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- PDB-1xls: Crystal structure of the mouse CAR/RXR LBD heterodimer bound to T... -

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Basic information

Entry
Database: PDB / ID: 1xls
TitleCrystal structure of the mouse CAR/RXR LBD heterodimer bound to TCPOBOP and 9cRA and a TIF2 peptide containg the third LXXLL motifs
Components
  • Nuclear receptor coactivator 2
  • Orphan nuclear receptor NR1I3
  • Retinoic acid receptor RXR-alpha
KeywordsTRANSCRIPTION / LBD / nuclear receptor / CAR / xenobiotic
Function / homology
Function and homology information


HATs acetylate histones / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / Regulation of lipid metabolism by PPARalpha / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / positive regulation of glucocorticoid receptor signaling pathway ...HATs acetylate histones / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / Regulation of lipid metabolism by PPARalpha / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / positive regulation of glucocorticoid receptor signaling pathway / Cytoprotection by HMOX1 / 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 / nuclear glucocorticoid receptor binding / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine shuttle / nuclear retinoic acid receptor binding / retinoic acid binding / TGFBR3 expression / positive regulation of vitamin D receptor signaling pathway / positive regulation of female receptivity / nuclear vitamin D receptor binding / nuclear thyroid hormone receptor binding / 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 / LBD domain binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / 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 / nuclear retinoid X receptor binding / DNA polymerase binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / Recycling of bile acids and salts / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / transcription coregulator binding / response to progesterone / nuclear receptor binding / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / 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 / 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 / osteoblast differentiation / RNA polymerase II transcription regulator complex / circadian rhythm / male gonad development / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / response to estradiol / double-stranded DNA binding / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / dendritic spine / 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 / DNA-binding transcription factor activity
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 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking ...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 / 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
(9cis)-retinoic acid / Chem-TCD / Nuclear receptor subfamily 1 group I member 3 / Retinoic acid receptor RXR-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsSuino, K. / peng, L. / Reynolds, R. / Li, Y. / Cha, J.-Y. / Repa, J.J. / Kliewer, S.A. / Xu, H.E.
CitationJournal: Mol.Cell / Year: 2004
Title: The nuclear xenobiotic receptor CAR: structural determinants of constitutive activation and heterodimerization.
Authors: Suino, K. / Peng, L. / Reynolds, R. / Li, Y. / Cha, J.Y. / Repa, J.J. / Kliewer, S.A. / Xu, H.E.
History
DepositionSep 30, 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 9, 2016Group: Non-polymer description / Source and taxonomy
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 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: Retinoic acid receptor RXR-alpha
C: Retinoic acid receptor RXR-alpha
D: Retinoic acid receptor RXR-alpha
E: Orphan nuclear receptor NR1I3
F: Orphan nuclear receptor NR1I3
G: Orphan nuclear receptor NR1I3
H: Orphan nuclear receptor NR1I3
I: Nuclear receptor coactivator 2
J: Nuclear receptor coactivator 2
K: Nuclear receptor coactivator 2
L: Nuclear receptor coactivator 2
M: Nuclear receptor coactivator 2
N: Nuclear receptor coactivator 2
O: Nuclear receptor coactivator 2
P: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,87524
Polymers233,06516
Non-polymers2,8108
Water1,58588
1
A: Retinoic acid receptor RXR-alpha
E: Orphan nuclear receptor NR1I3
I: Nuclear receptor coactivator 2
M: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9696
Polymers58,2664
Non-polymers7022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-48 kcal/mol
Surface area22230 Å2
MethodPISA
2
B: Retinoic acid receptor RXR-alpha
F: Orphan nuclear receptor NR1I3
J: Nuclear receptor coactivator 2
N: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9696
Polymers58,2664
Non-polymers7022
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-47 kcal/mol
Surface area22180 Å2
MethodPISA
3
C: Retinoic acid receptor RXR-alpha
G: Orphan nuclear receptor NR1I3
K: Nuclear receptor coactivator 2
O: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9696
Polymers58,2664
Non-polymers7022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-47 kcal/mol
Surface area22220 Å2
MethodPISA
4
D: Retinoic acid receptor RXR-alpha
H: Orphan nuclear receptor NR1I3
L: Nuclear receptor coactivator 2
P: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9696
Polymers58,2664
Non-polymers7022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-47 kcal/mol
Surface area22270 Å2
MethodPISA
5
B: Retinoic acid receptor RXR-alpha
F: Orphan nuclear receptor NR1I3
J: Nuclear receptor coactivator 2
N: Nuclear receptor coactivator 2
hetero molecules

