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- PDB-3hvl: Tethered PXR-LBD/SRC-1p complexed with SR-12813 -

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Basic information

Entry
Database: PDB / ID: 3hvl
TitleTethered PXR-LBD/SRC-1p complexed with SR-12813
ComponentsPregnane X receptor, Linker, Steroid receptor coactivator 1
KeywordsTranscription / Transferase / PXR / SRC-1 / TETHERED / ENGINEERED / DRUG-DRUG INTERACTIONS / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


cellular response to molecule of bacterial origin / intestinal epithelial structure maintenance / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / hypothalamus development / male mating behavior / steroid metabolic process ...cellular response to molecule of bacterial origin / intestinal epithelial structure maintenance / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / hypothalamus development / male mating behavior / steroid metabolic process / progesterone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / 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 / protein-lysine-acetyltransferase activity / xenobiotic catabolic process / xenobiotic transport / nuclear retinoid X receptor binding / estrous cycle / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / lactation / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / cellular response to hormone stimulus / intracellular receptor signaling pathway / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / response to progesterone / cerebellum development / positive regulation of adipose tissue development / positive regulation of neuron differentiation / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of cellular response to insulin stimulus / xenobiotic metabolic process / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Heme signaling / male gonad development / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional activation of mitochondrial biogenesis / cerebral cortex development / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / mRNA transcription by RNA polymerase II / 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 / transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription coactivator activity / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / 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 / DNA-templated transcription / nucleoplasm / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-SRL / Nuclear receptor subfamily 1 group I member 2 / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsLesburg, C.A. / Wang, W. / Prosise, W.W. / Chen, J. / Taremi, S.S. / Le, H.V. / Madison, V. / Cui, X. / Thomas, A. / Cheng, K.C.
CitationJournal: Protein Eng.Des.Sel. / Year: 2008
Title: Construction and characterization of a fully active PXR/SRC-1 tethered protein with increased stability
Authors: Wang, W. / Prosise, W.W. / Chen, J. / Taremi, S.S. / Le, H.V. / Madison, V. / Cui, X. / Thomas, A. / Cheng, K.C. / Lesburg, C.A.
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionAug 4, 2009ID: 3CTC
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 2, 2014Group: Source and taxonomy
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 21, 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

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Assembly

Deposited unit
A: Pregnane X receptor, Linker, Steroid receptor coactivator 1
B: Pregnane X receptor, Linker, Steroid receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3774
Polymers78,3682
Non-polymers1,0092
Water4,630257
1
A: Pregnane X receptor, Linker, Steroid receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6892
Polymers39,1841
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pregnane X receptor, Linker, Steroid receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6892
Polymers39,1841
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-28 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.440, 88.840, 105.390
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, Linker, Steroid receptor coactivator 1 / Nuclear receptor subfamily 1 group I member 2 / Orphan nuclear receptor PXR / Orphan nuclear ...Nuclear receptor subfamily 1 group I member 2 / Orphan nuclear receptor PXR / Orphan nuclear receptor PAR1 / Steroid and xenobiotic receptor / SXR / NCoA-1 / SRC-1 / RIP160 / Protein Hin-2 / Renal carcinoma antigen NY-REN-52 / Nuclear receptor coactivator 1


Mass: 39184.035 Da / Num. of mol.: 2
Fragment: PXR, residues 130-434, linker, SRC-1, residues 678-700
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: THE PEPTIDE FROM STEROID RECEPTOR COACTIVATOR 1 WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
Gene: NR1I2, PXR / Production host: Escherichia coli (E. coli)
References: UniProt: O75469, UniProt: Q15788, histone acetyltransferase
#2: Chemical ChemComp-SRL / [2-(3,5-DI-TERT-BUTYL-4-HYDROXY-PHENYL)-1-(DIETHOXY-PHOSPHORYL)-VINYL]-PHOSPHONIC ACID DIETHLYL ESTER / SR12813


Mass: 504.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H42O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 10-30% MPD OR ISOPROPANOL, 100 mM IMIDAZOLE, 1 mM SR12813, pH 7, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54182 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 27, 2005 / Details: MULTILAYER
RadiationMonochromator: MULTILAYER MIRRORS VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54182 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. all: 47572 / Num. obs: 46716 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.68 % / Biso Wilson estimate: 56.367 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.66 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.469 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
BUSTER-TNT1.3.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
BUSTER-TNT1.3.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→67.42 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 2351 5.04 %RANDOM
Rwork0.2203 ---
all0.2226 46640 --
obs0.2226 46640 97.97 %-
Displacement parametersBiso mean: 61.51 Å2
Baniso -1Baniso -2Baniso -3
1-3.63034718 Å20 Å20 Å2
2---0.81681636 Å20 Å2
3----2.81353081 Å2
Refine analyzeLuzzati coordinate error obs: 0.2877 Å
Refinement stepCycle: LAST / Resolution: 2.1→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 66 257 5031
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01149002
X-RAY DIFFRACTIONt_angle_deg1.20865812
X-RAY DIFFRACTIONt_dihedral_angle_d21.35310820
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_trig_c_planes0.011282
X-RAY DIFFRACTIONt_gen_planes0.0167465
X-RAY DIFFRACTIONt_it1.892490020
X-RAY DIFFRACTIONt_nbd0.059785
LS refinement shellResolution: 2.1→2.23 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2645 379 5.14 %
Rwork0.2239 6993 -
all0.2259 7372 -
obs-7372 97.97 %

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