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(-) Description

Authors :  W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  12 Dec 05  (Deposition) - 12 Jun 06  (Release) - 24 Feb 09  (Revision)
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structure Genomics, Zf-Ccch Domain, Target Of Egr1, Member 1(Nuclear), 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. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of The Zf-Ccch Domain Of Target Of Egr1, Member 1 (Nuclear)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TARGET OF EGR1, MEMBER 1
    Expression System PlasmidP050302-22
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FC6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FC6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FC6)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
1ZF_C3H1PS50103 Zinc finger C3H1-type profile.TOE1_HUMAN294-322  1A:17-44

(-) Exons   (2, 2)

NMR Structure (2, 2)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.7eENST000003720907eENSE00000905992chr1:45808515-45808674160TOE1_HUMAN251-304541A:1-27 (gaps)49
1.8bENST000003720908bENSE00001813606chr1:45808754-45809647894TOE1_HUMAN305-5102061A:28-50 (gaps)55

(-) 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:50
 aligned with TOE1_HUMAN | Q96GM8 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:104
                                   265       275       285       295       305       315       325       335       345       355    
               SCOP domains -----------------------------d2fc6a1 A:8-44                       -------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......----------------------.................hhhh......hhh........-------------------------------.-.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------ZF_C3H1  PDB: A:17-44        ------------------------------------- PROSITE
               Transcript 1 Exon 1.7e  PDB: A:1-27 (gaps) UniProt: 251-304   Exon 1.8b  PDB: A:28-50 (gaps) UniProt: 305-510         Transcript 1
                 2fc6 A   1 GSSGSSG----------------------CCLPPATHRPHPTSICDNFSAYGWCPLGPQCPQSHDIS-------------------------------G-PSSG  50
                                  |  -         -         8        18        28        38      |  -         -         -        |-|   
                                  7                      8                                   45                              46 |   

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  - → 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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FC6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FC6)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (TOE1_HUMAN | Q96GM8)
molecular function
    GO:0000175    3'-5'-exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
    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:0004535    poly(A)-specific ribonuclease activity    Catalysis of the exonucleolytic cleavage of poly(A) to 5'-AMP.
    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).
biological process
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
cellular component
    GO:0015030    Cajal body    A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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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