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- PDB-6jnr: RXRa structure complexed with CU-6PMN and SRC1 peptide. -

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Basic information

Entry
Database: PDB / ID: 6jnr
TitleRXRa structure complexed with CU-6PMN and SRC1 peptide.
Components
  • HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / Retinoid X receptor alpha / fluorescent agonist / dimer form
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 / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / labyrinthine layer morphogenesis / regulation of thyroid hormone 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 / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / positive regulation of vitamin D receptor signaling pathway / TGFBR3 expression / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / DNA binding domain binding / positive regulation of lipid metabolic process / male mating behavior / hypothalamus development / LBD domain binding / positive regulation of lipoprotein transport / nuclear steroid receptor activity / progesterone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of cholesterol efflux / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / monocyte differentiation / response to retinoic acid / cellular response to low-density lipoprotein particle stimulus / positive regulation of bone mineralization / protein-lysine-acetyltransferase activity / nuclear retinoid X receptor binding / estrous cycle / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / retinoic acid receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to hormone stimulus / estrogen receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / lactation / peptide binding / peroxisome proliferator activated receptor signaling pathway / cell maturation / response to progesterone / hormone-mediated signaling pathway / positive regulation of adipose tissue development / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / positive regulation of neuron differentiation / SUMOylation of transcription cofactors / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / cerebellum development / nuclear estrogen receptor binding / nuclear receptor binding / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / hippocampus development / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / cerebral cortex development / mRNA transcription by RNA polymerase II / male gonad development / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / response to estradiol / nervous system development / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription coactivator activity / signaling receptor complex / protein dimerization activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of apoptotic process / DNA-binding transcription factor activity / chromatin binding / positive regulation of DNA-templated transcription
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / 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 ...Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / 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
Chem-WY5 / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: To Be Published
Title: RXRa structure complexed with CU-6PMN and SRC1 peptide.
Authors: Kawasaki, M. / Nakano, S. / Motoyama, T. / Yamada, S. / Watanabe, M. / Takamura, Y. / Fujihara, M. / Tokiwa, H. / Kakuta, H. / Ito, S.
History
DepositionMar 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoic acid receptor RXR-alpha
B: Retinoic acid receptor RXR-alpha
C: HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN
D: HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9316
Polymers57,1184
Non-polymers8132
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-19 kcal/mol
Surface area19660 Å2
Unit cell
Length a, b, c (Å)64.390, 64.390, 111.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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.: 2
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: Protein/peptide HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN


Mass: 1434.686 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788*PLUS
#3: 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.: 2 / Source method: obtained synthetically / Formula: C25H26O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30%(v/v) Polyethylene glycol monomethyl ether 550, 0.1M HEPES-NaOH (pH 7.5), 0.05M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→64.4 Å / Num. obs: 19042 / % possible obs: 99.8 % / Redundancy: 13.6 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Net I/σ(I): 24
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.428 / Num. unique obs: 996 / CC1/2: 0.968 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OAP

3oap


Resolution: 2.3→64.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.82 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.393 / ESU R Free: 0.246 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 943 4.7 %RANDOM
Rwork0.17853 ---
obs0.18139 19042 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.221 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.3→64.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 60 91 3709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193697
X-RAY DIFFRACTIONr_bond_other_d0.0010.023671
X-RAY DIFFRACTIONr_angle_refined_deg2.3442.0035013
X-RAY DIFFRACTIONr_angle_other_deg1.19238440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.765442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75423.585159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57315660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8621526
X-RAY DIFFRACTIONr_chiral_restr0.1370.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214032
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02808
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_it3.8773.2591786
X-RAY DIFFRACTIONr_mcbond_other3.8773.2561785
X-RAY DIFFRACTIONr_mcangle_it5.2274.8542222
X-RAY DIFFRACTIONr_mcangle_other5.2264.8572223
X-RAY DIFFRACTIONr_scbond_it5.3183.6881911
X-RAY DIFFRACTIONr_scbond_other5.3173.6881912
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3125.3442792
X-RAY DIFFRACTIONr_long_range_B_refined8.38525.8674297
X-RAY DIFFRACTIONr_long_range_B_other8.38425.8684298
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.304→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 80 -
Rwork0.188 1353 -
obs--97.82 %

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