[English] 日本語
Yorodumi
- PDB-5z12: A structure of FXR/RXR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z12
TitleA structure of FXR/RXR
Components
  • (Peptide from Nuclear receptor coactivator ...) x 2
  • Bile acid receptor
  • Retinoic acid receptor RXR-alpha
KeywordsNUCLEAR PROTEIN / complex
Function / homology
Function and homology information


: / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / : / positive regulation of ammonia assimilation cycle / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / negative regulation of interleukin-1 production / negative regulation of very-low-density lipoprotein particle remodeling ...: / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / : / positive regulation of ammonia assimilation cycle / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / negative regulation of interleukin-1 production / negative regulation of very-low-density lipoprotein particle remodeling / 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 / regulation of bile acid biosynthetic process / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of monocyte chemotactic protein-1 production / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / toll-like receptor 9 signaling pathway / nuclear receptor-mediated bile acid signaling pathway / bile acid nuclear receptor activity / Carnitine shuttle / retinoic acid binding / bile acid binding / bile acid metabolic process / cellular response to fatty acid / cell-cell junction assembly / positive regulation of vitamin D receptor signaling pathway / TGFBR3 expression / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / regulation of cholesterol metabolic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of interleukin-2 production / DNA binding domain binding / positive regulation of lipid metabolic process / bile acid and bile salt transport / LBD domain binding / locomotor rhythm / positive regulation of lipoprotein transport / positive regulation of interleukin-17 production / nuclear steroid receptor activity / aryl hydrocarbon receptor binding / negative regulation of type II interferon production / cellular response to Thyroglobulin triiodothyronine / negative regulation of interleukin-6 production / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / regulation of lipid metabolic process / negative regulation of tumor necrosis factor production / 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 / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / response to retinoic acid / cellular response to low-density lipoprotein particle stimulus / positive regulation of bone mineralization / negative regulation of tumor necrosis factor-mediated signaling pathway / nuclear retinoid X receptor binding / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / transcription regulator inhibitor activity / retinoic acid receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to hormone stimulus / intracellular receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / Notch signaling pathway / cell maturation / peroxisome proliferator activated receptor signaling pathway / peptide binding / 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 / 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 / intracellular glucose homeostasis / ciliary tip / cholesterol homeostasis / nuclear receptor binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / transcription coregulator binding / negative regulation of canonical NF-kappaB signal transduction / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / circadian regulation of gene expression / negative regulation of smoothened signaling pathway / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1
Similarity search - Function
Bile acid receptor, ligand binding domain / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Thyroid hormone receptor / Retinoid X receptor/HNF4 / : / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 ...Bile acid receptor, ligand binding domain / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Thyroid hormone receptor / 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 / 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-33Y / (9cis)-retinoic acid / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 2 / Bile acid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLu, Y. / Li, Y.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural insights into the heterodimeric complex of the nuclear receptors FXR and RXR
Authors: Zheng, W. / Lu, Y. / Tian, S. / Ma, F. / Wei, Y. / Xu, S. / Li, Y.
History
DepositionDec 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 25, 2019Group: Derived calculations / Refinement description / Category: pdbx_struct_assembly_gen / refine_hist
Item: _pdbx_struct_assembly_gen.asym_id_list / _refine_hist.d_res_low
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bile acid receptor
C: Retinoic acid receptor RXR-alpha
F: Peptide from Nuclear receptor coactivator 2
J: Peptide from Nuclear receptor coactivator 2
D: Bile acid receptor
H: Peptide from Nuclear receptor coactivator 2
B: Retinoic acid receptor RXR-alpha
I: Peptide from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,55612
Polymers109,0788
Non-polymers1,4784
Water1,24369
1
A: Bile acid receptor
J: Peptide from Nuclear receptor coactivator 2
B: Retinoic acid receptor RXR-alpha
I: Peptide from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2786
Polymers54,5394
Non-polymers7392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Retinoic acid receptor RXR-alpha
F: Peptide from Nuclear receptor coactivator 2
D: Bile acid receptor
H: Peptide from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2786
Polymers54,5394
Non-polymers7392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.873, 95.484, 116.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ADCB

