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- PDB-1yow: human Steroidogenic Factor 1 LBD with bound Co-factor Peptide -

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Basic information

Entry
Database: PDB / ID: 1yow
Titlehuman Steroidogenic Factor 1 LBD with bound Co-factor Peptide
Components
  • Steroidogenic factor 1
  • TIF2 peptide
KeywordsTRANSCRIPTION / Steroidogenic factor 1 / SF1 / phospholipid / phosphatidyl ethanolamine / phosphatidyl glycerol
Function / homology
Function and homology information


primary sex determination / response to gonadotropin-releasing hormone / Sertoli cell differentiation / negative regulation of female gonad development / sex determination / regulation of steroid biosynthetic process / positive regulation of male gonad development / Transcriptional regulation of testis differentiation / luteinization / calcineurin-mediated signaling ...primary sex determination / response to gonadotropin-releasing hormone / Sertoli cell differentiation / negative regulation of female gonad development / sex determination / regulation of steroid biosynthetic process / positive regulation of male gonad development / Transcriptional regulation of testis differentiation / luteinization / calcineurin-mediated signaling / Transcriptional regulation of pluripotent stem cells / tissue development / Leydig cell differentiation / male sex determination / maintenance of protein location in nucleus / hormone metabolic process / adrenal gland development / female gonad development / hormone-mediated signaling pathway / transcription coregulator binding / phospholipid binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / sequence-specific double-stranded DNA binding / 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 / chromatin binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
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 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
PHOSPHATIDYL ETHANOL / Steroidogenic factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsKrylova, I.N. / Sablin, E.P. / Xu, R.X. / Waitt, G.M. / Juzumiene, D. / Williams, J.D. / Ingraham, H.A. / Willson, T.M. / Williams, S.P. / Montana, V. ...Krylova, I.N. / Sablin, E.P. / Xu, R.X. / Waitt, G.M. / Juzumiene, D. / Williams, J.D. / Ingraham, H.A. / Willson, T.M. / Williams, S.P. / Montana, V. / Madauss, K.P. / Moore, J. / Bynum, J.M. / Lebedeva, L. / MacKay, J.A. / Suzawa, M. / Guy, R.K. / Thornton, J.W.
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. / Xu, R.X. / Waitt, G.M. / MacKay, J.A. / Juzumiene, D. / Bynum, J.M. / Madauss, K.P. / Montana, V. / Lebedeva, L. / Suzawa, M. / Williams, J.D. / Williams, S.P. ...Authors: Krylova, I.N. / Sablin, E.P. / Xu, R.X. / Waitt, G.M. / MacKay, J.A. / Juzumiene, D. / Bynum, J.M. / Madauss, K.P. / 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 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
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_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

Downloads & links

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Assembly

Deposited unit
A: Steroidogenic factor 1
B: TIF2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5013
Polymers28,7842
Non-polymers7171
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-21 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.335, 73.335, 139.021
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 Steroidogenic factor 1 / / STF-1 / SF-1 / Adrenal 4 binding protein / Steroid hormone receptor Ad4BP / Fushi tarazu factor homolog 1


Mass: 27742.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A1, AD4BP, FTZF1, SF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 [DE3] / References: UniProt: Q13285
#2: Protein/peptide TIF2 peptide


Mass: 1041.264 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
#3: Chemical ChemComp-P0E / PHOSPHATIDYL ETHANOL / (2S)-2-[(9E)-HEXADEC-9-ENOYLOXY]-3-{[HYDROXY(2-HYDROXYETHOXY)PHOSPHORYL]OXY}PROPYL (9E)-OCTADEC-9-ENOATE


Mass: 716.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H73O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M NaCitrate pH5.6, 0.2M Li2SO4, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID11
SYNCHROTRONAPS 17-ID21.0, 0.979, 0.985
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2002 / Details: mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
30.9851
ReflectionResolution: 3→20 Å / Num. obs: 8888 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10 % / Biso Wilson estimate: 86.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 36
Reflection shellResolution: 3→3.1 Å / Redundancy: 10 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.8 / Num. unique all: 869 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNX library / Details: Simulated annealing followed by CG minimization
RfactorNum. reflection% reflectionSelection details
Rfree0.29 596 -Random
Rwork0.246 ---
all0.25 8898 --
obs0.25 8080 90.8 %-
Displacement parametersBiso mean: -0.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3----0.24 Å2
Refine analyzeLuzzati coordinate error obs: 0.302 Å / Luzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 46 96 1998
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.01
X-RAY DIFFRACTIONc_angle_deg1.34

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