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- PDB-6jno: RXRa structure complexed with CU-6PMN -

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Basic information

Entry
Database: PDB / ID: 6jno
TitleRXRa structure complexed with CU-6PMN
ComponentsRetinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / Retinoid x receptor alpha / Ligand binding domain / fluorescent reagent / inactive form
Function / homology
Function and homology information


positive regulation of transporter activity / retinoic acid-responsive element binding / 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 gluconeogenesis / 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 transporter activity / retinoic acid-responsive element binding / 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 gluconeogenesis / 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 / nuclear steroid receptor activity / LBD domain binding / 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 / positive regulation of bone mineralization / response to retinoic acid / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / Recycling of bile acids and salts / 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 / BMAL1:CLOCK,NPAS2 activates circadian expression / peptide binding / 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 / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / nuclear receptor activity / 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 / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / 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
Chem-WY5 / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKawasaki, M. / Nakano, S. / Motoyama, T. / Yamada, S. / Watanabe, M. / Takamura, Y. / Fujihara, M. / Tokiwa, H. / Kakuta, H. / Ito, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K18688 Japan
Japan Society for the Promotion of Science18K14391 Japan
Japan Society for the Promotion of Science12J06716 Japan
CitationJournal: J.Med.Chem. / Year: 2019
Title: Competitive Binding Assay with an Umbelliferone-Based Fluorescent Rexinoid for Retinoid X Receptor Ligand Screening.
Authors: Yamada, S. / Kawasaki, M. / Fujihara, M. / Watanabe, M. / Takamura, Y. / Takioku, M. / Nishioka, H. / Takeuchi, Y. / Makishima, M. / Motoyama, T. / Ito, S. / Tokiwa, H. / Nakano, S. / Kakuta, H.
History
DepositionMar 17, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 20, 2019ID: 5GYM
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)108,9045
Polymers108,4974
Non-polymers4061
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-51 kcal/mol
Surface area35080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.615, 99.386, 110.158
Angle α, β, γ (deg.)90.00, 99.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA264 - 45845 - 239
21PROPROBB264 - 45845 - 239
12METMETAA264 - 45445 - 235
22METMETCC264 - 45445 - 235
13METMETAA264 - 45445 - 235
23METMETDD264 - 45445 - 235
14METMETBB264 - 45445 - 235
24METMETCC264 - 45445 - 235
15METMETBB264 - 45445 - 235
25METMETDD264 - 45445 - 235
16LEULEUCC231 - 45512 - 236
26LEULEUDD231 - 45512 - 236

NCS ensembles :
ID
1
2
3
4
5
6

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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: 27124.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19793
#2: Chemical ChemComp-WY5 / 7-oxidanyl-2-oxidanylidene-6-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)chromene-3-carboxylic acid


Mass: 406.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (w/v) Polyethylene glycol 3350, 0.2M Mg(OAc)2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→46 Å / Num. obs: 27286 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 10.7
Reflection shellResolution: 2.65→2.72 Å / Rmerge(I) obs: 0.716 / Num. unique obs: 1438 / CC1/2: 0.706 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GYM

5gym
PDB Unreleased entry


Resolution: 2.65→46 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.883 / SU B: 15.419 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R: 1.107 / ESU R Free: 0.358 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27442 1425 5 %RANDOM
Rwork0.22345 ---
obs0.22596 27286 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.01 Å2
2--0.05 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.65→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6262 0 30 57 6349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136424
X-RAY DIFFRACTIONr_bond_other_d00.0176281
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.6328683
X-RAY DIFFRACTIONr_angle_other_deg1.0831.57314522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.495782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90621.447318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.783151163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3921546
X-RAY DIFFRACTIONr_chiral_restr0.0460.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026995
X-RAY DIFFRACTIONr_gen_planes_other00.021334
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4325.0873155
X-RAY DIFFRACTIONr_mcbond_other5.4265.0863154
X-RAY DIFFRACTIONr_mcangle_it7.9537.6213928
X-RAY DIFFRACTIONr_mcangle_other7.9537.6233929
X-RAY DIFFRACTIONr_scbond_it5.8715.6033269
X-RAY DIFFRACTIONr_scbond_other5.8715.6043270
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9888.2114756
X-RAY DIFFRACTIONr_long_range_B_refined12.03260.4387171
X-RAY DIFFRACTIONr_long_range_B_other12.03160.4357172
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A62300.05
12B62300.05
21A60000.08
22C60000.08
31A60370.08
32D60370.08
41B59860.08
42C59860.08
51B60360.08
52D60360.08
61C64210.09
62D64210.09
LS refinement shellResolution: 2.654→2.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 88 -
Rwork0.328 1973 -
obs--95.82 %

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