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- PDB-4n8r: Crystal structure of RXRa LBD complexed with a synthetic modulato... -

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Basic information

Entry
Database: PDB / ID: 4n8r
TitleCrystal structure of RXRa LBD complexed with a synthetic modulator K-8008
ComponentsRetinoic acid receptor RXR-alpha
KeywordsSIGNALING PROTEIN / RETINOID X RECEPTOR / ALPHA NUCLEAR RECEPTOR / NUCLEUS
Function / homology
Function and homology information


DNA binding domain binding / 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 / LBD domain binding / Carnitine metabolism ...DNA binding domain binding / 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 / LBD domain binding / Carnitine metabolism / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Synthesis of bile acids and bile salts / hormone-mediated signaling pathway / peroxisome proliferator activated 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 / RORA activates gene expression / transcription coregulator binding / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / Heme signaling / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / Circadian Clock / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / receptor complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / chromatin / 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 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 / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Ligand-binding domain of nuclear hormone receptor / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-K08 / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsAleshin, A.E. / Su, Y. / Zhang, X. / Liddington, R.C.
CitationJournal: Chem.Biol. / Year: 2014
Title: Sulindac-Derived RXR alpha Modulators Inhibit Cancer Cell Growth by Binding to a Novel Site.
Authors: Chen, L. / Wang, Z.G. / Aleshin, A.E. / Chen, F. / Chen, J. / Jiang, F. / Alitongbieke, G. / Zeng, Z. / Ma, Y. / Huang, M. / Zhou, H. / Cadwell, G. / Zheng, J.F. / Huang, P.Q. / Liddington, ...Authors: Chen, L. / Wang, Z.G. / Aleshin, A.E. / Chen, F. / Chen, J. / Jiang, F. / Alitongbieke, G. / Zeng, Z. / Ma, Y. / Huang, M. / Zhou, H. / Cadwell, G. / Zheng, J.F. / Huang, P.Q. / Liddington, R.C. / Zhang, X.K. / Su, Y.
History
DepositionOct 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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)109,7916
Polymers109,0784
Non-polymers7132
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-62 kcal/mol
Surface area34500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.038, 99.347, 93.971
Angle α, β, γ (deg.)90.00, 98.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: ligand binding domain (UNP residues 223-462)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P19793
#2: Chemical ChemComp-K08 / 5-(2-{(1Z)-2-methyl-1-[4-(propan-2-yl)benzylidene]-1H-inden-3-yl}ethyl)-1H-tetrazole


Mass: 356.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG3330, 0.2M Mg Formate, 100 MM NACL, 20 MM TRIS-CL, 0.5 MM LIGAND K-8008, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2013
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→68 Å / Num. all: 59800 / Num. obs: 58010 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.6
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.014 / Mean I/σ(I) obs: 1 / % possible all: 92

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G1U

1g1u


Resolution: 2.03→50.4 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 1859 3.33 %RANDOM
Rwork0.1916 ---
obs0.1932 55829 94.4 %-
all-59140 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.4 Å2
Refinement stepCycle: LAST / Resolution: 2.03→50.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6224 0 54 641 6919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076479
X-RAY DIFFRACTIONf_angle_d1.0488770
X-RAY DIFFRACTIONf_dihedral_angle_d12.7872433
X-RAY DIFFRACTIONf_chiral_restr0.073991
X-RAY DIFFRACTIONf_plane_restr0.0051116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.05350.34651210.32493414X-RAY DIFFRACTION81
2.0535-2.08060.34871310.32793908X-RAY DIFFRACTION93
2.0806-2.10910.33641340.29894005X-RAY DIFFRACTION94
2.1091-2.13920.28941380.27573923X-RAY DIFFRACTION93
2.1392-2.17110.36791420.27973925X-RAY DIFFRACTION94
2.1711-2.2050.29041410.27354003X-RAY DIFFRACTION93
2.205-2.24120.30331250.26783814X-RAY DIFFRACTION90
2.2412-2.27980.3271210.26853878X-RAY DIFFRACTION91
2.2798-2.32130.32821350.26053868X-RAY DIFFRACTION90
2.3213-2.3660.28571350.23683991X-RAY DIFFRACTION95
2.366-2.41420.31181450.23114131X-RAY DIFFRACTION97
2.4142-2.46670.25071420.22424081X-RAY DIFFRACTION98
2.4667-2.52410.27311380.23254135X-RAY DIFFRACTION98
2.5241-2.58720.27461420.21974067X-RAY DIFFRACTION96
2.5872-2.65720.29891420.21144054X-RAY DIFFRACTION95
2.6572-2.73540.28161410.2034009X-RAY DIFFRACTION95
2.7354-2.82370.2391400.18423904X-RAY DIFFRACTION92
2.8237-2.92460.26271360.1874081X-RAY DIFFRACTION96
2.9246-3.04160.24391460.19084111X-RAY DIFFRACTION98
3.0416-3.18010.25621470.18684217X-RAY DIFFRACTION98
3.1801-3.34770.24921370.17734110X-RAY DIFFRACTION98
3.3477-3.55740.21781460.16214029X-RAY DIFFRACTION96
3.5574-3.8320.19951410.14473925X-RAY DIFFRACTION92
3.832-4.21740.14891360.13934181X-RAY DIFFRACTION99
4.2174-4.82730.18681480.13624127X-RAY DIFFRACTION98
4.8273-6.08020.21300.17763960X-RAY DIFFRACTION93
6.0802-50.46930.18511390.15834088X-RAY DIFFRACTION96

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