#1: Protein Bile acid receptor / Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group H ...Farnesoid X-activated receptor / Farnesol receptor HRR-1 / Nuclear receptor subfamily 1 group H member 4 / Retinoid X receptor-interacting protein 14 / RXR-interacting protein 14


Mass: 26673.674 Da / Num. of mol.: 2 / Fragment: UNP residues 259-486 / Mutation: C480Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H4, BAR, FXR, HRR1, RIP14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RI1
#2: Protein Retinoic acid receptor RXR-alpha / Nuclear receptor subfamily 2 group B member 1 / Retinoid X receptor alpha


Mass: 25897.021 Da / Num. of mol.: 2 / Fragment: UNP residues 228-458
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

-
Peptide from Nuclear receptor coactivator ... , 2 types, 4 molecules FIJH

#3: Protein/peptide Peptide from Nuclear receptor coactivator 2


Mass: 1161.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS
#4: Protein/peptide Peptide from Nuclear receptor coactivator 2


Mass: 806.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS

-
Non-polymers , 3 types, 73 molecules

#5: Chemical ChemComp-33Y / 1-methylethyl 3-[(3,4-difluorophenyl)carbonyl]-1,1-dimethyl-1,2,3,6-tetrahydroazepino[4,5-b]indole-5-carboxylate


Mass: 438.466 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C25H24F2N2O3
#6: Chemical ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4% v/v Tacsimate pH 8.0, 12% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 25979 / % possible obs: 97.2 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.043 / Rrim(I) all: 0.138 / Χ2: 0.981 / Net I/σ(I): 3.5 / Num. measured all: 320129
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.89.20.94510210.9360.3030.9961.00877.7
2.8-2.859.70.92910930.920.2980.9790.97983.9
2.85-2.910.411960.9490.3120.96689.7
2.9-2.9611.312230.9020.3520.97894.7
2.96-3.0311.612810.9420.3120.95998.1
3.03-3.1120.87213210.950.2580.9110.95899.4
3.1-3.1712.50.66113120.990.1930.690.988100
3.17-3.2612.90.66513190.9810.1910.6920.997100
3.26-3.36130.55613280.9850.160.5790.993100
3.36-3.4613.10.38313090.9920.110.3991.006100
3.46-3.5912.30.31113440.9930.0920.3241.026100
3.59-3.7312.40.24113130.9930.0710.2511.042100
3.73-3.913.50.19813310.9980.0560.2051.047100
3.9-4.1113.90.15613340.9980.0430.1621.029100
4.11-4.3613.70.1313360.9980.0360.1351.032100
4.36-4.713.40.10813480.9980.0310.1131.006100
4.7-5.1712.60.10213400.9980.030.1071.004100
5.17-5.9212.20.09213680.9980.0270.0960.928100
5.92-7.4613.40.07913860.9990.0220.0820.915100
7.46-5011.80.03914760.9990.0120.0410.769100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.858 / SU B: 20.894 / SU ML: 0.409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.586 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2901 968 5.1 %RANDOM
Rwork0.2297 ---
obs0.2329 17944 70.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.06 Å2 / Biso mean: 43.757 Å2 / Biso min: 8.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å20 Å2
2---0.45 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7228 0 108 69 7405
Biso mean--27.84 25.93 -
Num. residues----896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197487
X-RAY DIFFRACTIONr_bond_other_d0.0060.027172
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.99110116
X-RAY DIFFRACTIONr_angle_other_deg1.065316633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.90524.26338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.401151381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9141543
X-RAY DIFFRACTIONr_chiral_restr0.0760.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218081
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021472
LS refinement shellResolution: 2.753→2.824 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 26 -
Rwork0.302 435 -
all-461 -
obs--23.75 %

+
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