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- PDB-4jyg: Crystal structure of RARbeta LBD in complex with agonist BMS411 [... -

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Basic information

Entry
Database: PDB / ID: 4jyg
TitleCrystal structure of RARbeta LBD in complex with agonist BMS411 [4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)carbonyl]amino}benzoic acid]
Components
  • Retinoic acid receptor beta
  • Steroid Receptor Coactivator 1
KeywordsTranscription/Agonist / Ligand binding domain / Nuclear hormone receptor / Transcription-Agonist complex
Function / homology
Function and homology information


ventricular cardiac muscle cell differentiation / embryonic eye morphogenesis / growth plate cartilage development / glandular epithelial cell development / embryonic digestive tract development / striatum development / outflow tract septum morphogenesis / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway ...ventricular cardiac muscle cell differentiation / embryonic eye morphogenesis / growth plate cartilage development / glandular epithelial cell development / embryonic digestive tract development / striatum development / outflow tract septum morphogenesis / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / negative regulation of chondrocyte differentiation / embryonic hindlimb morphogenesis / neural precursor cell proliferation / regulation of myelination / Signaling by Retinoic Acid / ureteric bud development / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / hypothalamus development / male mating behavior / heterocyclic compound binding / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / response to retinoic acid / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / negative regulation of stem cell proliferation / 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 / estrogen receptor signaling pathway / positive regulation of adipose tissue development / neurogenesis / : / 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) / hippocampus development / response to progesterone / stem cell proliferation / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / multicellular organism growth / cerebral cortex development / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / sequence-specific double-stranded DNA binding / : / response to estradiol / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription regulator complex / Estrogen-dependent gene expression / cell differentiation / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process
Similarity search - Function
: / : / Retinoic acid 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 ...: / : / Retinoic acid 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 / 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-1NY / CITRATE ANION / Retinoic acid receptor beta / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsNadendla, E.K. / Teyssier, C. / Germain, P. / Delfosse, V. / Bourguet, W.
CitationJournal: Plos One / Year: 2015
Title: An Unexpected Mode Of Binding Defines BMS948 as A Full Retinoic Acid Receptor beta (RAR beta , NR1B2) Selective Agonist.
Authors: Nadendla, E. / Teyssier, C. / Delfosse, V. / Vivat, V. / Krishnasamy, G. / Gronemeyer, H. / Bourguet, W. / Germain, P.
History
DepositionMar 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: Retinoic acid receptor beta
B: Retinoic acid receptor beta
F: Steroid Receptor Coactivator 1
G: Steroid Receptor Coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9168
Polymers63,5784
Non-polymers1,3384
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-29 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.240, 84.830, 108.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein Retinoic acid receptor beta / RAR-beta / HBV-activated protein / Nuclear receptor subfamily 1 group B member 2 / RAR-epsilon


Mass: 30197.000 Da / Num. of mol.: 2 / Fragment: Ligand binding domain, UNP residues 176-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARB, HAP, NR1B2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P10826
#2: Protein/peptide Steroid Receptor Coactivator 1 / SRC-1


Mass: 1591.880 Da / Num. of mol.: 2 / Fragment: UNP residues 686-698 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase

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Non-polymers , 4 types, 205 molecules

#3: Chemical ChemComp-1NY / 4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)carbonyl]amino}benzoic acid


Mass: 397.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H23NO3
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsLEU 414 to MET CONFLICT IN UNP ENTRY P10826

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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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 200 mM Tri Sodium Citrate pH 5.5, 25 % PEG 4000, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979759 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2010 / Details: Mirror
RadiationMonochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979759 Å / Relative weight: 1
ReflectionResolution: 2.35→48.03 Å / Num. obs: 22384 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rsym value: 0.057 / Net I/σ(I): 19.59
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.35-2.483.53.7928690.289185.2
2.48-2.654.75.6634470.254198.2
2.65-2.864.98.2532230.177199.8
2.86-3.134.812.4830030.115199.9
3.13-3.54.820.2427380.068199.7
3.5-4.044.833.4824550.038199.4
4.04-4.944.742.4320740.029199.3
4.94-6.954.640.7216210.031198.7
6.95-48.034.454.979540.017196.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→39.5 Å / SU ML: 0.35 / σ(F): 2.01 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1119 5 %Random
Rwork0.1986 ---
obs0.2016 22371 97.09 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.633 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.2778 Å20 Å20 Å2
2--13.3649 Å2-0 Å2
3---3.9129 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 97 201 4175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044067
X-RAY DIFFRACTIONf_angle_d0.8355514
X-RAY DIFFRACTIONf_dihedral_angle_d13.0991559
X-RAY DIFFRACTIONf_chiral_restr0.086656
X-RAY DIFFRACTIONf_plane_restr0.004693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.45690.32531190.26182260X-RAY DIFFRACTION84
2.4569-2.58650.28951360.24882582X-RAY DIFFRACTION96
2.5865-2.74850.32911420.23052689X-RAY DIFFRACTION100
2.7485-2.96060.29071420.2322695X-RAY DIFFRACTION100
2.9606-3.25840.29661440.22072727X-RAY DIFFRACTION100
3.2584-3.72960.27621420.19772715X-RAY DIFFRACTION100
3.7296-4.69770.21361450.16332741X-RAY DIFFRACTION99
4.6977-39.50550.21681490.17662843X-RAY DIFFRACTION98

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