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- PDB-8svn: Crystal structure of the apo form of pregnane X receptor ligand b... -

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Basic information

Entry
Database: PDB / ID: 8svn
TitleCrystal structure of the apo form of pregnane X receptor ligand binding domain
ComponentsPregnane X receptor ligand binding domain fused to SRC-1 coactivator peptide
KeywordsTRANSCRIPTION / Pregnane X receptor (PXR) / promiscuous ligand-activated protein / nuclear receptor subfamily 1 / transcriptional regulator / and drug metabolism.
Function / homology
Function and homology information


cellular response to molecule of bacterial origin / intestinal epithelial structure maintenance / intermediate filament cytoskeleton / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / xenobiotic transport / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / male mating behavior ...cellular response to molecule of bacterial origin / intestinal epithelial structure maintenance / intermediate filament cytoskeleton / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / xenobiotic transport / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / male mating behavior / hypothalamus development / steroid metabolic process / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / progesterone receptor signaling pathway / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / xenobiotic catabolic process / estrous cycle / nuclear retinoid X receptor binding / histone acetyltransferase activity / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / estrogen receptor signaling pathway / lactation / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / regulation of cellular response to insulin stimulus / xenobiotic metabolic process / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / cerebellum development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / response to estradiol / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription coactivator activity / protein dimerization activity / nuclear body / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
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 / : ...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 / 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 / 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
Similarity search - Domain/homology
Nuclear receptor subfamily 1 group I member 2 / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsGarcia-Maldonado, E. / Huber, A.D. / Nithianantham, S. / Miller, D.J. / Chen, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118041 United States
CitationJournal: Nat Commun / Year: 2024
Title: Chemical manipulation of an activation/inhibition switch in the nuclear receptor PXR.
Authors: Garcia-Maldonado, E. / Huber, A.D. / Chai, S.C. / Nithianantham, S. / Li, Y. / Wu, J. / Poudel, S. / Miller, D.J. / Seetharaman, J. / Chen, T.
History
DepositionMay 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pregnane X receptor ligand binding domain fused to SRC-1 coactivator peptide
B: Pregnane X receptor ligand binding domain fused to SRC-1 coactivator peptide


Theoretical massNumber of molelcules
Total (without water)79,7912
Polymers79,7912
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-16 kcal/mol
Surface area27580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.990, 89.653, 106.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pregnane X receptor ligand binding domain fused to SRC-1 coactivator peptide


Mass: 39895.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR, NCOA1, BHLHE74, SRC1 / Plasmid: pET-3A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O75469, UniProt: Q15788, histone acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: H2O
Has ligand of interestN

