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- PDB-5uan: Crystal structure of multi-domain RAR-beta-RXR-alpha heterodimer ... -

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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


ventricular cardiac muscle cell differentiation / embryonic eye morphogenesis / glandular epithelial cell development / growth plate cartilage development / 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 / embryonic digestive tract development ...ventricular cardiac muscle cell differentiation / embryonic eye morphogenesis / glandular epithelial cell development / growth plate cartilage development / 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 / embryonic digestive tract development / positive regulation of thyroid hormone mediated signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / striatum development / Carnitine metabolism / neural precursor cell proliferation / anatomical structure development / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / negative regulation of chondrocyte differentiation / positive regulation of vitamin D receptor signaling pathway / embryonic hindlimb morphogenesis / nuclear vitamin D receptor binding / ureteric bud development / regulation of myelination / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / heterocyclic compound binding / LBD domain binding / locomotor rhythm / aryl hydrocarbon receptor binding / positive regulation of cholesterol efflux / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / retinoic acid receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / negative regulation of stem cell proliferation / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / neurogenesis / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / response to progesterone / stem cell proliferation / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / circadian regulation of gene expression / multicellular organism growth / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / HATs acetylate histones / double-stranded DNA binding / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / cell differentiation / transcription coactivator activity / protein dimerization activity / nuclear body / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding
Similarity search - Function
: / : / Retinoic acid receptor / Erythroid Transcription Factor GATA-1, subunit A / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Erythroid Transcription Factor GATA-1; Chain A / Retinoid X receptor/HNF4 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 ...: / : / Retinoic acid receptor / Erythroid Transcription Factor GATA-1, subunit A / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Erythroid Transcription Factor GATA-1; Chain A / 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 / 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 / PAS domain superfamily / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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Components

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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

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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

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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)

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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 / Alitretinoin


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#8: Chemical ChemComp-REA / RETINOIC ACID / Retinoic acid


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

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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