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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DNA BINDING ETS DOMAIN OF HUMAN PROTEIN FEV
 
Authors :  C. K. Allerston, C. Cooper, M. Vollmar, T. Krojer, F. Von Delft, J. Weig C. H. Arrowsmith, C. Bountra, A. Edwards, O. Gileadi
Date :  31 Oct 12  (Deposition) - 16 Jan 13  (Release) - 10 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. D. O. Cooper, J. A. Newman, H. Aitkenhead, C. K. Allerston, O. Gileadi
Structures Of The Ets Domains Of Transcription Factors Etv1 Etv4, Etv5 And Fev: Determinants Of Dna Binding And Redox Regulation By Disulfide Bond Formation.
J. Biol. Chem. V. 290 13692 2015
PubMed-ID: 25866208  |  Reference-DOI: 10.1074/JBC.M115.646737

(-) Compounds

Molecule 1 - PROTEIN FEV
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    Expression System Vector TypePLASMID
    FragmentETS DOMAIN, RESIDUES 42-141
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFIFTH EWING VARIANT PROTEIN, PC12 ETS DOMAIN-CONTAINING TRANSCRIPTION FACTOR 1, PC12 ETS FACTOR 1, PET-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:121 , TYR A:122BINDING SITE FOR RESIDUE GOL A1138

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:43 -Ser A:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ETS_DOMAIN_3PS50061 Ets-domain profile.FEV_HUMAN47-127
 
  2A:47-127
B:47-127
2ETS_DOMAIN_1PS00345 Ets-domain signature 1.FEV_HUMAN49-57
 
  2A:49-57
B:49-57
3ETS_DOMAIN_2PS00346 Ets-domain signature 2.FEV_HUMAN93-108
 
  2A:93-108
B:93-108

(-) Exons   (0, 0)

(no "Exon" information available for 2YPR)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:96
 aligned with FEV_HUMAN | Q99581 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:96
                                    51        61        71        81        91       101       111       121       131      
            FEV_HUMAN    42 KGSGQIQLWQFLLELLADRANAGCIAWEGGHGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRYYYDKNIMSKVHGKRYAYRFDFQGLAQACQP 137
               SCOP domains d2ypra_ A: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh...ee.....eee..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eee......eeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----ETS_DOMAIN_3  PDB: A:47-127 UniProt: 47-127                                      ---------- PROSITE (1)
                PROSITE (2) -------ETS_DOMAI-----------------------------------ETS_DOMAIN_2    ----------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 2ypr A  42 KGSGQIQLWQFLLELLADRANAGCIAWEGGHGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRYYYDKNIMSKVHGKRYAYRFDFQGLAQACQP 137
                                    51        61        71        81        91       101       111       121       131      

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with FEV_HUMAN | Q99581 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:92
                                    55        65        75        85        95       105       115       125       135  
            FEV_HUMAN    46 QIQLWQFLLELLADRANAGCIAWEGGHGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRYYYDKNIMSKVHGKRYAYRFDFQGLAQACQP 137
               SCOP domains d2yprb_ B: automated matches                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...ee.....eee..hhhhhhhhhhhhh.....hhhhhhhhhhhh.....eee......eeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ETS_DOMAIN_3  PDB: B:47-127 UniProt: 47-127                                      ---------- PROSITE (1)
                PROSITE (2) ---ETS_DOMAI-----------------------------------ETS_DOMAIN_2    ----------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 2ypr B  46 QIQLWQFLLELLADRANAGCIAWEGGHGEFKLTDPDEVARRWGERKSKPNMNYDKLSRALRYYYDKNIMSKVHGKRYAYRFDFQGLAQACQP 137
                                    55        65        75        85        95       105       115       125       135  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YPR)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FEV_HUMAN | Q99581)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    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:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    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.
biological process
    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:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:1903507    negative regulation of nucleic acid-templated transcription    Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0048665    neuron fate specification    The process in which a cell becomes capable of differentiating autonomously into a neuron in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed.
    GO:0042551    neuron maturation    A developmental process, independent of morphogenetic (shape) change, that is required for a neuron to attain its fully functional state.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    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: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: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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FEV_HUMAN | Q995813zp5

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