[English] 日本語
Yorodumi
- PDB-2ff0: Solution Structure of Steroidogenic Factor 1 DNA Binding Domain B... -

+
Open data


ID or keywords:

Loading...

-
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 / luteinization / tissue development / Leydig cell differentiation ...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 / luteinization / tissue development / Leydig cell differentiation / male sex determination / maintenance of protein location in nucleus / hormone metabolic process / adrenal gland development / female gonad development / calcineurin-mediated signaling / hormone-mediated signaling pathway / transcription coregulator binding / phospholipid binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / transcription by RNA polymerase II / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / 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 / Double treble clef zinc finger, C4 type / 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 / Double treble clef zinc finger, C4 type / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more