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- PDB-1ymt: Mouse SF-1 LBD -

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Basic information

Entry
Database: PDB / ID: 1ymt
TitleMouse SF-1 LBD
Components
  • Nuclear receptor 0B2
  • Steroidogenic factor 1
KeywordsTRANSCRIPTION / nuclear receptor / SF-1 / ligand-binding domain / ligand / phosphatidyl glycerol / co-repressor peptide
Function / homology
Function and homology information


response to gonadotropin-releasing hormone / Sertoli cell differentiation / reproductive process / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / negative regulation of female gonad development / 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 / Nuclear Receptor transcription pathway / negative regulation of female gonad development / sex determination / positive regulation of male gonad development / luteinization / calcineurin-mediated signaling / 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 / phospholipid binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / negative regulation of DNA-binding transcription factor activity / positive regulation of insulin secretion / 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 / intracellular membrane-bounded organelle / 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
Chem-DR9 / 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: 1.2 Å
AuthorsKrylova, I.N. / Sablin, E.P. / Moore, J. / Xu, R.X. / Waitt, G.M. / Juzumiene, D. / Bynum, J.M. / Fletterick, R.J. / Willson, T.M. / Ingraham, H.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Structural analyses reveal phosphatidyl inositols as ligands for the NR5 orphan receptors SF-1 and LRH-1
Authors: Krylova, I.N. / Sablin, E.P. / Moore, J. / Xu, R.X. / Waitt, G.M. / MacKay, J.A. / Juzumiene, D. / Bynum, J.M. / Madauss, K. / Montana, V. / Lebedeva, L. / Suzawa, M. / Williams, J.D. / ...Authors: Krylova, I.N. / Sablin, E.P. / Moore, J. / Xu, R.X. / Waitt, G.M. / MacKay, J.A. / Juzumiene, D. / Bynum, J.M. / Madauss, K. / Montana, V. / Lebedeva, L. / Suzawa, M. / Williams, J.D. / Williams, S.P. / Guy, R.K. / Thornton, J.W. / Fletterick, R.J. / Willson, T.M. / Ingraham, H.A.
History
DepositionJan 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 23, 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: Steroidogenic factor 1
B: Nuclear receptor 0B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3253
Polymers29,5782
Non-polymers7471
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-27 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.853, 73.853, 117.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-946-

HOH

DetailsPolypeptide monomer (chain A) bound to phospholipid (chain C) represents biological assembly

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Components

#1: Protein Steroidogenic factor 1 / / STF-1 / SF-1 / Adrenal 4 binding protein / Steroid hormone receptor Ad4BP / Fushi tarazu factor ...STF-1 / SF-1 / Adrenal 4 binding protein / Steroid hormone receptor Ad4BP / Fushi tarazu factor homolog 1 / Embryonal LTR binding protein / ELP / Embryonal long terminal repeat- binding protein / Steroid hydroxylase positive regulator


Mass: 27992.281 Da / Num. of mol.: 1 / Fragment: mSF-1 LBD (residues 219-462) / Mutation: C302S, C408S, C413S, C423S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr5a1, Ftzf1 / Production host: Escherichia coli (E. coli) / References: UniProt: P33242
#2: Protein/peptide Nuclear receptor 0B2 / Orphan nuclear receptor SHP / Small heterodimer partner


Mass: 1585.889 Da / Num. of mol.: 1 / Fragment: mSHP peptide (residues 17-30) / Source method: obtained synthetically / Details: mSHP peptide, RPTILYALLSPSPR (a.a. 17-30) / References: UniProt: Q62227
#3: Chemical ChemComp-DR9 / 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL / (2R)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(9E)-HEXADEC-9-ENOYLOXY]PROPYL (9E)-OCTADEC-9-ENOATE


Mass: 746.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H75O10P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.7 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8 mg/ml mSF-1, 6X molar excess of mSHP peptide, 0.1 M Tris, 14% PEG 8000, 5% isopropanol, 15% xylitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03326 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03326 Å / Relative weight: 1
ReflectionResolution: 1.2→25 Å / Num. all: 101414 / Num. obs: 95280 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 38
Reflection shellResolution: 1.2→1.32 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PK5 (mLRH-1 LBD)

1pk5


Resolution: 1.2→24.09 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 339886.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4822 5.1 %RANDOM
Rwork0.197 ---
all0.203 101414 --
obs0.197 95280 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.4456 Å2 / ksol: 0.360209 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.7 Å20 Å2
3----1.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.2→24.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 51 467 2751
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d2.39
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.972
X-RAY DIFFRACTIONc_scangle_it4.062.5
LS refinement shellResolution: 1.2→1.32 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.307 1122 5.3 %
Rwork0.311 20170 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3C16_1_C18_1.PARC16_1_C18_1.TOP

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