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- PDB-5tbp: Crystal Structure of RXR-alpha ligand binding domain complexed wi... -

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Basic information

Entry
Database: PDB / ID: 5tbp
TitleCrystal Structure of RXR-alpha ligand binding domain complexed with synthetic modulator K8003
ComponentsRetinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / nuclear receptor / Sulindac / AKT activation / Complex / tetramer / RXR / LBD
Function / homology
Function and homology information


positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex ...positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / 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. ...Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / 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
Chem-7A4 / ACETATE ION / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAleshin, A.E. / Liddington, R.C. / Su, Y. / Zhang, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM089927 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA140980 United States
CitationJournal: Nat Commun / Year: 2017
Title: Modulation of nongenomic activation of PI3K signalling by tetramerization of N-terminally-cleaved RXR alpha.
Authors: Chen, L. / Aleshin, A.E. / Alitongbieke, G. / Zhou, Y. / Zhang, X. / Ye, X. / Hu, M. / Ren, G. / Chen, Z. / Ma, Y. / Zhang, D. / Liu, S. / Gao, W. / Cai, L. / Wu, L. / Zeng, Z. / Jiang, F. / ...Authors: Chen, L. / Aleshin, A.E. / Alitongbieke, G. / Zhou, Y. / Zhang, X. / Ye, X. / Hu, M. / Ren, G. / Chen, Z. / Ma, Y. / Zhang, D. / Liu, S. / Gao, W. / Cai, L. / Wu, L. / Zeng, Z. / Jiang, F. / Liu, J. / Zhou, H. / Cadwell, G. / Liddington, R.C. / Su, Y. / Zhang, X.K.
History
DepositionSep 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
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: Retinoic acid receptor RXR-alpha
B: Retinoic acid receptor RXR-alpha
C: Retinoic acid receptor RXR-alpha
D: Retinoic acid receptor RXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,77220
Polymers109,0784
Non-polymers2,69416
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14090 Å2
ΔGint-59 kcal/mol
Surface area33460 Å2
2
A: Retinoic acid receptor RXR-alpha
C: Retinoic acid receptor RXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,95511
Polymers54,5392
Non-polymers1,4169
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-31 kcal/mol
Surface area19030 Å2
MethodPISA
3
B: Retinoic acid receptor RXR-alpha
D: Retinoic acid receptor RXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8179
Polymers54,5392
Non-polymers1,2787
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-31 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.640, 99.380, 109.860
Angle α, β, γ (deg.)90.00, 99.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Retinoic acid receptor RXR-alpha / Nuclear receptor subfamily 2 group B member 1 / Retinoid X receptor alpha


Mass: 27269.514 Da / Num. of mol.: 4 / Fragment: UNP residues 223-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P19793

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Non-polymers , 5 types, 150 molecules

#2: Chemical
ChemComp-7A4 / [(1Z)-5-fluoro-2-methyl-1-{[4-(propan-2-yl)phenyl]methylidene}-1H-inden-3-yl]acetic acid


Mass: 336.399 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H21FO2
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.2 ul of 0.35 mM protein and 0.6 mM ligand in 100 mM NaCl, 20 mM Tris-Cl were mixed with 0.2 ul of the well solution (20% PEG3330 and 0.2M Na Acetate)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: AREA DETECTOR / Date: Apr 7, 2013 / Details: VariMax optic
RadiationMonochromator: VariMax optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→36.15 Å / Num. obs: 30187 / % possible obs: 98.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.1
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.56 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX(DEV_2645: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N8R

4n8r


Resolution: 2.6→36.15 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1501 4.97 %Random selection
Rwork0.196 ---
obs0.198 30181 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6493 0 194 134 6821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026968
X-RAY DIFFRACTIONf_angle_d0.6059451
X-RAY DIFFRACTIONf_dihedral_angle_d14.0424226
X-RAY DIFFRACTIONf_chiral_restr0.0351042
X-RAY DIFFRACTIONf_plane_restr0.0021212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.68390.34321230.30852317X-RAY DIFFRACTION88
2.6839-2.77980.3071290.27662603X-RAY DIFFRACTION100
2.7798-2.89110.32521440.24392632X-RAY DIFFRACTION100
2.8911-3.02260.26491400.2432600X-RAY DIFFRACTION100
3.0226-3.18190.30641400.25232633X-RAY DIFFRACTION100
3.1819-3.38110.28251420.21942616X-RAY DIFFRACTION100
3.3811-3.64190.25941350.19732648X-RAY DIFFRACTION100
3.6419-4.0080.21481320.1782647X-RAY DIFFRACTION100
4.008-4.5870.21681370.16552648X-RAY DIFFRACTION100
4.587-5.77530.22911400.1782658X-RAY DIFFRACTION100
5.7753-36.15750.19871390.17412678X-RAY DIFFRACTION100

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