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- PDB-1xiu: Crystal structure of the agonist-bound ligand-binding domain of B... -

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Basic information

Entry
Database: PDB / ID: 1xiu
TitleCrystal structure of the agonist-bound ligand-binding domain of Biomphalaria glabrata RXR
Components
  • Nuclear receptor coactivator 1
  • RXR-like protein
KeywordsTRANSCRIPTION/TRANSFERASE / Nuclear Receptor / Protein-Ligand complex / Retinoid Receptor / TRANSCRIPTION-TRANSFERASE COMPLEX
Function / homology
Function and homology information


retinal binding / 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 / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H2AK5 acetyltransferase activity ...retinal binding / 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 / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H3K4 acetyltransferase activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3K9 acetyltransferase activity / male mating behavior / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K122 acetyltransferase activity / hypothalamus development / histone H3K18 acetyltransferase activity / histone H3K27 acetyltransferase activity / nuclear steroid receptor activity / 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 / estrous cycle / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to hormone stimulus / Recycling of bile acids and salts / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / lactation / estrogen receptor signaling pathway / positive regulation of adipose tissue development / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of neuron differentiation / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / response to progesterone / Activation of gene expression by SREBF (SREBP) / cerebellum development / hippocampus development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / : / male gonad development / 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 / sequence-specific DNA binding / transcription coactivator activity / protein dimerization activity / positive regulation of apoptotic process / chromatin binding / chromatin / protein-containing complex binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Retinoid X receptor/HNF4 / : / 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 ...Retinoid X receptor/HNF4 / : / 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
(9cis)-retinoic acid / : / Nuclear receptor coactivator 1 / Retinoic acid receptor RXR
Similarity search - Component
Biological speciesBiomphalaria glabrata (bloodfluke planorb)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDe Groot, A. / De Rosny, E. / Juillan-Binard, C. / Ferrer, J.-L. / Laudet, V. / Pebay-Peroula, E. / Fontecilla-Camps, J.-C. / Borel, F.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of a Novel Tetrameric Complex of Agonist-bound Ligand-binding Domain of Biomphalaria glabrata Retinoid X Receptor.
Authors: de Groot, A. / de Rosny, E. / Juillan-Binard, C. / Ferrer, J.-L. / Laudet, V. / Pierce, R.J. / Pebay-Peyroula, E. / Fontecilla-Camps, J.-C. / Borel, F.
History
DepositionSep 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 16, 2016Group: Non-polymer description
Revision 1.4Aug 23, 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_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

Downloads & links

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Assembly

Deposited unit
A: RXR-like protein
B: RXR-like protein
E: Nuclear receptor coactivator 1
F: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9556
Polymers55,3544
Non-polymers6012
Water84747
1
A: RXR-like protein
B: RXR-like protein
E: Nuclear receptor coactivator 1
F: Nuclear receptor coactivator 1
hetero molecules

A: RXR-like protein
B: RXR-like protein
E: Nuclear receptor coactivator 1
F: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,91012
Polymers110,7088
Non-polymers1,2024
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Unit cell
Length a, b, c (Å)87.100, 87.100, 320.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -x+1+y,y,-z+1/2

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Components

#1: Protein RXR-like protein / retinoid X receptor ligand-binding domain / 9-cis retinoic acid


Mass: 25901.029 Da / Num. of mol.: 2 / Fragment: Ligand-binding domain (LBD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Biomphalaria glabrata (bloodfluke planorb)
Gene: RXR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: GenBank: 19386469, UniProt: Q8T5C6*PLUS
#2: Protein/peptide Nuclear receptor coactivator 1 / NCoA-1 / Steroid receptor coactivator-1 / SRC-1 / RIP160 / Hin-2 protein


Mass: 1776.072 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is derived from human SRC-1 coactivator.
References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, sodium formate, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 21, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 25831 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.6 % / Rsym value: 0.094 / Net I/σ(I): 19.5
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 15.8 % / Mean I/σ(I) obs: 5.98 / Rsym value: 0.54 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FBY

1fby


Resolution: 2.5→24.4 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 17.471 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24332 1292 5 %RANDOM
Rwork0.19326 ---
obs0.1958 24538 100 %-
all-24537 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.191 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å21.03 Å20 Å2
2--2.07 Å20 Å2
3----3.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3691 0 44 47 3782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0223803
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5891.9975140
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1495463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31324.012162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.76715695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.6671525
X-RAY DIFFRACTIONr_chiral_restr0.1620.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022795
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2670.21885
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.340.22646
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.41.52396
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3123746
X-RAY DIFFRACTIONr_scbond_it3.82431566
X-RAY DIFFRACTIONr_scangle_it5.9744.51394
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 91 -
Rwork0.257 1729 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 23.2564 Å / Origin y: 51.2523 Å / Origin z: 84.2538 Å
111213212223313233
T-0.0673 Å2-0.0593 Å2-0.0093 Å2--0.0092 Å20.0208 Å2---0.0714 Å2
L1.1223 °2-0.4044 °20.3496 °2-0.4323 °2-0.0528 °2--0.4167 °2
S0.0744 Å °-0.0373 Å °0.0817 Å °-0.0047 Å °-0.0847 Å °-0.0332 Å °0.0548 Å °-0.0407 Å °0.0103 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA210 - 4304 - 224
2X-RAY DIFFRACTION1BB210 - 4324 - 226

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