[English] 日本語
Yorodumi
- PDB-3kfc: Complex Structure of LXR with an agonist -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kfc
TitleComplex Structure of LXR with an agonist
ComponentsOxysterols receptor LXR-beta
KeywordsTRANSCRIPTION / Nuclear Receptor / LXR / Liver X receptor / LXR agonist / LXR ligand / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


positive regulation of secretion of lysosomal enzymes / positive regulation of high-density lipoprotein particle assembly / positive regulation of pancreatic juice secretion / phosphatidylcholine acyl-chain remodeling / positive regulation of cholesterol transport / negative regulation of response to endoplasmic reticulum stress / negative regulation of pinocytosis / positive regulation of lipoprotein lipase activity / apolipoprotein A-I receptor binding / positive regulation of triglyceride biosynthetic process ...positive regulation of secretion of lysosomal enzymes / positive regulation of high-density lipoprotein particle assembly / positive regulation of pancreatic juice secretion / phosphatidylcholine acyl-chain remodeling / positive regulation of cholesterol transport / negative regulation of response to endoplasmic reticulum stress / negative regulation of pinocytosis / positive regulation of lipoprotein lipase activity / apolipoprotein A-I receptor binding / positive regulation of triglyceride biosynthetic process / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of lipid storage / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / positive regulation of fatty acid biosynthetic process / negative regulation of lipid transport / negative regulation of cold-induced thermogenesis / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / VLDLR internalisation and degradation / positive regulation of protein metabolic process / hormone-mediated signaling pathway / cholesterol homeostasis / negative regulation of proteolysis / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / PPARA activates gene expression / chromatin DNA binding / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Liver X receptor / 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 ...Liver X receptor / 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-61X / Oxysterols receptor LXR-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOlland, A. / Bernotas, R.C. / Unwalla, R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: 4-(3-Aryloxyaryl)quinoline sulfones are potent liver X receptor agonists.
Authors: Bernotas, R.C. / Singhaus, R.R. / Kaufman, D.H. / Travins, J.M. / Ullrich, J.W. / Unwalla, R. / Quinet, E. / Evans, M. / Nambi, P. / Olland, A. / Kauppi, B. / Wilhelmsson, A. / Goos-Nilsson, A. / Wrobel, J.
History
DepositionOct 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Feb 21, 2024Group: 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: Oxysterols receptor LXR-beta
B: Oxysterols receptor LXR-beta
C: Oxysterols receptor LXR-beta
D: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,5597
Polymers116,2294
Non-polymers1,3303
Water25214
1
A: Oxysterols receptor LXR-beta
B: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0014
Polymers58,1152
Non-polymers8872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-11 kcal/mol
Surface area22420 Å2
MethodPISA
2
C: Oxysterols receptor LXR-beta
D: Oxysterols receptor LXR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5583
Polymers58,1152
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-13 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.993, 99.286, 174.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Oxysterols receptor LXR-beta / Liver X receptor beta / Nuclear orphan receptor LXR-beta / Nuclear receptor subfamily 1 group H ...Liver X receptor beta / Nuclear orphan receptor LXR-beta / Nuclear receptor subfamily 1 group H member 2 / Ubiquitously-expressed nuclear receptor / Nuclear receptor NER


Mass: 29057.283 Da / Num. of mol.: 4 / Fragment: Ligand binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H2, LXRB, NER, UNR / Production host: Escherichia coli (E. coli) / References: UniProt: P55055
#2: Chemical ChemComp-61X / 4-{3-[3-(methylsulfonyl)phenoxy]phenyl}-8-(trifluoromethyl)quinoline


Mass: 443.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H16F3NO3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M Hepes, 15% PEG4K, 5.33% iso-propanol, 6.4% glycerol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→87.37 Å / Num. all: 39025 / Num. obs: 36586 / % possible obs: 93.75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.462 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3023 / Rsym value: 0.488 / % possible all: 100

-
Processing

Software
NameVersionClassification
CBASSdata collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 23.631 / SU ML: 0.252 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.59 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28384 1930 5 %RANDOM
Rwork0.23751 ---
obs0.23986 36586 93.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.212 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7197 0 93 14 7304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227433
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.98710059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6445875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05923.75368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.496151343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0741568
X-RAY DIFFRACTIONr_chiral_restr0.0730.21123
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025601
X-RAY DIFFRACTIONr_nbd_refined0.1910.23261
X-RAY DIFFRACTIONr_nbtor_refined0.2970.25078
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.28
X-RAY DIFFRACTIONr_mcbond_it0.4521.54588
X-RAY DIFFRACTIONr_mcangle_it0.76927178
X-RAY DIFFRACTIONr_scbond_it1.08733238
X-RAY DIFFRACTIONr_scangle_it1.7744.52881
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 130 -
Rwork0.268 2566 -
obs--89.36 %
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)
12.2814-0.375-0.54973.8441-0.18981.64380.2640.1686-0.0984-0.4593-0.2186-0.1397-0.2027-0.0236-0.0455-0.2580.06780.0088-0.11180.0015-0.14814.69444.98930.583
22.79540.68710.6442.87780.57512.01430.1124-0.0682-0.00790.1223-0.00080.03170.03580.1196-0.1116-0.36690.05720.0234-0.17940.026-0.069938.76629.28638.696
32.79980.3148-0.35823.88231.22513.7932-0.06460.35390.3315-0.91420.101-0.1129-0.01620.4648-0.0364-0.03490.132-0.0402-0.08910.043-0.247549.304107.12910.499
44.1351-1.83320.73145.5241-1.00343.40350.28150.3513-0.5145-1.163-0.38250.42230.49360.16890.1010.03420.1756-0.1168-0.2095-0.2009-0.263545.44779.00513.431
50.08960.10150.1371.23560.03880.22150.11450.0760.1303-0.1221-0.17240.4320.0090.06240.05790.09970.0376-0.08920.3816-0.01640.461922.35549.43932.638
60.6501-1.19680.97292.2832-0.98719.54470.06140.1292-0.0163-0.6831-0.1596-0.4527-0.5131-0.30230.09820.29220.17340.04720.38010.04260.305515.87653.13629.099
74.91022.5555-1.50944.8035-6.986811.5354-0.08-0.39450.24710.3271-0.67420.601-0.06440.91580.75420.24630.0674-0.00580.51360.05440.379644.75434.12243.925
80.3613-1.4014-0.275111.9502-6.39798.76340.74481.3331-2.3896-0.5679-0.8663-0.71210.29660.28930.12150.54290.28720.11310.3631-0.09780.450151.3173.9718.311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A220 - 458
2X-RAY DIFFRACTION2B220 - 458
3X-RAY DIFFRACTION3C220 - 439
4X-RAY DIFFRACTION4D220 - 458
5X-RAY DIFFRACTION5A2 - 19
6X-RAY DIFFRACTION5C1 - 14
7X-RAY DIFFRACTION5B3 - 8
8X-RAY DIFFRACTION6A1
9X-RAY DIFFRACTION7B1
10X-RAY DIFFRACTION8D1

+
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