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- PDB-1zh7: Structural and Biochemical Basis for Selective Repression of the ... -

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Basic information

Entry
Database: PDB / ID: 1zh7
TitleStructural and Biochemical Basis for Selective Repression of the Orphan Nuclear Receptor LRH-1 by SHP
Components
  • Orphan nuclear receptor NR5A2
  • nuclear receptor subfamily 0, group B, member 2
KeywordsTRANSCRIPTION / protein-peptide complex
Function / homology
Function and homology information


SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / Nuclear Receptor transcription pathway / tissue development / nuclear retinoic acid receptor binding / bile acid metabolic process / bile acid and bile salt transport ...SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / Nuclear Receptor transcription pathway / tissue development / nuclear retinoic acid receptor binding / bile acid metabolic process / bile acid and bile salt transport / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / positive regulation of viral genome replication / animal organ regeneration / response to glucose / nuclear retinoid X receptor binding / Notch signaling pathway / hormone-mediated signaling pathway / cellular response to leukemia inhibitory factor / transcription coregulator binding / cholesterol homeostasis / circadian regulation of gene expression / positive regulation of insulin secretion / response to organic cyclic compound / negative regulation of DNA-binding transcription factor activity / phospholipid binding / circadian rhythm / RNA polymerase II transcription regulator complex / transcription corepressor activity / nuclear receptor activity / regulation of cell population proliferation / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / protein-containing complex binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear receptor subfamily 0 group B member 1/2 / Nuclear hormone receptor family 5 / Retinoid X Receptor / Retinoid X Receptor / 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 receptor subfamily 0 group B member 1/2 / Nuclear hormone receptor family 5 / Retinoid X Receptor / Retinoid X Receptor / 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
Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor subfamily 0 group B member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, Y. / Choi, M. / Suino, K. / Kovach, A. / Daugherty, J. / Kliewer, S.A. / Xu, H.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structural and biochemical basis for selective repression of the orphan nuclear receptor liver receptor homolog 1 by small heterodimer partner
Authors: Li, Y. / Choi, M. / Suino, K. / Kovach, A. / Daugherty, J. / Kliewer, S.A. / Xu, H.E.
History
DepositionApr 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orphan nuclear receptor NR5A2
B: Orphan nuclear receptor NR5A2
C: nuclear receptor subfamily 0, group B, member 2
D: nuclear receptor subfamily 0, group B, member 2


Theoretical massNumber of molelcules
Total (without water)58,9004
Polymers58,9004
Non-polymers00
Water3,081171
1
A: Orphan nuclear receptor NR5A2
C: nuclear receptor subfamily 0, group B, member 2


Theoretical massNumber of molelcules
Total (without water)29,4502
Polymers29,4502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-11 kcal/mol
Surface area13000 Å2
MethodPISA
2
B: Orphan nuclear receptor NR5A2
D: nuclear receptor subfamily 0, group B, member 2


Theoretical massNumber of molelcules
Total (without water)29,4502
Polymers29,4502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-11 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.765, 35.126, 134.205
Angle α, β, γ (deg.)90.00, 92.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Orphan nuclear receptor NR5A2 / Liver receptor homolog / LRH-1


Mass: 28204.438 Da / Num. of mol.: 2 / Fragment: LRH-1 Ligand Binding Domain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P45448
#2: Protein/peptide nuclear receptor subfamily 0, group B, member 2


Mass: 1245.445 Da / Num. of mol.: 2 / Fragment: SHP 1st LXXLL motif / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P97947
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.2 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, tri-Lithium Citrate tetrahydrate, pH 7.0, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.99998 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2004
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.5→30.2 Å / Num. all: 21170 / Num. obs: 21170 / % possible obs: 100 % / Observed criterion σ(F): 31.58 / Observed criterion σ(I): 3953 / Biso Wilson estimate: 62.8 Å2
Reflection shellResolution: 2.5→2.6 Å / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30.2 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1351581.44 / 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
Rfree0.285 1465 7.8 %RANDOM
Rwork0.226 ---
all0.226 18729 --
obs0.226 18729 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.6474 Å2 / ksol: 0.351688 e/Å3
Displacement parametersBiso mean: 84.8 Å2
Baniso -1Baniso -2Baniso -3
1-31.16 Å20 Å2-7.19 Å2
2---9.97 Å20 Å2
3----21.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-6 Å
Luzzati sigma a0.48 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.5→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 0 0 171 4315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d0.85
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 239 7.8 %
Rwork0.354 2828 -
obs-2322 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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