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- PDB-8e3n: Crystal structure of pregnane X receptor ligand binding domain co... -

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Basic information

Entry
Database: PDB / ID: 8e3n
TitleCrystal structure of pregnane X receptor ligand binding domain complexed with rifamycin S
ComponentsNuclear receptor subfamily 1 group I member 2
KeywordsTRANSCRIPTION / nuclear receptor / transcription factor / metabolism / antibiotic
Function / homology
Function and homology information


cellular response to molecule of bacterial origin / intestinal epithelial structure maintenance / intermediate filament cytoskeleton / xenobiotic transport / steroid metabolic process / xenobiotic catabolic process / intracellular receptor signaling pathway / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding ...cellular response to molecule of bacterial origin / intestinal epithelial structure maintenance / intermediate filament cytoskeleton / xenobiotic transport / steroid metabolic process / xenobiotic catabolic process / intracellular receptor signaling pathway / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / 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 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
Rifamycin S / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHuber, A.D. / Poudel, S. / Seetharaman, J. / Miller, D.J. / Lin, W. / 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: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structure-guided approach to modulate small molecule binding to a promiscuous ligand-activated protein.
Authors: Lin, W. / Huber, A.D. / Poudel, S. / Li, Y. / Seetharaman, J. / Miller, D.J. / Chen, T.
History
DepositionAug 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor subfamily 1 group I member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9042
Polymers36,2091
Non-polymers6961
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.893, 91.893, 85.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Nuclear receptor subfamily 1 group I member 2 / Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and ...Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and xenobiotic receptor / SXR


Mass: 36208.742 Da / Num. of mol.: 1 / Fragment: UNP residues 153-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Production host: Escherichia coli (E. coli) / References: UniProt: O75469
#2: Chemical ChemComp-VA0 / Rifamycin S / (2S,12Z,14Z,16S,17S,18R,19R,20R,21S,22R,23S,24E)-5,17,19-trihydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-1,6,9,11-tetraoxo-1,2,6,9-tetrahydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl acetate


Mass: 695.753 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H45NO12 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 100 mM imidazole (pH 7.2), 14% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.2→32.49 Å / Num. obs: 22158 / % possible obs: 99.6 % / Redundancy: 10.5 % / Biso Wilson estimate: 42.54 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.046 / Rrim(I) all: 0.148 / Rsym value: 0.092 / Net I/σ(I): 4.3
Reflection shellResolution: 2.2→2.26 Å / Num. unique obs: 1082 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M13

1m13


Resolution: 2.25→32.49 Å / SU ML: 0.235 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.7104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2349 913 5.07 %
Rwork0.2084 17105 -
obs0.2099 18018 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.73 Å2
Refinement stepCycle: LAST / Resolution: 2.25→32.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 50 111 2357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512299
X-RAY DIFFRACTIONf_angle_d0.80523109
X-RAY DIFFRACTIONf_chiral_restr0.0499341
X-RAY DIFFRACTIONf_plane_restr0.0043396
X-RAY DIFFRACTIONf_dihedral_angle_d16.221870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.370.28071310.23472392X-RAY DIFFRACTION100
2.37-2.520.27781180.23862388X-RAY DIFFRACTION100
2.52-2.710.2751200.22642424X-RAY DIFFRACTION100
2.71-2.980.2563990.22082438X-RAY DIFFRACTION100
2.98-3.420.26451530.2242421X-RAY DIFFRACTION100
3.42-4.30.22331260.19162467X-RAY DIFFRACTION99.88
4.3-32.490.20831660.19772575X-RAY DIFFRACTION99.85

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