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- PDB-2ff0: Solution Structure of Steroidogenic Factor 1 DNA Binding Domain B... -

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Basic information

Entry
Database: PDB / ID: 2ff0
TitleSolution Structure of Steroidogenic Factor 1 DNA Binding Domain Bound to its Target Sequence in the Inhibin alpha-subunit Promoter
Components
  • CTGTGGCCCTGAGCC
  • GGCTCAGGGCCACAG
  • Steroidogenic factor 1
KeywordsHormone/Growth factor/DNA / Nuclear Hormone Receptor / Protein-DNA complex / Monomeric Receptor-DNA complex / Hormone-Growth factor-DNA COMPLEX
Function / homology
Function and homology information


response to gonadotropin-releasing hormone / Sertoli cell differentiation / SUMOylation of intracellular receptors / negative regulation of female gonad development / Nuclear Receptor transcription pathway / sex determination / positive regulation of male gonad development / calcineurin-mediated signaling / luteinization / tissue development ...response to gonadotropin-releasing hormone / Sertoli cell differentiation / SUMOylation of intracellular receptors / negative regulation of female gonad development / Nuclear Receptor transcription pathway / sex determination / positive regulation of male gonad development / calcineurin-mediated signaling / luteinization / 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 regulator complex / nuclear receptor activity / male gonad development / double-stranded DNA binding / sequence-specific DNA binding / transcription by RNA polymerase II / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Nuclear hormone receptor family 5 / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Steroidogenic factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / Simulated annealing, cartesian molecular dynamics
AuthorsLittle, T.H. / Zhang, Y. / Matulis, C.K. / Weck, J. / Zhang, Z. / Ramachandran, A. / Mayo, K.E. / Radhakrishnan, I.
CitationJournal: Mol.Endocrinol. / Year: 2006
Title: Sequence-specific deoxyribonucleic Acid (DNA) recognition by steroidogenic factor 1: a helix at the carboxy terminus of the DNA binding domain is necessary for complex stability.
Authors: Little, T.H. / Zhang, Y. / Matulis, C.K. / Weck, J. / Zhang, Z. / Ramachandran, A. / Mayo, K.E. / Radhakrishnan, I.
History
DepositionDec 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX AUTHOR DETERMINED HELIX RECORDS BASED ON PROCHECK OUTPUT OF ENTIRE NMR ENSEMBLE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: GGCTCAGGGCCACAG
C: CTGTGGCCCTGAGCC
A: Steroidogenic factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2045
Polymers21,0733
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 200lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
RepresentativeModel #1best captures the intermolecular interactions observed in the ensemble

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Components

#1: DNA chain GGCTCAGGGCCACAG


Mass: 4620.000 Da / Num. of mol.: 1 / Fragment: Inhibin Alpha-Subunit Promoter / Source method: obtained synthetically
Details: The DNA sequence was synthesized via automated methods
#2: DNA chain CTGTGGCCCTGAGCC


Mass: 4561.947 Da / Num. of mol.: 1 / Fragment: Inhibin Alpha-Subunit Promoter / Source method: obtained synthetically
Details: The DNA sequence was synthesized via automated methods
#3: 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: 11890.955 Da / Num. of mol.: 1 / Fragment: DNA Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr5a1, Ftzf1 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33242
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D aliphatic 13C-separated NOESY
1323D aromatic 13C-separated NOESY
1422D 15N,13C-double-half-filtered NOESY
1532D 15N,13C-double-half-filtered NOESY
1623D 13C-filtered 13C-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N-steroidogenic factor 1 DBD:NA-duplex DNA complex90% H2O/10% D2O
2U-15N,U-13C-steroidogenic factor 1 DBD:NA-duplex DNA complex90% H2O/10% D2O
3U-15N,U-13C-steroidogenic factor 1 DBD:NA-duplex DNA complex100% D2O
Sample conditionsIonic strength: 20 mM Tris acetate, 50 uM ZnCl2, 2 mM DTT, 1% glycerol
pH: 6 / Pressure: ambient / Temperature: 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix98Accelrys Incprocessing
ARIA1.2Nilges et al.refinement
CNS1.1Brunger et al.refinement
VNMR6.1Varian Inccollection
RefinementMethod: Simulated annealing, cartesian molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: best captures the intermolecular interactions observed in the ensemble
NMR ensembleConformer selection criteria: lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
Conformers calculated total number: 200 / Conformers submitted total number: 16

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