[English] 日本語
Yorodumi
- PDB-1fm6: THE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE HETERODIMER ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fm6
TitleTHE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE HETERODIMER OF THE HUMAN RXRALPHA AND PPARGAMMA LIGAND BINDING DOMAINS RESPECTIVELY BOUND WITH 9-CIS RETINOIC ACID AND ROSIGLITAZONE AND CO-ACTIVATOR PEPTIDES.
Components
  • PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
  • RETINOIC ACID RECEPTOR RXR-ALPHA
  • STEROID RECEPTOR COACTIVATOR
KeywordsTRANSCRIPTION / the heterodimer of the nuclear receptor ligand binding domains of RXRalpha and PPARgamma bound respectively with 9-cis Retinoic Acid and Rosiglitazone and co-activator peptides
Function / homology
Function and homology information


DNA binding domain binding / 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 / LBD domain binding / Carnitine metabolism ...DNA binding domain binding / 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 / LBD domain binding / Carnitine metabolism / 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 vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / positive regulation of female receptivity / Signaling by Retinoic Acid / nuclear steroid receptor activity / positive regulation of cholesterol efflux / hypothalamus development / male mating behavior / retinoic acid receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / Complex I biogenesis / positive regulation of adipose tissue development / hormone-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Respiratory electron transport / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / response to retinoic acid / mitochondrial ATP synthesis coupled electron transport / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / mitochondrial respiratory chain complex I assembly / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / transcription coregulator binding / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / peptide binding / : / mitochondrial electron transport, NADH to ubiquinone / SUMOylation of intracellular receptors / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / mRNA transcription by RNA polymerase II / response to progesterone / nuclear receptor binding / NADH dehydrogenase (ubiquinone) activity / hippocampus development / nuclear estrogen receptor binding / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / Heme signaling / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / mitochondrial membrane / aerobic respiration / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / cerebral cortex development / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / male gonad development / sequence-specific double-stranded DNA binding / Circadian Clock / response to estradiol / double-stranded DNA binding / HATs acetylate histones / transcription regulator complex / sequence-specific DNA binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / receptor complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / mitochondrial inner membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding
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 / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / 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 / 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 / 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 / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Ligand-binding domain of nuclear hormone receptor / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(9cis)-retinoic acid / Chem-BRL / Nuclear receptor coactivator 1 / Retinoic acid receptor RXR-alpha / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsGampe Jr., R.T. / Montana, V.G. / Lambert, M.H. / Miller, A.B. / Bledsoe, R.K. / Milburn, M.V. / Kliewer, S.A. / Willson, T.M. / Xu, H.E.
CitationJournal: Mol.Cell / Year: 2000
Title: Asymmetry in the PPARgamma/RXRalpha crystal structure reveals the molecular basis of heterodimerization among nuclear receptors.
Authors: Gampe Jr., R.T. / Montana, V.G. / Lambert, M.H. / Miller, A.B. / Bledsoe, R.K. / Milburn, M.V. / Kliewer, S.A. / Willson, T.M. / Xu, H.E.
History
DepositionAug 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 26, 2012Group: Non-polymer description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RETINOIC ACID RECEPTOR RXR-ALPHA
D: PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
U: RETINOIC ACID RECEPTOR RXR-ALPHA
X: PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
B: STEROID RECEPTOR COACTIVATOR
V: STEROID RECEPTOR COACTIVATOR
E: STEROID RECEPTOR COACTIVATOR
Y: STEROID RECEPTOR COACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,06412
Polymers126,7498
Non-polymers1,3164
Water8,143452
1
A: RETINOIC ACID RECEPTOR RXR-ALPHA
D: PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
B: STEROID RECEPTOR COACTIVATOR
E: STEROID RECEPTOR COACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0326
Polymers63,3744
Non-polymers6582
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
U: RETINOIC ACID RECEPTOR RXR-ALPHA
X: PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA
V: STEROID RECEPTOR COACTIVATOR
Y: STEROID RECEPTOR COACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0326
Polymers63,3744
Non-polymers6582
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.255, 222.364, 55.289
Angle α, β, γ (deg.)90.00, 98.59, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules AUDX

#1: Protein RETINOIC ACID RECEPTOR RXR-ALPHA


Mass: 26667.857 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN - RESIDUES 225 -462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PACYC184 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19793
#2: Protein PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA


Mass: 31094.135 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN - RESIDUES 206 - 477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37231

-
Protein/peptide , 1 types, 4 molecules BVEY

#3: Protein/peptide
STEROID RECEPTOR COACTIVATOR


Mass: 2806.163 Da / Num. of mol.: 4 / Fragment: SRC-1 PEPTIDE / Source method: obtained synthetically
Details: Chemically synthesized 25mer portion of human src-1 coactivator peptide
References: UniProt: O43793, UniProt: Q15788*PLUS

-
Non-polymers , 3 types, 456 molecules

#4: Chemical ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#5: Chemical ChemComp-BRL / 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) / BRL49653 / ROSIGLITAZONE


Mass: 357.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19N3O3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsrosiglitazone is a synthetic antidiabetic agonist for PPARgamma

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 4K, 200mM NaSCN, 8% Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal
*PLUS
Density % sol: 39 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
217 %PEG40001reservoir
3200 mM1reservoirNaSCN
48 %ethylene glycol1reservoir
58 %glycerol1reservoir

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 64772 / % possible obs: 94.9 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.7
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.6

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
MAR345data collection
HKL-2000data scaling
RefinementResolution: 2.1→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 372436.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.292 6054 10.1 %RANDOM
Rwork0.25 ---
obs0.25 59851 87.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.72 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso mean: 55.5 Å2
Baniso -1Baniso -2Baniso -3
1-28.2 Å20 Å26.25 Å2
2---14.96 Å20 Å2
3----13.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8292 0 94 452 8838
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 898 10.3 %
Rwork0.386 7798 -
obs--76.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2BSXPI3.XPL
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION49CRA_LOCAL3.XPL
X-RAY DIFFRACTION5RSG_LOCAL3.XPL
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.242 / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 55.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03
LS refinement shell
*PLUS
Rfactor Rfree: 0.386 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.386

+
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