[English] 日本語
Yorodumi
- PDB-5uan: Crystal structure of multi-domain RAR-beta-RXR-alpha heterodimer ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uan
TitleCrystal structure of multi-domain RAR-beta-RXR-alpha heterodimer on DNA
Components
  • (Retinoic acid receptor ...) x 2
  • DNA (5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*G)-3')
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION/DNA / nuclear receptors / transcription / protein-DNA complex / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


glandular epithelial cell development / embryonic eye morphogenesis / ventricular cardiac muscle cell differentiation / growth plate cartilage development / 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 / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / embryonic digestive tract development ...glandular epithelial cell development / embryonic eye morphogenesis / ventricular cardiac muscle cell differentiation / growth plate cartilage development / 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 / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / embryonic digestive tract development / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / striatum development / Carnitine shuttle / retinoic acid binding / outflow tract septum morphogenesis / positive regulation of vitamin D receptor signaling pathway / TGFBR3 expression / negative regulation of chondrocyte differentiation / embryonic hindlimb morphogenesis / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / heterocyclic compound binding / ureteric bud development / neural precursor cell proliferation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of myelination / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / DNA binding domain binding / positive regulation of lipid metabolic process / LBD domain binding / locomotor rhythm / positive regulation of lipoprotein transport / nuclear steroid receptor activity / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / regulation of lipid metabolic process / 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 / response to retinoic acid / cellular response to low-density lipoprotein particle stimulus / positive regulation of bone mineralization / nuclear retinoid X receptor binding / negative regulation of stem cell proliferation / 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 / Regulation of lipid metabolism by PPARalpha / peptide binding / cell maturation / peroxisome proliferator activated receptor signaling pathway / 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 / neurogenesis / stem cell proliferation / nuclear receptor binding / transcription coregulator binding / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / mRNA transcription by RNA polymerase II / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / multicellular organism growth / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / rhythmic process / nervous system development / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / double-stranded DNA binding / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription coactivator activity
Similarity search - Function
: / : / Retinoic acid receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / : / Nuclear receptor coactivator 2 ...: / : / Retinoic acid receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(9cis)-retinoic acid / RETINOIC ACID / DNA / DNA (> 10) / Nuclear receptor coactivator 2 / Retinoic acid receptor beta / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.508 Å
AuthorsChandra, V. / Wu, D. / Kim, Y. / Rastinejad, F.
CitationJournal: Nat Commun / Year: 2017
Title: The quaternary architecture of RAR beta-RXR alpha heterodimer facilitates domain-domain signal transmission.
Authors: Chandra, V. / Wu, D. / Li, S. / Potluri, N. / Kim, Y. / Rastinejad, F.
History
DepositionDec 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinoic acid receptor RXR-alpha
B: Retinoic acid receptor beta
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
E: DNA (5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*GP*C)-3')
F: DNA (5'-D(*GP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,76812
Polymers98,9066
Non-polymers8636
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-96 kcal/mol
Surface area32670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.470, 77.403, 112.113
Angle α, β, γ (deg.)90.000, 90.370, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Retinoic acid receptor ... , 2 types, 2 molecules AB

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


Mass: 41120.352 Da / Num. of mol.: 1 / Fragment: UNP residues 98-462
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
#2: Protein Retinoic acid receptor beta / RAR-beta / HBV-activated protein / Nuclear receptor subfamily 1 group B member 2 / RAR-epsilon


Mass: 44817.578 Da / Num. of mol.: 1 / Fragment: UNP residues 98-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARB, HAP, NR1B2 / Production host: Escherichia coli (E. coli) / References: UniProt: P10826

-
Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide Nuclear receptor coactivator 2


Mass: 1276.530 Da / Num. of mol.: 2 / Fragment: UNP residues 687-696 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: E7EWM1, UniProt: Q15596*PLUS

-
DNA chain , 2 types, 2 molecules EF

#4: DNA chain DNA (5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*GP*C)-3')


Mass: 5236.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*G)-3')


Mass: 5178.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 3 types, 6 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2
#8: Chemical ChemComp-REA / RETINOIC ACID


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES, PEG300

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 9550 / % possible obs: 84 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.057 / Rrim(I) all: 0.125 / Χ2: 0.765 / Net I/σ(I): 7.1 / Num. measured all: 38824
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.5-3.562.50.4310.78152.2
3.56-3.632.60.3070.895155.8
3.63-3.692.60.2880.934159.7
3.69-3.772.80.2690.86164.5
3.77-3.852.90.3250.891172.8
3.85-3.9430.3050.858173.9
3.94-4.043.10.280.928179.3
4.04-4.153.20.2990.911180.7
4.15-4.273.30.2610.924184.4
4.27-4.413.40.2510.922187.1
4.41-4.573.60.2140.942187.8
4.57-4.753.60.2090.98190.6
4.75-4.973.90.2090.939193
4.97-5.234.20.2340.934197.9
5.23-5.554.80.2510.96199.1
5.55-5.985.40.250.97199.8
5.98-6.585.70.2070.968199.8
6.58-7.535.80.1230.956199.8
7.53-9.485.50.0670.9781100
9.48-505.40.0470.974199

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
Cootmodel building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DSZ, 1XDK

1dsz

1xdk


Resolution: 3.508→47.405 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.81
RfactorNum. reflection% reflection
Rfree0.2703 1341 10.02 %
Rwork0.2211 --
obs0.2225 13381 60.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 194.15 Å2 / Biso mean: 61.6256 Å2 / Biso min: 13.55 Å2
Refinement stepCycle: final / Resolution: 3.508→47.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 691 48 0 5560
Biso mean--51.89 --
Num. residues----639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035745
X-RAY DIFFRACTIONf_angle_d0.5467848
X-RAY DIFFRACTIONf_chiral_restr0.037882
X-RAY DIFFRACTIONf_plane_restr0.003881
X-RAY DIFFRACTIONf_dihedral_angle_d14.3723394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5077-3.6330.3477350.305431334816
3.633-3.77850.3162540.26845751123
3.7785-3.95030.2627670.231266973633
3.9503-4.15850.2829940.230989298645
4.1585-4.41890.26961280.20641093122154
4.4189-4.75970.29561340.20841317145167
4.7597-5.23820.28721930.20291580177380
5.2382-5.99490.26351910.23251813200493
5.9949-7.5480.28972270.24391978220599
7.548-47.40890.22012180.19081928214697
Refinement TLS params.Method: refined / Origin x: -9.6616 Å / Origin y: 20.0592 Å / Origin z: -31.9392 Å
111213212223313233
T0.0417 Å20.1826 Å2-0.0296 Å2-0.219 Å2-0.112 Å2--0.2954 Å2
L1.4051 °2-0.1855 °20.3545 °2-1.6757 °2-0.7645 °2--1.9401 °2
S-0.5157 Å °-0.0691 Å °-0.0527 Å °0.4562 Å °0.4112 Å °-0.245 Å °-0.1285 Å °-0.0068 Å °0.0636 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA133 - 457
2X-RAY DIFFRACTION1allA501 - 601
3X-RAY DIFFRACTION1allB80 - 408
4X-RAY DIFFRACTION1allB501 - 601
5X-RAY DIFFRACTION1allC687 - 696
6X-RAY DIFFRACTION1allD687 - 695
7X-RAY DIFFRACTION1allE1 - 17
8X-RAY DIFFRACTION1allF1 - 17

+
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