[English] 日本語
Yorodumi
- PDB-3fal: humanRXR alpha & mouse LXR alpha complexed with Retenoic acid and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fal
TitlehumanRXR alpha & mouse LXR alpha complexed with Retenoic acid and GSK2186
Components
  • Oxysterols receptor LXR-alpha
  • Retinoic acid receptor RXR-alpha
KeywordsSIGNALING PROTEIN / Nuclear hormone receptor nonsteroidal LXR agonist choloestorol metabolism / DNA-binding / Host-virus interaction / Metal-binding / Nucleus / Polymorphism / Receptor / Transcription / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger
Function / homology
Function and homology information


negative regulation of secretion of lysosomal enzymes / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / sterol response element binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SUMOylation of intracellular receptors / negative regulation of macrophage activation / negative regulation of pancreatic juice secretion / Nuclear Receptor transcription pathway / phosphatidylcholine acyl-chain remodeling / : ...negative regulation of secretion of lysosomal enzymes / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / sterol response element binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SUMOylation of intracellular receptors / negative regulation of macrophage activation / negative regulation of pancreatic juice secretion / Nuclear Receptor transcription pathway / phosphatidylcholine acyl-chain remodeling / : / negative regulation of response to endoplasmic reticulum stress / negative regulation of pinocytosis / sterol homeostasis / VLDLR internalisation and degradation / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of triglyceride biosynthetic process / positive regulation of transporter activity / regulation of fatty acid metabolic process / 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 / positive regulation of fatty acid biosynthetic process / negative regulation of lipid transport / Carnitine shuttle / retinoic acid binding / TGFBR3 expression / triglyceride homeostasis / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / apoptotic cell clearance / negative regulation of cold-induced thermogenesis / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / negative regulation of cholesterol storage / lipid homeostasis / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / retinoic acid receptor signaling pathway / positive regulation of bone mineralization / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / positive regulation of protein metabolic process / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / cholesterol homeostasis / transcription coregulator binding / response to progesterone / negative regulation of proteolysis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / negative regulation of inflammatory response / fatty acid biosynthetic process / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / sequence-specific DNA binding / transcription regulator complex / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein-containing complex binding / chromatin / nucleolus / positive regulation of DNA-templated transcription
Similarity search - Function
Liver X receptor / 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. ...Liver X receptor / 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 / 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-LO2 / RETINOIC ACID / Retinoic acid receptor RXR-alpha / Oxysterols receptor LXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsChao, E.Y. / Caravella, J.A. / Watson, M.A. / Campobasso, N. / Ghisletti, S. / Billin, A.N. / Galardi, C. / Willson, T.M. / Zuercher, W.J. / Collins, J.L.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Structure-guided design of N-phenyl tertiary amines as transrepression-selective liver X receptor modulators with anti-inflammatory activity.
Authors: Chao, E.Y. / Caravella, J.A. / Watson, M.A. / Campobasso, N. / Ghisletti, S. / Billin, A.N. / Galardi, C. / Wang, P. / Laffitte, B.A. / Iannone, M.A. / Goodwin, B.J. / Nichols, J.A. / Parks, ...Authors: Chao, E.Y. / Caravella, J.A. / Watson, M.A. / Campobasso, N. / Ghisletti, S. / Billin, A.N. / Galardi, C. / Wang, P. / Laffitte, B.A. / Iannone, M.A. / Goodwin, B.J. / Nichols, J.A. / Parks, D.J. / Stewart, E. / Wiethe, R.W. / Williams, S.P. / Smallwood, A. / Pearce, K.H. / Glass, C.K. / Willson, T.M. / Zuercher, W.J. / Collins, J.L.
History
DepositionNov 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: Oxysterols receptor LXR-alpha
C: Retinoic acid receptor RXR-alpha
D: Oxysterols receptor LXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0668
Polymers115,4654
Non-polymers1,6014
Water28816
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-50 kcal/mol
Surface area37300 Å2
MethodPISA
2
A: Retinoic acid receptor RXR-alpha
D: Oxysterols receptor LXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5334
Polymers57,7332
Non-polymers8002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-16 kcal/mol
Surface area20570 Å2
MethodPISA
3
B: Oxysterols receptor LXR-alpha
C: Retinoic acid receptor RXR-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5334
Polymers57,7332
Non-polymers8002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-15 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.212, 90.002, 101.311
Angle α, β, γ (deg.)90.00, 111.88, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 27114.465 Da / Num. of mol.: 2 / Fragment: residues 225-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRA, NR2B1 / Plasmid: T7RXRaLBD_-pACYC184, pRSETa-H6.-thr.mLXRa2-00-455 / Production host: Escherichia coli (E. coli) / References: UniProt: P19793
#2: Protein Oxysterols receptor LXR-alpha / Liver X receptor alpha / Nuclear orphan receptor LXR-alpha / Nuclear receptor subfamily 1 group H member 3


