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- PDB-1h9u: The structure of the human retinoid-X-receptor beta ligand bindin... -

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Basic information

Entry
Database: PDB / ID: 1h9u
TitleThe structure of the human retinoid-X-receptor beta ligand binding domain in complex with the specific synthetic agonist LG100268
ComponentsRETINOID X RECEPTOR, BETA
KeywordsNUCLEAR RECEPTOR / RXR / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


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 / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / anatomical structure development / positive regulation of vitamin D receptor signaling pathway / Signaling by Retinoic Acid / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis ...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 / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / anatomical structure development / positive regulation of vitamin D receptor signaling pathway / Signaling by Retinoic Acid / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / retinoic acid receptor signaling pathway / positive regulation of bone mineralization / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / hormone-mediated signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mRNA transcription by RNA polymerase II / PPARA activates gene expression / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
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 ...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-LG2 / NICKEL (II) ION / Retinoic acid receptor RXR-beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchwabe, J.W.R. / Love, J.D. / Gooch, J.T.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The Structural Basis for the Specificity of Retinoid-X Receptor-Selective Agonists: New Insights Into the Role of Helix H12
Authors: Love, J.D. / Gooch, J.T. / Benko, S. / Li, C. / Nagy, L. / Chatterjee, V.K.K. / Evans, R.M. / Schwabe, J.W.R.
History
DepositionMar 21, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: RETINOID X RECEPTOR, BETA
B: RETINOID X RECEPTOR, BETA
C: RETINOID X RECEPTOR, BETA
D: RETINOID X RECEPTOR, BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,13014
Polymers99,3714
Non-polymers1,76010
Water724
1
A: RETINOID X RECEPTOR, BETA
B: RETINOID X RECEPTOR, BETA
C: RETINOID X RECEPTOR, BETA
D: RETINOID X RECEPTOR, BETA
hetero molecules

A: RETINOID X RECEPTOR, BETA
B: RETINOID X RECEPTOR, BETA
C: RETINOID X RECEPTOR, BETA
D: RETINOID X RECEPTOR, BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,26028
Polymers198,7418
Non-polymers3,51920
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
MethodPQS
Unit cell
Length a, b, c (Å)123.886, 106.882, 100.587
Angle α, β, γ (deg.)90.00, 122.56, 90.00
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL. THE RETINOID X RECEPTOR IS ACTIVE AS DIMERIC

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Components

#1: Protein
RETINOID X RECEPTOR, BETA / / RXRB


Mass: 24842.645 Da / Num. of mol.: 4 / Fragment: LIGAND BINDING DOMAIN RESIDUES 299-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P28702
#2: Chemical
ChemComp-LG2 / 6-[1-(3,5,5,8,8-PENTAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)CYCLOPROPYL]PYRIDINE-3-CARBOXYLIC ACID


Mass: 363.493 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H29NO2
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBINDS TO 9-CIS RETINOIC ACID (9C-RA). INVOLVED IN RETINOIC ACID RESPONSE PATHWAY. THE C-TERMINAL ...BINDS TO 9-CIS RETINOIC ACID (9C-RA). INVOLVED IN RETINOIC ACID RESPONSE PATHWAY. THE C-TERMINAL DOMAIN IS INVOLVED IN STEROID-BINDING.

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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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growpH: 7.6 / Details: pH 7.60
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris-HCl1droppH8.0
250 mM1dropNaCl
31.0 mMdithiothreitol1drop
40.125 %(v/v)Triton X-1001drop
57.4 mg/mlprotein1drop
61.4 Mammonium formate1reservoirpH7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: QUANTUM / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→38 Å / Num. obs: 29713 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 55.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 5.1
Reflection
*PLUS
Lowest resolution: 38 Å / % possible obs: 97.8 % / Num. measured all: 87647
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.87 Å / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LBD

1lbd
PDB Unreleased entry


Resolution: 2.7→38.14 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2064073.76 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.306 2929 9.9 %RANDOM
Rwork0.273 ---
obs0.273 29621 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.2394 Å2 / ksol: 0.35528 e/Å3
Displacement parametersBiso mean: 50.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.68 Å20 Å219.66 Å2
2---13.83 Å20 Å2
3---11.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.43 Å
Luzzati d res low-6 Å
Luzzati sigma a0.54 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.7→38.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6220 0 114 4 6338
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it1.712
X-RAY DIFFRACTIONc_scangle_it2.672.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 483 9.8 %
Rwork0.354 4461 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMLG2.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4LG2.PAR
Refinement
*PLUS
Rfactor obs: 0.277 / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.277
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08

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