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(-) Description

Title :  SOLUTION STRUCTURE OF THE 3RD C2H2 ZINC FINGER OF HUMAN ZINC FINGER PROTEIN 406
 
Authors :  N. Tochio, M. Yoneyama, S. Koshiba, S. Watanabe, T. Harada, T. Umehara, A. Tanaka, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  27 Mar 07  (Deposition) - 01 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Zfat Zinc Finger 1, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Tochio, M. Yoneyama, S. Koshiba, S. Watanabe, T. Harada, T. Umehara, A. Tanaka, T. Kigawa, S. Yokoyama
Solution Structure Of The 3Rd C2H2 Zinc Finger Of Human Zinc Finger Protein 406
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN 406
    ChainsA
    EngineeredYES
    Expression System PlasmidP060718-01
    Expression System Vector TypePLASMID
    FragmentZF-C2H2
    GeneZFAT1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymZFAT ZINC FINGER 1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:12 , PRO A:13 , GLN A:14 , CYS A:15 , TYR A:17 , HIS A:28BINDING SITE FOR RESIDUE ZN A 181

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ELT)

(-) Exons   (0, 0)

(no "Exon" information available for 2ELT)

(-) 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:36
 aligned with ZFAT_HUMAN | Q9P243 from UniProtKB/Swiss-Prot  Length:1243

    Alignment length:99
                                   236       246       256       266       276       286       296       306       316         
           ZFAT_HUMAN   227 GATNSETTSADLVPRRGYQEYAIQQTPYEQPMKSSRLGPTQLKIFTCEYCNKVFKFKHSLQAHLRIHTNEKPYKCPQCSYASAIKANLNVHLRKHTGEK 325
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-------------.----------------..--.--------------------------------..ee......ee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 2elt A   1 GSS-------------G----------------SS--G--------------------------------KPYKCPQCSYASAIKANLNVHLRKHTGEK  36
                              |      -      |  -         -   ||  | -         -         -         -|       17        27         
                              3             4                5|  7                                8                            
                                                              6                                                                

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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (ZFAT_HUMAN | Q9P243)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0002244    hematopoietic progenitor cell differentiation    The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells.
    GO:0030097    hemopoiesis    The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
    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: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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0060712    spongiotrophoblast layer development    The process in which the spongiotrophoblast layer of the placenta progresses from its formation to its mature state.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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
        ZFAT_HUMAN | Q9P2432elm 2eln 2elo 2elp 2elq 2elr 2els 2elu 2elv 2rsh 2rsi 2rsj 2rut 2ruu 2ruv 2ruw 2rux 2ruy 2ruz 2rv0 2rv1 2rv2 2rv3 2rv6 2rv7

(-) Related Entries Specified in the PDB File

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