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- PDB-6hl0: Crystal Structure of Farnesoid X receptor (FXR) with bound NCoA-2... -

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Basic information

Entry
Database: PDB / ID: 6hl0
TitleCrystal Structure of Farnesoid X receptor (FXR) with bound NCoA-2 peptide
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 / intracellular bile acid receptor signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / bile acid receptor activity / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid ...regulation of urea metabolic process / intracellular bile acid receptor signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / bile acid receptor activity / 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 / cellular response to organonitrogen compound / toll-like receptor 9 signaling pathway / negative regulation of monocyte chemotactic protein-1 production / intracellular receptor signaling pathway / bile acid metabolic process / nitrogen catabolite activation of transcription from RNA polymerase II promoter / cell-cell junction assembly / bile acid binding / bile acid signaling pathway / negative regulation of interleukin-2 production / cellular response to fatty acid / 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 / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor-mediated signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / fatty acid homeostasis / nuclear retinoid X receptor binding / negative regulation of canonical NF-kappaB signal transduction / positive regulation of insulin receptor signaling pathway / Recycling of bile acids and salts / Notch signaling pathway / positive regulation of adipose tissue development / cholesterol homeostasis / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / euchromatin / SUMOylation of intracellular receptors / 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 / chromatin / regulation of DNA-templated transcription / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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
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


Theoretical massNumber of molelcules
Total (without water)28,7532
Polymers28,7532
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein/Peptide Complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-7 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.359, 34.558, 82.880
Angle α, β, γ (deg.)90.00, 103.05, 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 / 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 / Details: Polypeptide / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.28 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting 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: 0.91841 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: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.66→41.58 Å / Num. obs: 26862 / % possible obs: 95.5 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.073 / Rrim(I) all: 0.14 / Net I/σ(I): 6.8
Reflection shellResolution: 1.66→1.75 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 2941 / CC1/2: 0.123 / % possible all: 74

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QE6

4qe6
PDB Unreleased entry


Resolution: 1.66→41.578 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.32
RfactorNum. reflection% reflection
Rfree0.2458 760 2.83 %
Rwork0.2153 --
obs0.2161 26860 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.66→41.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 0 141 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072055
X-RAY DIFFRACTIONf_angle_d0.8982774
X-RAY DIFFRACTIONf_dihedral_angle_d19.2071264
X-RAY DIFFRACTIONf_chiral_restr0.054311
X-RAY DIFFRACTIONf_plane_restr0.007356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6601-1.78820.36341140.35274132X-RAY DIFFRACTION76
1.7882-1.96820.35851550.31265390X-RAY DIFFRACTION99
1.9682-2.2530.29241400.2385476X-RAY DIFFRACTION100
2.253-2.83840.2451760.21285488X-RAY DIFFRACTION100
2.8384-41.59060.20881750.17525614X-RAY DIFFRACTION100
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)
12.51280.3439-1.25793.6040.27336.76720.0131-0.0233-0.03430.0860.0226-0.11460.57480.4158-0.01090.2645-0.00850.02850.150.00190.1989-20.382-26.8942113.5393
28.18982.1088-4.72643.6738-1.76035.3273-0.14770.0106-1.130.3539-0.2890.26520.0322-0.20770.38630.33790.02240.09410.28930.01790.4767-8.0396-23.931484.5477
33.3222-0.1304-2.20361.51670.24234.4157-0.07110.1069-0.1017-0.0679-0.12790.1378-0.0428-0.30770.16210.18680.0072-0.03990.1672-0.00840.1703-19.8146-13.224395.639
44.2399-1.8858-0.70245.27651.11633.4809-0.01350.1358-0.3148-0.4522-0.0419-0.35410.07220.320.01110.2195-0.07520.03740.30910.01390.2453-8.4805-16.873899.2411
51.11360.8692-0.15041.28710.33323.4257-0.09480.1291-0.16640.09150.0642-0.251-0.04110.19190.05090.16490.0177-0.00270.38440.0630.31930.5935-15.594294.7281
64.8162-3.39481.44886.8332-1.07673.1335-0.22780.1627-0.0760.36470.1596-0.1296-0.1825-0.00820.08270.2322-0.0410.00490.1507-0.02420.1278-16.6006-13.2709108.0456
72.4124-0.85562.07172.0349-1.48922.9303-0.1814-0.19540.00250.43490.1407-0.0847-0.2174-0.1232-0.00840.2235-0.0018-0.0090.1069-0.01010.1435-15.1687-17.745117.6585
80.1805-0.73880.87054.0062-5.85798.7675-0.11060.18460.17060.2906-0.1141-0.2915-0.60450.47590.29710.2385-0.0658-0.0440.24960.00650.2704-6.5053-7.4434104.5181
92.71860.61250.67283.6187-0.14742.74080.09490.71160.4577-0.7141-0.05-0.27390.2769-0.0554-0.01520.3250.0450.030.35940.0460.2826-12.482-4.360585.2451
107.497-0.08880.35532.557-0.1338.8616-0.0002-0.46220.09580.96540.113-0.0023-0.1234-0.0432-0.04960.24680.0032-0.0430.2685-0.00390.2303-29.6133-10.176591.9101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 241 through 262 )
2X-RAY DIFFRACTION2chain 'A' and (resid 263 through 279 )
3X-RAY DIFFRACTION3chain 'A' and (resid 280 through 323 )
4X-RAY DIFFRACTION4chain 'A' and (resid 324 through 338 )
5X-RAY DIFFRACTION5chain 'A' and (resid 339 through 375 )
6X-RAY DIFFRACTION6chain 'A' and (resid 376 through 400 )
7X-RAY DIFFRACTION7chain 'A' and (resid 401 through 428 )
8X-RAY DIFFRACTION8chain 'A' and (resid 429 through 452 )
9X-RAY DIFFRACTION9chain 'A' and (resid 453 through 471 )
10X-RAY DIFFRACTION10chain 'B' and (resid 740 through 752 )

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