Mass: 30618.035 Da / Num. of mol.: 2 / Fragment: residues 200-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr1h3, Lxra / Plasmid: T7RXRaLBD_-pACYC184, pRSETa-H6.-thr.mLXRa2-00-455 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z0Y9
#3: Chemical ChemComp-REA / RETINOIC ACID


Mass: 300.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O2
#4: Chemical ChemComp-LO2 / 2-{4-[butyl(3-chloro-4,5-dimethoxybenzyl)amino]phenyl}-1,1,1,3,3,3-hexafluoropropan-2-ol / 2-[4-(Butyl{[3-chloro-4,5-bis(methyloxy)phenyl]methyl}amino)phenyl]-1,1,1,3,3,3-hexafluoro-2-propanol


Mass: 499.874 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24ClF6NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DIFFERENCE IS DESCRIBED AS CONFLICT OR VARIANT BETWEEN DIFFERENT REFERENCES IN UNP REFERENCE Q9Z0Y9

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 3uL 6.6mgs/ml protein + 3 uL well containing 21 % - 23 % PEG 3550, 200mM Ammonium Acetate, 100 mM Bis Tris pH 6.5 and 10 mM DTT, VAPOR DIFFUSION, SITTING DROP

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→42.342 Å / Num. obs: 41753
Reflection shellHighest resolution: 2.35 Å / % possible all: 98.5

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→42.342 Å / SU ML: 0.39 / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2777 2106 5.04 %
Rwork0.2194 --
obs0.2223 41749 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.928 Å2 / ksol: 0.396 e/Å3
Refinement stepCycle: LAST / Resolution: 2.36→42.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6968 0 110 16 7094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3596-2.41450.33951280.24522245X-RAY DIFFRACTION85
2.4145-2.47490.34681480.23832676X-RAY DIFFRACTION100
2.4749-2.54180.30241430.23222679X-RAY DIFFRACTION100
2.5418-2.61660.31841610.2312634X-RAY DIFFRACTION100
2.6166-2.7010.31311470.22032659X-RAY DIFFRACTION100
2.701-2.79750.27851320.22442671X-RAY DIFFRACTION100
2.7975-2.90950.28131450.22592676X-RAY DIFFRACTION100
2.9095-3.04190.30681460.23822671X-RAY DIFFRACTION100
3.0419-3.20220.33631370.24082671X-RAY DIFFRACTION100
3.2022-3.40280.28791330.23032675X-RAY DIFFRACTION100
3.4028-3.66530.25011130.20832703X-RAY DIFFRACTION100
3.6653-4.03390.23391500.18882672X-RAY DIFFRACTION100
4.0339-4.61710.20451350.18592698X-RAY DIFFRACTION100
4.6171-5.81460.25831340.19562699X-RAY DIFFRACTION100
5.8146-42.34850.2471540.22614X-RAY DIFFRACTION95

+
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://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