52890.6663-0.20830.49030.0848-0.00020.4381-0.04160.40079.4365-23.70224.9492
32.6044-0.0836-0.63020.7908-0.18774.8678-0.04190.2078-0.1294-0.0624-0.0346-0.0730.12330.47870.09120.1693-0.0052-0.00070.1601-0.01580.15735.5895-14.34314.4547
43.6232.1738-2.40197.2246-5.44636.8728-0.19880.1903-0.0104-0.0687-0.1742-0.396-0.19731.16340.46860.2598-0.1346-0.05690.72440.02130.260620.0176-11.198519.9855
57.4994-6.43770.27519.05450.19153.2071-0.0603-0.05850.21420.05110.1439-0.1435-0.09140.0124-0.03180.1557-0.0240.00610.1255-0.01790.13822.3492-12.852827.5172
63.2826-1.81532.32874.0969-2.7243.8666-0.2073-0.1477-0.02190.50430.1222-0.15-0.1949-0.05310.04220.1847-0.0143-0.01720.0807-0.02250.15274.1591-17.492837.0771
70.1297-0.32410.31757.4968-6.38285.3748-0.19110.29440.1640.28130.1256-0.1978-0.79850.40460.03630.3827-0.137-0.03360.2690.01660.310111.9347-6.879325.2285
86.6293.6637-2.86333.4637-1.17875.49870.20490.57440.66980.1854-0.03730.1141-1.05480.2957-0.27870.3095-0.0729-0.01840.29980.0610.20366.1968-4.0135.0335
97.08650.4614-0.83961.90780.43658.5481-0.0769-0.13770.23470.09390.13310.5084-0.5556-1.23250.06940.29370.0842-0.0270.43970.0080.2466-10.2032-10.091211.5018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 242 through 260 )
2X-RAY DIFFRACTION2chain 'A' and (resid 261 through 279 )
3X-RAY DIFFRACTION3chain 'A' and (resid 280 through 358 )
4X-RAY DIFFRACTION4chain 'A' and (resid 359 through 375 )
5X-RAY DIFFRACTION5chain 'A' and (resid 376 through 400 )
6X-RAY DIFFRACTION6chain 'A' and (resid 401 through 428 )
7X-RAY DIFFRACTION7chain 'A' and (resid 429 through 451 )
8X-RAY DIFFRACTION8chain 'A' and (resid 452 through 472 )
9X-RAY DIFFRACTION9chain 'B' and (resid 740 through 752 )

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