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- PDB-6a5w: FXR-LBD with HNC143 and SRC1 -

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Basic information

Entry
Database: PDB / ID: 6a5w
TitleFXR-LBD with HNC143 and SRC1
Components
  • Bile acid receptor
  • Nuclear receptor coactivator 1
KeywordsTRANSCRIPTION / nuclear receptor / coactivator / agonist / 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 / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / bile acid binding / cell-cell junction assembly / positive regulation of female receptivity / bile acid signaling pathway / cellular response to fatty acid / negative regulation of interleukin-2 production / regulation of cholesterol metabolic process / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / 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 / cellular response to Thyroglobulin triiodothyronine / negative regulation of tumor necrosis factor-mediated signaling pathway / estrous cycle / 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 / response to retinoic acid / negative regulation of canonical NF-kappaB signal transduction / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / Notch signaling pathway / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / transcription coregulator binding / response to progesterone / cholesterol homeostasis / hippocampus development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / Circadian Clock / response to estradiol / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity
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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / 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 / 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
Chem-9R0 / Nuclear receptor coactivator 1 / Nuclear receptor coactivator 1 / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.88 Å
AuthorsWang, N. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
31770817 China
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Ligand binding and heterodimerization with retinoid X receptor alpha (RXR alpha ) induce farnesoid X receptor (FXR) conformational changes affecting coactivator binding
Authors: Wang, N. / Zou, Q. / Xu, J. / Zhang, J. / Liu, J.
History
DepositionJun 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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: Nuclear receptor coactivator 1
C: Bile acid receptor
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6586
Polymers56,5174
Non-polymers1,1412
Water724
1
A: Bile acid receptor
B: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8293
Polymers28,2582
Non-polymers5701
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-5 kcal/mol
Surface area12190 Å2
MethodPISA
2
C: Bile acid receptor
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8293
Polymers28,2582
Non-polymers5701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-5 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.380, 98.770, 119.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUVALVALAA244 - 4711 - 228
21GLUGLUVALVALCC244 - 4711 - 228
12ASPASPASPASPBB745 - 7561 - 12
22ASPASPASPASPDD745 - 7561 - 12

NCS ensembles :
ID
1
2

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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: 26726.600 Da / Num. of mol.: 2 / Fragment: ligand binding domain / Mutation: C432E, C466E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H4, BAR, FXR, HRR1, RIP14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96RI1
#2: Protein/peptide Nuclear receptor coactivator 1


Mass: 1531.733 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: B5MCN7, UniProt: Q15788*PLUS
#3: Chemical ChemComp-9R0 / 2-[2-[[3-[2,6-bis(chloranyl)phenyl]-5-cyclopropyl-1,2-oxazol-4-yl]methoxy]-6-azaspiro[3.4]octan-6-yl]-1,3-benzothiazole-6-carboxylic acid


Mass: 570.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H25Cl2N3O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.13 Å3/Da / Density % sol: 70.19 % / Mosaicity: 1.08 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 0.1 M Sodium citrate tribasic dihydrate , 2% v/v Tacsimate pH 5.0, 16% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.88→98.77 Å / Num. obs: 21858 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.934 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.086 / Rrim(I) all: 0.217 / Net I/σ(I): 6.9 / Num. measured all: 134970 / Scaling rejects: 197
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.88-3.046.41.1871996331400.6680.5071.2941.6100
9.11-98.775.50.09643347890.9050.0470.10816.199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.23data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DCT

3dct


Resolution: 2.88→76.07 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.861 / SU B: 16.881 / SU ML: 0.291 / SU R Cruickshank DPI: 0.5786 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.579 / ESU R Free: 0.339
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 1050 4.8 %RANDOM
Rwork0.2115 ---
obs0.2139 20743 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 143.54 Å2 / Biso mean: 60.155 Å2 / Biso min: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.55 Å2-0 Å20 Å2
2---2.73 Å2-0 Å2
3----2.82 Å2
Refinement stepCycle: final / Resolution: 2.88→76.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 76 4 4030
Biso mean--53.5 37.42 -
Num. residues----480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194120
X-RAY DIFFRACTIONr_bond_other_d0.0020.023806
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9665582
X-RAY DIFFRACTIONr_angle_other_deg1.0292.9848871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3755476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08325.024205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.33115759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6031520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214460
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02784
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A150400.06
12C150400.06
21B6440.14
22D6440.14
LS refinement shellResolution: 2.88→2.955 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 62 -
Rwork0.371 1502 -
all-1564 -
obs--100 %

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