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(-) Description

Title :  SOLUTION STRUCTURE OF CCCH TYPE ZINC-FINGER DOMAIN 2 IN CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR
 
Authors :  C. Abe, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  12 Dec 05  (Deposition) - 12 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ccch Zinc-Finger, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Abe, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of Ccch Type Zinc-Finger Domain 2 In Cleavage And Polyadenylation Specificity Factor
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 30 KDA SUBUNIT
    Chains: A
    Engineered: YES
    Expression System Plasmid: P050302-51
    Expression System Vector Type: PLASMID
    Fragment: CCCH-TYPE ZINC FINGER MOTIF
    Gene: CPSF4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: CPSF 30 KDA SUBUNIT, NS1 EFFECTOR DOMAIN-BINDING PROTEIN 1, NEB-1, NO ARCHES HOMOLOG

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

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:68 , CYS A:76 , CYS A:82 , HIS A:86BINDING SITE FOR RESIDUE ZN A 256
2AC2SOFTWARECYS A:96 , CYS A:105 , CYS A:110 , HIS A:114BINDING SITE FOR RESIDUE ZN A 456

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D9N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D9N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D9N)

(-) PROSITE Motifs  (1, 4)

NMR Structure (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_C3H1PS50103 Zinc finger C3H1-type profile.CPSF4_HUMAN62-89
35-59
90-117
143-169
118-142		  4A:62-89
-
A:90-117
A:128-130
A:118-126

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1dENST000002924761dENSE00001842942chr7:99036696-99036808113CPSF4_HUMAN1-35350--
1.4bENST000002924764bENSE00001631953chr7:99042412-9904246251CPSF4_HUMAN35-52181A:56-583
1.6ENST000002924766ENSE00001605972chr7:99045744-99045896153CPSF4_HUMAN52-103521A:58-103 (gaps)52
1.7aENST000002924767aENSE00001766366chr7:99047899-9904799496CPSF4_HUMAN103-135331A:103-12725
1.8aENST000002924768aENSE00002178878chr7:99048325-9904841894CPSF4_HUMAN135-166321A:128-1325
1.9aENST000002924769aENSE00001805918chr7:99049991-9905006373CPSF4_HUMAN166-190250--
1.11cENST0000029247611cENSE00001055437chr7:99051589-99051759171CPSF4_HUMAN191-247570--
1.12fENST0000029247612fENSE00001055438chr7:99054055-99054994940CPSF4_HUMAN248-269220--

(-) 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:77
 aligned with CPSF4_HUMAN | O95639 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:114
                                    59        69        79        89        99       109       119       129       139       149       159    
          CPSF4_HUMAN    50 GKGGMCPFRHISGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHIDPESKIKDCPWYDRGFCKHGPLCRHRHTRRVICVNYLVGFCPEGPSCK 163
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....------.......hhhhhh......................hhhhhhh.........................-------------------------------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ZF_C3H1   --ZF_C3H1  PDB: A:62-89       ZF_C3H1  PDB: A:90-117      ZF_C3H1  PDB: A:118-126  ZF_C3H1               PROSITE
           Transcript 1 (1) 1.4--------------------------------------------------Exon 1.7a  PDB: A:103-127        ---------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.6  PDB: A:58-103 (gaps) UniProt: 52-103      -------------------------------Exon 1.8a  PDB: A:128-132     Transcript 1 (2)
                 2d9n A  56 GSSGS------SGEKTVVCKHWLRGLCKKGDQCEFLHEYDMTKMPECYFYSKFGECSNKECPFLHIDPESKIKDCPWS-------------------------------GPSSG 132
                                |    - |      69        79        89        99       109       119       | -         -         -       128    
                               60     61                                                               127                             128
   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  (0, 0)

(no "SCOP Domain" information available for 2D9N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D9N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D9N)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (CPSF4_HUMAN | O95639)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0046778    modification by virus of host mRNA processing    Any viral process that interferes with the processing of mRNA in the host cell.
    GO:0006388    tRNA splicing, via endonucleolytic cleavage and ligation    Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005847    mRNA cleavage and polyadenylation specificity factor complex    A multisubunit complex that binds to the canonical AAUAAA hexamer and to U-rich upstream sequence elements on the pre-mRNA, thereby stimulating the otherwise weakly active and nonspecific polymerase to elongate efficiently RNAs containing a poly(A) signal.
    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

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UniProtKB/Swiss-Prot
        CPSF4_HUMAN | O95639: 2rhk

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