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(-) Description

Title :  SOLUTION STRUCTURE OF STEROIDOGENIC FACTOR 1 DNA BINDING DOMAIN BOUND TO ITS TARGET SEQUENCE IN THE INHIBIN ALPHA-SUBUNIT PROMOTER
 
Authors :  T. H. Little, Y. Zhang, C. K. Matulis, J. Weck, Z. Zhang, A. Ramachandran, K. E. Mayo, I. Radhakrishnan
Date :  17 Dec 05  (Deposition) - 11 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (16x)
Keywords :  Nuclear Hormone Receptor, Protein-Dna Complex, Monomeric Receptor-Dna Complex, Hormone/Growth Factor/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. H. Little, Y. Zhang, C. K. Matulis, J. Weck, Z. Zhang, A. Ramachandran, K. E. Mayo, I. Radhakrishnan
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.
Mol. Endocrinol. V. 20 831 2006
PubMed-ID: 16339274  |  Reference-DOI: 10.1210/ME.2005-0384
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STEROIDOGENIC FACTOR 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN
    Gene: NR5A1, FTZF1
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: 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
 
Molecule 2 - GGCTCAGGGCCACAG
    Chains: B
    Engineered: YES
    Fragment: INHIBIN ALPHA-SUBUNIT PROMOTER
    Other Details: THE DNA SEQUENCE WAS SYNTHESIZED VIA AUTOMATED METHODS
    Synthetic: YES
 
Molecule 3 - CTGTGGCCCTGAGCC
    Chains: C
    Engineered: YES
    Fragment: INHIBIN ALPHA-SUBUNIT PROMOTER
    Other Details: THE DNA SEQUENCE WAS SYNTHESIZED VIA AUTOMATED METHODS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (16x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:13 , CYS A:16 , CYS A:30 , CYS A:33BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWARECYS A:49 , SER A:52 , CYS A:55 , CYS A:65 , CYS A:68BINDING SITE FOR RESIDUE ZN A 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FF0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FF0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FF0)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUCLEAR_REC_DBD_2PS51030 Nuclear hormone receptors DNA-binding domain profile.STF1_MOUSE10-85  1A:10-85
2NUCLEAR_REC_DBD_1PS00031 Nuclear hormones receptors DNA-binding region signature.STF1_MOUSE13-39  1A:13-39

(-) Exons   (0, 0)

(no "Exon" information available for 2FF0)

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:102
 aligned with STF1_MOUSE | P33242 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:102
                                    19        29        39        49        59        69        79        89        99       109  
           STF1_MOUSE    10 DELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCPFCRFQKCLTVGMRLEAVRADRMRGGRNKFGPMYKRDRALKQQKKA 111
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2ff0A00 A:10-111 Erythroid Transcription Factor GATA-1, subunit A                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eee..eee.hhhhhhhhhhhh.......................hhhhhhhhhhh...hhh.............hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) NUCLEAR_REC_DBD_2  PDB: A:10-85 UniProt: 10-85                              -------------------------- PROSITE (1)
                PROSITE (2) ---NUCLEAR_REC_DBD_1          ------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2ff0 A  10 DELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCPFCRFQKCLTVGMRLEAVRADRMRGGRNKFGPMYKRDRALKQQKKA 111
                                    19        29        39        49        59        69        79        89        99       109  


Chain B from PDB  Type:DNA  Length:15
                                               
                 2ff0 B   1 GGCTCAGGGCCACAG  15
                                    10     


Chain C from PDB  Type:DNA  Length:15
                                               
                 2ff0 C  16 CTGTGGCCCTGAGCC  30
                                    25
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2FF0)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FF0)

(-) Gene Ontology  (38, 38)

NMR Structure(hide GO term definitions)
Chain A   (STF1_MOUSE | P33242)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    GO:0004879    RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding    Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003707    steroid hormone receptor activity    Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.
    GO:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030325    adrenal gland development    The process whose specific outcome is the progression of the adrenal gland over time, from its formation to the mature structure. This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0008585    female gonad development    The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure.
    GO:0042445    hormone metabolic process    The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone.
    GO:0009755    hormone-mediated signaling pathway    A series of molecular signals mediated by the detection of a hormone.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0001553    luteinization    The set of processes resulting in differentiation of theca and granulosa cells into luteal cells and in the formation of a corpus luteum after ovulation.
    GO:0051457    maintenance of protein location in nucleus    Any process in which a protein is maintained in the nucleus and prevented from moving elsewhere. These include sequestration within the nucleus, protein stabilization to prevent transport elsewhere and the active retrieval of proteins that escape the nucleus.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0010259    multicellular organism aging    An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700).
    GO:2000195    negative regulation of female gonad development    Any process that stops, prevents, or reduces the frequency, rate or extent of female gonad development.
    GO:2000020    positive regulation of male gonad development    Any process that activates or increases the frequency, rate or extent of male gonad development.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0022414    reproductive process    A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    GO:0009888    tissue development    The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0090575    RNA polymerase II transcription factor complex    A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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UniProtKB/Swiss-Prot
        STF1_MOUSE | P33242: 1ymt 1yp0 3f7d

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