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- PDB-3ruu: FXR with SRC1 and GSK237 -

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Basic information

Entry
Database: PDB / ID: 3ruu
TitleFXR with SRC1 and GSK237
Components
  • Bile acid receptor
  • Nuclear receptor coactivator 1
KeywordsTRANSCRIPTION REGULATOR / nuclear receptor / alpha-helical sandwich / transcription factor / RXR / transcription co-factors / bile acid / farnesoid
Function / homology
Function and homology information


regulation of urea metabolic process / 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 urea metabolic process / 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 / 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 metabolic process / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / cell-cell junction assembly / positive regulation of female receptivity / bile acid binding / regulation of cholesterol metabolic process / cellular response to fatty acid / negative regulation of interleukin-2 production / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / bile acid and bile salt transport / hypothalamus development / positive regulation of interleukin-17 production / intracellular glucose homeostasis / negative regulation of interleukin-6 production / negative regulation of type II interferon production / intracellular receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / fatty acid homeostasis / nuclear retinoid X receptor binding / : / progesterone receptor signaling pathway / positive regulation of insulin receptor signaling pathway / response to retinoic acid / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of canonical NF-kappaB signal transduction / estrogen receptor signaling pathway / positive regulation of adipose tissue development / Notch signaling pathway / : / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of neuron differentiation / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / cholesterol homeostasis / hippocampus development / transcription coregulator binding / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / euchromatin / PPARA activates gene expression / Cytoprotection by HMOX1
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 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-37G / Nuclear receptor coactivator 1 / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.502 Å
AuthorsWilliams, S.P. / Madauss, K.P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Conformationally constrained farnesoid X receptor (FXR) agonists: Alternative replacements of the stilbene.
Authors: Akwabi-Ameyaw, A. / Caravella, J.A. / Chen, L. / Creech, K.L. / Deaton, D.N. / Madauss, K.P. / Marr, H.B. / Miller, A.B. / Navas, F. / Parks, D.J. / Spearing, P.K. / Todd, D. / Williams, S.P. / Wisely, G.B.
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,9335
Polymers28,2192
Non-polymers7143
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-27 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.605, 159.605, 159.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23

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Components

#1: Protein Bile acid receptor / FXR / Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group ...FXR / 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: 26802.789 Da / Num. of mol.: 1 / Fragment: ligand binding domain (UNP residues 258-486)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAR, FXR, HRR1, NR1H4, RIP14 / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96RI1
#2: Protein/peptide Nuclear receptor coactivator 1 / SRC1 / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / ...SRC1 / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1


Mass: 1416.645 Da / Num. of mol.: 1 / Fragment: UNP residues 745-755 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-37G / 6-(4-{[3-(2,6-dichlorophenyl)-5-(propan-2-yl)-1,2-oxazol-4-yl]methoxy}phenyl)-1H-indole-3-carboxylic acid


Mass: 521.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H22Cl2N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6.5
Details: 25% PEG3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 15, 2005
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 11725 / % possible obs: 99.7 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.065 / Χ2: 1.007 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5910.10.46311530.8581100
2.59-2.6911.10.3711680.9131100
2.69-2.8211.40.24111740.7871100
2.82-2.9611.40.17911680.8041100
2.96-3.1511.50.12711580.8431100
3.15-3.3911.40.09311820.9551100
3.39-3.7311.20.07211651.1651100
3.73-4.2711.20.0511801.2031100
4.27-5.3811.20.04111801.2371100
5.38-5010.70.03711971.309196.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.69 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.5 Å
Translation2.5 Å19.5 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.502→19.499 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8184 / SU ML: 0.33 / σ(F): 0 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 858 7.46 %
Rwork0.213 --
obs0.216 11498 98 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.736 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 201.43 Å2 / Biso mean: 63.844 Å2 / Biso min: 20.28 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.502→19.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 46 15 1928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031959
X-RAY DIFFRACTIONf_angle_d0.6652671
X-RAY DIFFRACTIONf_chiral_restr0.043303
X-RAY DIFFRACTIONf_plane_restr0.002342
X-RAY DIFFRACTIONf_dihedral_angle_d14.687695
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5024-2.65880.32831300.25761693182394
2.6588-2.86350.28891580.22821724188297
2.8635-3.15060.26851360.21821769190598
3.1506-3.6040.28341390.216517921931100
3.604-4.53120.2211400.187618121952100
4.5312-19.49940.23771550.218218502005100
Refinement TLS params.Method: refined / Origin x: 33.3694 Å / Origin y: -0.7808 Å / Origin z: -24.4602 Å
111213212223313233
T0.227 Å20.0536 Å20.1266 Å2-0.2236 Å2-0.0394 Å2--0.2587 Å2
L1.61 °2-0.2619 °2-0.698 °2-2.0207 °20.6434 °2--2.001 °2
S-0.1652 Å °-0.1353 Å °-0.0084 Å °-0.1412 Å °0.0841 Å °-0.2706 Å °0.2307 Å °0.3193 Å °-0.0708 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA244 - 2
2X-RAY DIFFRACTION1allB745 - 755
3X-RAY DIFFRACTION1allA1 - 15
4X-RAY DIFFRACTION1allA1

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