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(-) Description

Title :  SOLUTION STRUCTURE OF THE 4TH ZINC FINGER DOMAIN OF ZINC FINGER PROTEIN 278
 
Authors :  W. Tanabe, S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  C2H2, Zinc Finger Domain, 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 :  W. Tanabe, S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The 4Th Zinc Finger Domain Of Zinc Finger Protein 278
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POZ-, AT HOOK-, AND ZINC FINGER-CONTAINING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression System PlasmidP061204-08
    Expression System Vector TypePLASMID
    FragmentZINC FINGER DOMAIN, UNP RESIDUES 408-448
    GenePATZ1, PATZ, RIAZ, ZBTB19, ZNF278, ZSG
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymZINC FINGER PROTEIN 278, ZINC FINGER SARCOMA GENE PROTEIN, BTB-POZ DOMAIN ZINC FINGER TRANSCRIPTION FACTOR, PROTEIN KINASE A RI-SUBUNIT ALPHA- ASSOCIATED PROTEIN, ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 19

 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  (0, 0)

(no "Site" information available for 2EPS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

NMR Structure (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.PATZ1_HUMAN294-314
357-377
385-405
415-436
444-464
497-518
607-628
  3-
-
-
A:415-436
A:444-445
A:454-454
-

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002662691aENSE00001361762chr22:31742218-317403181901PATZ1_HUMAN1-4244241A:401-424 (gaps)49
1.2cENST000002662692cENSE00000911167chr22:31738946-3173888364PATZ1_HUMAN424-445221A:424-44522
1.4aENST000002662694aENSE00000653152chr22:31731849-31731678172PATZ1_HUMAN446-503581A:446-454 (gaps)58
1.5aENST000002662695aENSE00001361736chr22:31724910-31724773138PATZ1_HUMAN503-549471A:454-4541
1.6bENST000002662696bENSE00001742345chr22:31723295-317217901506PATZ1_HUMAN549-6871390--

(-) 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:54
 aligned with PATZ1_HUMAN | Q9HBE1 from UniProtKB/Swiss-Prot  Length:687

    Alignment length:128
                                   385       395       405       415       425       435       445       455       465       475       485       495        
          PATZ1_HUMAN   376 SHSGEKPYSCPVCGLRFKRKDRMSYHVRSHDGSVGKPYICQSCGKGFSRPDHLNGHIKQVHTSERPHKCQTCNASFATRDRLRSHLACHEDKVPCQVCGKYLRAAYMADHLKKHSEGPSNFCSICNRG 503
               SCOP domains --------------------------------d2epsa1 A:408-446 PATZ1                --------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-------------------------.......ee......ee.hhhhhhhhhhhh..............------------------------------------------...-------.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZI-------ZINC_FINGER_C2H2_1   ---------ZINC_FINGER_C2H2_1    -------ZINC_FINGER_C2H2_1   --------------------------------ZINC_FI PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:401-424 (gaps) UniProt: 1-424  ---------------------Exon 1.4a  PDB: A:446-454 (gaps) UniProt: 446-503          Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.2c             ---------------------------------------------------------1 Transcript 1 (2)
                 2eps A 401 GSSGS-------------------------SGSVGKPYICQSCGKGFSRPDHLNGHIKQVHTSERPHKCQVWVS------------------------------------------GPS-------SG 454
                                |    -         -         -|      415       425       435       445   |     -         -         -         -      | |-      | 
                              405                       406                                        449                                        450 |     453 
                                                                                                                                                452         

   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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (PATZ1_HUMAN | Q9HBE1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA 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.
    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: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: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:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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:0010468    regulation of gene expression    Any process that modulates 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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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
        PATZ1_HUMAN | Q9HBE12epp 2epq 2epr 2yt9

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