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- PDB-1yp0: Structure of the steroidogenic factor-1 ligand binding domain bou... -

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Basic information

Entry
Database: PDB / ID: 1yp0
TitleStructure of the steroidogenic factor-1 ligand binding domain bound to phospholipid and a SHP peptide motif
Components
  • Nuclear receptor subfamily 0, group B, member 2
  • nuclear receptor subfamily 5, group A, member 1
KeywordsTRANSCRIPTION / Ligand dependent nuclear receptor / Steroidogenic factor-1 / NR5A1 / helical sandwich fold / LBD fold
Function / homology
Function and homology information


response to gonadotropin-releasing hormone / Sertoli cell differentiation / reproductive process / SUMOylation of intracellular receptors / negative regulation of female gonad development / Nuclear Receptor transcription pathway / sex determination / positive regulation of male gonad development / luteinization / calcineurin-mediated signaling ...response to gonadotropin-releasing hormone / Sertoli cell differentiation / reproductive process / SUMOylation of intracellular receptors / negative regulation of female gonad development / Nuclear Receptor transcription pathway / sex determination / positive regulation of male gonad development / luteinization / calcineurin-mediated signaling / Nuclear Receptor transcription pathway / tissue development / Leydig cell differentiation / male sex determination / nuclear retinoic acid receptor binding / maintenance of protein location in nucleus / bile acid and bile salt transport / hormone metabolic process / transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / adrenal gland development / female gonad development / animal organ regeneration / response to glucose / nuclear retinoid X receptor binding / Notch signaling pathway / hormone-mediated signaling pathway / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / phospholipid binding / circadian regulation of gene expression / positive regulation of insulin secretion / negative regulation of DNA-binding transcription factor activity / response to organic cyclic compound / circadian rhythm / RNA polymerase II transcription regulator complex / male gonad development / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / double-stranded DNA binding / response to ethanol / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / chromatin / protein-containing complex binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
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
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Steroidogenic factor 1 / Nuclear receptor subfamily 0 group B member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLi, Y. / Choi, M. / Cavey, G. / Daugherty, J. / Suino, K. / Kovach, A. / Bingham, N. / Kliewer, S. / Xu, H.
CitationJournal: Mol.Cell / Year: 2005
Title: Crystallographic identification and functional characterization of phospholipids as ligands for the orphan nuclear receptor steroidogenic factor-1.
Authors: Li, Y. / Choi, M. / Cavey, G. / Daugherty, J. / Suino, K. / Kovach, A. / Bingham, N. / Kliewer, S. / Xu, H.
History
DepositionJan 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: nuclear receptor subfamily 5, group A, member 1
B: Nuclear receptor subfamily 0, group B, member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5183
Polymers28,8262
Non-polymers6921
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-29 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.175, 73.175, 115.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein nuclear receptor subfamily 5, group A, member 1


Mass: 27513.010 Da / Num. of mol.: 1 / Fragment: ligand binding domain (Residues: 223-461)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P33242
#2: Protein/peptide Nuclear receptor subfamily 0, group B, member 2


Mass: 1312.534 Da / Num. of mol.: 1 / Fragment: SHP LXXLL / Source method: obtained synthetically
Details: peptide synthesis, the sequence of the peptide is naturally found in Rattus norvegicus (Norway rat)
References: UniProt: P97947
#3: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL / Phosphatidylethanolamine


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Oct 21, 2004
RadiationMonochromator: diamond crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 51068 / Num. obs: 51068 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 34.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: mLRH-1/SHP complex

Resolution: 1.5→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1729788.93 / 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
Rfree0.231 4116 8.1 %RANDOM
Rwork0.223 ---
obs0.223 50759 99.8 %-
all-50759 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.1241 Å2 / ksol: 0.498201 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-6 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 47 196 2218
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.34
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 690 8.3 %
Rwork0.274 7598 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PLD2.PARPLD.TOP

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