D: Retinoic acid receptor RXR-alpha
H: Orphan nuclear receptor NR1I3
L: Nuclear receptor coactivator 2
P: Nuclear receptor coactivator 2
hetero molecules

A: Retinoic acid receptor RXR-alpha
C: Retinoic acid receptor RXR-alpha
E: Orphan nuclear receptor NR1I3
G: Orphan nuclear receptor NR1I3
I: Nuclear receptor coactivator 2
K: Nuclear receptor coactivator 2
M: Nuclear receptor coactivator 2
O: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,87524
Polymers233,06516
Non-polymers2,8108
Water27015
TypeNameSymmetry operationNumber
crystal symmetry operation1_546x,y-1,z+11
crystal symmetry operation1_646x+1,y-1,z+11
identity operation1_555x,y,z1
Buried area32370 Å2
ΔGint-219 kcal/mol
Surface area82680 Å2
MethodPISA
6
A: Retinoic acid receptor RXR-alpha
C: Retinoic acid receptor RXR-alpha
E: Orphan nuclear receptor NR1I3
G: Orphan nuclear receptor NR1I3
I: Nuclear receptor coactivator 2
K: Nuclear receptor coactivator 2
M: Nuclear receptor coactivator 2
O: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,93812
Polymers116,5338
Non-polymers1,4054
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15410 Å2
ΔGint-107 kcal/mol
Surface area42100 Å2
MethodPISA
7
B: Retinoic acid receptor RXR-alpha
F: Orphan nuclear receptor NR1I3
J: Nuclear receptor coactivator 2
N: Nuclear receptor coactivator 2
hetero molecules

D: Retinoic acid receptor RXR-alpha
H: Orphan nuclear receptor NR1I3
L: Nuclear receptor coactivator 2
P: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,93812
Polymers116,5338
Non-polymers1,4054
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area15520 Å2
ΔGint-105 kcal/mol
Surface area42030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.271, 88.381, 105.494
Angle α, β, γ (deg.)79.02, 85.81, 67.22
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
Retinoic acid receptor RXR-alpha


Mass: 26011.125 Da / Num. of mol.: 4 / Fragment: CAR LBD / Mutation: residues 116-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: human / Plasmid: PETDUET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P19793
#2: Protein
Orphan nuclear receptor NR1I3 / Constitutive androstane receptor / CAR


Mass: 28004.400 Da / Num. of mol.: 4 / Fragment: RXRalpha LBD / Mutation: residues 225-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: mouse / Plasmid: PET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O35627

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Protein/peptide , 1 types, 8 molecules IJKLMNOP

#3: Protein/peptide
Nuclear receptor coactivator 2 / NCoA-2 / Transcriptional intermediary factor 2


Mass: 2125.381 Da / Num. of mol.: 8 / Fragment: TIF2 / Mutation: the third LXXLL motif / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q9WUI9

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Non-polymers , 3 types, 96 molecules

#4: Chemical
ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#5: Chemical
ChemComp-TCD / 3,5-DICHLORO-2-{4-[(3,5-DICHLOROPYRIDIN-2-YL)OXY]PHENOXY}PYRIDINE


Mass: 402.059 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H8Cl4N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG2K, 3% 1,6 hexanediol, 0.1 M di-ammonium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2004 / Details: diamond crystal
RadiationMonochromator: diamond crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.96→20 Å / Num. all: 45946 / Num. obs: 42821 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.171 / Rsym value: 0.121 / Net I/σ(I): 10.2
Reflection shellResolution: 2.96→3.06 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4227 / Rsym value: 0.76 / % possible all: 92.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.96→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1528881.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.303 3463 8.1 %RANDOM
Rwork0.255 ---
all0.259 45946 --
obs0.255 42670 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.5547 Å2 / ksol: 0.295007 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å2-5.9 Å20 Å2
2---1.74 Å2-3.16 Å2
3---4.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.96→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16016 0 184 88 16288
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d0.96
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.96→3.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 518 8.2 %
Rwork0.366 5778 -
obs--80.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION39CRA.PAR9CRA.TOP
X-RAY DIFFRACTION4TCP.PARTCP.TOP

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