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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: 2.52 Å3/Da / Density % sol: 51.22 % / Description: Rectangular shaped crystal
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: in 0.1 M HEPES pH 7.0, and 14% Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→89.65 Å / Num. obs: 41701 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.028 / Rrim(I) all: 0.103 / Χ2: 1.02 / Net I/σ(I): 13.6
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 1.546 / Num. measured all: 50090 / Num. unique obs: 3574 / CC1/2: 0.753 / Rpim(I) all: 0.424 / Rrim(I) all: 1.603 / Χ2: 1.05 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
Aimlessdata scaling
XDSdata reduction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→53.44 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 2133 5.12 %Random selection
Rwork0.2104 ---
obs0.2141 41631 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→53.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4569 0 0 72 4641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034697
X-RAY DIFFRACTIONf_angle_d0.576344
X-RAY DIFFRACTIONf_dihedral_angle_d14.2471736
X-RAY DIFFRACTIONf_chiral_restr0.036708
X-RAY DIFFRACTIONf_plane_restr0.006810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.36161340.32592604X-RAY DIFFRACTION100
2.25-2.310.31271360.27412584X-RAY DIFFRACTION100
2.31-2.370.29191490.24872617X-RAY DIFFRACTION100
2.37-2.440.27081430.24032574X-RAY DIFFRACTION100
2.44-2.520.27041410.252601X-RAY DIFFRACTION100
2.52-2.610.29441310.25372609X-RAY DIFFRACTION100
2.61-2.710.30931580.28042615X-RAY DIFFRACTION100
2.71-2.840.31541350.25972601X-RAY DIFFRACTION100
2.84-2.990.26671330.23882631X-RAY DIFFRACTION100
2.99-3.170.25961660.24022591X-RAY DIFFRACTION100
3.17-3.420.28531490.24422636X-RAY DIFFRACTION100
3.42-3.760.26461570.20672634X-RAY DIFFRACTION100
3.76-4.310.23931340.19262663X-RAY DIFFRACTION100
4.31-5.420.19741390.17882698X-RAY DIFFRACTION100
5.42-53.440.19981280.19492840X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.1229-0.2362-6.36193.77992.2529.5678-0.2989-0.5849-0.63231.10910.21130.50121.16310.54940.6630.71330.1470.14970.47810.10720.65326.712513.935145.5141
21.8891.0949-1.4323.7552-1.20475.0936-0.25170.3771-0.3333-0.6308-0.5395-0.5690.18660.90540.48080.5978-0.00570.02620.6298-0.00180.536721.22825.837421.473
36.6458-0.77491.4611.35070.77715.0738-0.23580.99940.9083-0.3583-0.23730.1156-0.87450.0770.28960.7717-0.04850.09210.62820.21170.78118.06538.707617.0402
44.36721.4525-1.46153.1338-1.29674.4675-0.03550.1751-0.26120.2293-0.00810.10040.1437-0.12570.02270.47260.02260.0360.4987-0.05580.58558.34118.31427.7405
57.65281.4215-0.74393.7960.81235.56830.0367-0.02130.2222-0.1732-0.07540.1884-0.40180.16620.05230.41830.03850.06430.34630.06010.480711.603127.694630.7467
62.30850.0411-0.80664.4315-0.14663.8289-0.06540.90341.123-0.74690.09450.1849-2.74140.0027-0.0451.22410.0010.01940.58820.07430.69810.301740.862334.8823
73.0042-0.17150.16834.26491.42125.3734-0.03510.2883-0.31890.2391-0.03120.67610.2884-0.28120.18280.44020.0430.13860.5169-0.00120.69931.230623.166237.6255
80.9205-1.0512-1.5993.8463-0.00813.0341-0.3452-0.3197-0.20240.67220.01910.54430.4428-0.32940.32080.56060.05060.20120.52660.03640.5947-1.966824.376448.1902
90.90970.1464-1.70491.18131.59082.8716-0.07260.28680.0307-0.3612-0.32780.3987-0.7957-0.47350.55720.60530.1336-0.01960.5937-0.00770.63911.537933.785928.4984
105.18281.1873-1.96347.7677-1.61157.6095-0.30640.6797-0.5672-0.54170.18330.489-0.0349-0.95970.00570.57940.01120.01370.6987-0.11720.62153.876418.111416.7131
112.73420.9357-1.20735.757-3.2944.7906-0.09570.45190.1085-0.39980.20890.12540.0542-0.1724-0.19960.49480.02020.01070.5-0.07290.403948.194744.98230.1855
126.78821.2972-1.99664.96920.72643.4816-0.2803-0.6515-0.24270.852-0.118-0.81540.15751.10350.26270.749-0.0540.06320.91560.25740.617243.733433.057521.3585
133.51380.74640.01824.05840.14352.96780.0186-0.2388-0.16090.1568-0.0232-0.22740.06230.2995-0.04850.40240.0159-0.01820.43690.03160.38653.689143.77715.5693
142.49532.30942.57743.60730.27564.9356-0.26360.2729-0.0592-0.32970.2216-0.5541-0.2010.5748-0.10460.5168-0.11880.12460.63550.05830.641364.509957.7666-0.0168
152.1782.4004-1.7612.4225-2.18562.1178-0.0244-0.3311-0.4433-0.1023-0.0087-0.26920.55680.40420.01140.65110.0085-0.04750.69150.0820.667361.318540.293812.0682
163.53461.05640.49263.8955-0.56397.24850.11610.113-0.8326-0.288-0.0746-0.09911.08250.5545-0.080.88550.07180.11540.5149-0.060.720954.232227.8842-1.7777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 142 THROUGH 161 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 162 THROUGH 193 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 194 THROUGH 239 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 240 THROUGH 268 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 269 THROUGH 308 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 309 THROUGH 333 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 334 THROUGH 358 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 359 THROUGH 388 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 389 THROUGH 417 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 418 THROUGH 458 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 142 THROUGH 196 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 197 THROUGH 239 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 240 THROUGH 358 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 359 THROUGH 388 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 389 THROUGH 417 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 418 THROUGH 460 )

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