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- PDB-1xv9: crystal structure of CAR/RXR heterodimer bound with SRC1 peptide,... -

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Basic information

Entry
Database: PDB / ID: 1xv9
Titlecrystal structure of CAR/RXR heterodimer bound with SRC1 peptide, fatty acid, and 5b-pregnane-3,20-dione.
Components
  • Orphan nuclear receptor NR1I3
  • Retinoic acid receptor RXR-alpha
  • nuclear receptor coactivator 1 isoform 1
KeywordsDNA BINDING PROTEIN / CAR / RXR / SRC1 / pregnanedione
Function / homology
Function and homology information


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 / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / TGFBR3 expression ...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 / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / retinoic acid binding / TGFBR3 expression / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of vitamin D receptor signaling pathway / positive regulation of female receptivity / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / estrous cycle / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of bone mineralization / retinoic acid receptor signaling pathway / progesterone receptor signaling pathway / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / hippocampus development / transcription coregulator binding / response to progesterone / nuclear receptor binding / nuclear estrogen receptor binding / 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 / cerebral cortex development / 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 / osteoblast differentiation / male gonad development / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / response to estradiol / HATs acetylate histones / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / cell differentiation / cytoskeleton / receptor complex / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II
Similarity search - Function
Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Thyroid hormone receptor / Retinoid X receptor/HNF4 / : / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 ...Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Thyroid hormone receptor / Retinoid X receptor/HNF4 / : / Nuclear receptor coactivator 1 / 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 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 / 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
(5BETA)-PREGNANE-3,20-DIONE / PENTADECANOIC ACID / : / Retinoic acid receptor RXR-alpha / Nuclear receptor subfamily 1 group I member 3 / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsXu, R.X. / Lambert, M.H. / Wisely, B.B. / Warren, E.N. / Weinert, E.E. / Waitt, G.M. / Williams, J.D. / Moore, L.B. / Willson, T.M. / Moore, J.T.
CitationJournal: Mol.Cell / Year: 2004
Title: A Structural Basis for Constitutive Activity in the Human CAR/RXRalpha Heterodimer.
Authors: Xu, R.X. / Lambert, M.H. / Wisely, B.B. / Warren, E.N. / Weinert, E.E. / Waitt, G.M. / Williams, J.D. / Collins, J.L. / Moore, L.B. / Willson, T.M. / Moore, J.T.
History
DepositionOct 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 30, 2016Group: Other / Source and taxonomy
Revision 1.4Feb 14, 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

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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: Orphan nuclear receptor NR1I3
C: Retinoic acid receptor RXR-alpha
D: Orphan nuclear receptor NR1I3
E: nuclear receptor coactivator 1 isoform 1
F: nuclear receptor coactivator 1 isoform 1
G: nuclear receptor coactivator 1 isoform 1
H: nuclear receptor coactivator 1 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,91411
Polymers116,1138
Non-polymers8013
Water1,18966
1
A: Retinoic acid receptor RXR-alpha
B: Orphan nuclear receptor NR1I3
E: nuclear receptor coactivator 1 isoform 1
F: nuclear receptor coactivator 1 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2995
Polymers58,0564
Non-polymers2421
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Retinoic acid receptor RXR-alpha
D: Orphan nuclear receptor NR1I3
G: nuclear receptor coactivator 1 isoform 1
H: nuclear receptor coactivator 1 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6156
Polymers58,0564
Non-polymers5592
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.442, 128.442, 214.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Retinoic acid receptor RXR-alpha / Retinoid X receptor alpha


Mass: 26509.701 Da / Num. of mol.: 2 / Fragment: LBD domain
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 Orphan nuclear receptor NR1I3 / Constitutive androstane receptor / CAR / Orphan nuclear receptor MB67


Mass: 28278.959 Da / Num. of mol.: 2 / Fragment: LBD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q14994

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Protein/peptide , 1 types, 4 molecules EFGH

#3: Protein/peptide
nuclear receptor coactivator 1 isoform 1


Mass: 1633.916 Da / Num. of mol.: 4 / Fragment: peptide fragment-13 residues / Source method: obtained synthetically / Details: Chemically synthesized / Source: (synth.) Homo sapiens (human) / References: GenBank: 22538455, UniProt: Q15788*PLUS

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Non-polymers , 3 types, 69 molecules

#4: Chemical ChemComp-F15 / PENTADECANOIC ACID


Mass: 242.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30O2
#5: Chemical ChemComp-CI2 / (5BETA)-PREGNANE-3,20-DIONE


Mass: 316.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 4.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: potassium sodium phosphate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2004
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 56901 / Num. obs: 49180 / % possible obs: 86.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 37.4

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Refinement was done on data from twinned crystal. twinning operator= -k,-h,-l twinning fraction= 0.473
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2834 -random
Rwork0.181 ---
all0.181 56901 --
obs0.181 49180 86.4 %-
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8028 0 57 66 8151

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