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- PDB-1fby: CRYSTAL STRUCTURE OF THE HUMAN RXR ALPHA LIGAND BINDING DOMAIN BO... -

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Basic information

Entry
Database: PDB / ID: 1fby
TitleCRYSTAL STRUCTURE OF THE HUMAN RXR ALPHA LIGAND BINDING DOMAIN BOUND TO 9-CIS RETINOIC ACID
ComponentsRETINOIC ACID RECEPTOR RXR-ALPHA
KeywordsTRANSCRIPTION / NUCLEAR RECEPTOR / PROTEIN-LIGAND COMPLEX / RETINOID RECEPTOR
Function / homology
Function and homology information


retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / 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 shuttle / retinoic acid binding / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway ...retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / 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 shuttle / retinoic acid binding / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / nuclear steroid receptor activity / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / positive regulation of bone mineralization / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / hormone-mediated signaling pathway / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / peptide binding / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear receptor activity / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / : / nervous system development / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / receptor complex / transcription cis-regulatory region binding / 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 / Double treble clef zinc finger, C4 type ...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 / 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 / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsEgea, P.F. / Mitschler, A. / Rochel, N. / Ruff, M. / Chambon, P. / Moras, D.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of the human RXRalpha ligand-binding domain bound to its natural ligand: 9-cis retinoic acid.
Authors: Egea, P.F. / Mitschler, A. / Rochel, N. / Ruff, M. / Chambon, P. / Moras, D.
History
DepositionJul 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 9, 2016Group: Non-polymer description
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: RETINOIC ACID RECEPTOR RXR-ALPHA
B: RETINOIC ACID RECEPTOR RXR-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1114
Polymers53,5102
Non-polymers6012
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.325, 86.358, 90.527
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RETINOIC ACID RECEPTOR RXR-ALPHA


Mass: 26754.938 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P19793
#2: Chemical ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 295 K
Method: vapor diffusion, hanging drop, sitting drop with seeding
pH: 7
Details: Sodium Formate, Propane 1,2 Diol, Glycerol, Tris, pH 7, VAPOUR DIFFUSION, HANGING DROP and SITTING DROP with SEEDING, temperature 295K
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / Details: used micro and macroseeding / PH range low: 8.5 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-4.5 Msodium formate1reservoir
250 mMTris1reservoir
35-10 %glycerol1reservoir
417-23 %propane-1,2-diol1reservoir

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.25→15 Å / Num. all: 87788 / Num. obs: 22453 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 22.7
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.23 / Num. unique all: 963 / % possible all: 95.5
Reflection
*PLUS
Num. measured all: 87788
Reflection shell
*PLUS
% possible obs: 95.5 % / Mean I/σ(I) obs: 5.3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.25→14.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1917692.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 989 4.9 %RANDOM
Rwork0.228 ---
obs0.228 20250 80.2 %-
all-87788 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.73 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å20 Å2
2--11.71 Å20 Å2
3----14.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-15 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.25→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 44 203 3625
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.241.5
X-RAY DIFFRACTIONc_mcangle_it3.52
X-RAY DIFFRACTIONc_scbond_it3.422
X-RAY DIFFRACTIONc_scangle_it4.872.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 65 4.6 %
Rwork0.271 1359 -
obs--34.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION29CI.PARAM9CI.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 52 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.236 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.271

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