[English] 日本語
Yorodumi
- PDB-5lyq: Crystal structure of the Retinoic Acid Receptor alpha in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lyq
TitleCrystal structure of the Retinoic Acid Receptor alpha in complex with a synthetic spiroketal agonist and a fragment of the TIF2 co-activator.
Components
  • HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / nuclear receptor / RXR / spiroketal
Function / homology
Function and homology information


positive regulation of transporter activity / 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 / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex ...positive regulation of transporter activity / 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 / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / transcription coregulator binding / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / HATs acetylate histones / double-stranded DNA binding / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription regulator complex / transcription coactivator activity / cell differentiation / receptor complex / nuclear body / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / 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 / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 ...Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-7BE / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsAndrei, S.A. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
NWOECHO 711011017 Netherlands
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Designed Spiroketal Protein Modulation.
Authors: Scheepstra, M. / Andrei, S.A. / Unver, M.Y. / Hirsch, A.K.H. / Leysen, S. / Ottmann, C. / Brunsveld, L. / Milroy, L.G.
History
DepositionSep 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Aug 10, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.4Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,8423
Polymers28,4362
Non-polymers4071
Water2,972165
1
A: Retinoic acid receptor RXR-alpha
B: HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP
hetero molecules

A: Retinoic acid receptor RXR-alpha
B: HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6856
Polymers56,8724
Non-polymers8132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)64.632, 64.632, 113.207
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-670-

HOH

-
Components

#1: Protein Retinoic acid receptor RXR-alpha / Nuclear receptor subfamily 2 group B member 1 / Retinoid X receptor alpha


Mass: 26856.039 Da / Num. of mol.: 1 / Fragment: UNP residues 223-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19793
#2: Protein/peptide HIS-LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN-ASP


Mass: 1579.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS
#3: Chemical ChemComp-7BE / (2~{R})-6,6,9,9-tetramethylspiro[3,4,7,8-tetrahydrobenzo[g]chromene-2,2'-3,4-dihydrochromene]-6'-carboxylic acid


Mass: 406.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H30O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M MIB buffer pH 8, 25% (w/v) PEG 1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.17→45.7 Å / Num. obs: 13334 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.031 / Rrim(I) all: 0.102 / Net I/σ(I): 22.3 / Num. measured all: 136161
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.17-2.245.80.892639111080.8780.3920.9782.199
8.95-45.77.50.019182224410.0070.0279.298.8

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OC7

4oc7


Resolution: 2.17→42.582 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 625 4.75 %
Rwork0.212 12534 -
obs0.2138 13159 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.53 Å2 / Biso mean: 33.8891 Å2 / Biso min: 6.74 Å2
Refinement stepCycle: final / Resolution: 2.17→42.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 30 165 1956
Biso mean--30.59 39.15 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031952
X-RAY DIFFRACTIONf_angle_d0.562663
X-RAY DIFFRACTIONf_chiral_restr0.037295
X-RAY DIFFRACTIONf_plane_restr0.004344
X-RAY DIFFRACTIONf_dihedral_angle_d15.5271198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.17-2.38840.39421460.37312982312897
2.3884-2.73390.24771640.238730863250100
2.7339-3.44420.28571510.199131493300100
3.4442-42.59020.20321640.17033317348199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.7593-2.80270.86145.4843-2.06893.77920.25950.2079-0.5057-0.1407-0.24280.21880.6124-0.1676-0.15250.55660.0310.07030.16820.0080.2942-8.5737-19.8649-23.1542
20.75340.0643-0.78441.8795-0.71011.036-0.0245-0.1562-0.2710.19220.12670.30820.3233-0.2146-0.12050.304-0.02840.04290.14860.07220.2237-16.3933-11.4614-20.0532
32.0354-0.34460.34472.0278-1.5712.80760.07180.2431-0.1062-0.16730.00720.19760.4134-0.111-0.07380.2174-0.01670.01990.1498-0.01130.2109-12.0845-7.4614-33.0548
42.5652-0.615-0.79781.60370.64261.80960.06330.0499-0.0763-0.0026-0.0728-0.12710.38460.29860.02310.27030.02510.01060.1740.01670.2118-2.7984-5.8077-24.8283
57.10240.80743.1356.4085-1.83012.5601-0.2407-0.30.45030.58370.15750.7119-0.6939-0.53020.13580.34850.04190.12140.27910.04780.398-24.80350.914-20.7586
63.51672.652-1.64133.4942-1.87392.5536-0.053-0.3483-0.02230.48370.13440.5367-0.35120.3318-0.5250.473-0.13620.1950.3309-0.03250.3195-20.6063-8.4385-9.1121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 229 through 263 )A229 - 263
2X-RAY DIFFRACTION2chain 'A' and (resid 264 through 293 )A264 - 293
3X-RAY DIFFRACTION3chain 'A' and (resid 294 through 375 )A294 - 375
4X-RAY DIFFRACTION4chain 'A' and (resid 376 through 442 )A376 - 442
5X-RAY DIFFRACTION5chain 'A' and (resid 443 through 458 )A443 - 458
6X-RAY DIFFRACTION6chain 'B' and (resid 472 through 481 )B472 - 481

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more