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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 25KDA SUBUNIT OF HUMAN CLEAVAGE FACTOR IM WITH AP4A
 
Authors :  M. Coseno, S. Doublie
Date :  28 Nov 07  (Deposition) - 19 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cpsf5, Rna Processing, Cleavage Factor, Diadenosine Tetraphosphate, Mrna Processing, Nucleus, Phosphoprotein, Rna-Binding, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Coseno, G. Martin, C. Berger, G. Gilmartin, W. Keller, S. Doublie
Crystal Structure Of The 25 Kda Subunit Of Human Cleavage Factor Im.
Nucleic Acids Res. V. 36 3474 2008
PubMed-ID: 18445629  |  Reference-DOI: 10.1093/NAR/GKN079
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 5
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidHIS6-MBP FUSION VECTOR
    Expression System StrainROSETTA (DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypeHIS6-MBP FUSION VECTOR
    GeneNUDT21, CFIM25, CPSF25, CPSF5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 25 KDA SUBUNIT, CPSF 25 KDA SUBUNIT, PRE-MRNA CLEAVAGE FACTOR IM 25 KDA SUBUNIT, NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 21, NUDIX MOTIF 21

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1B4P1Ligand/IonBIS(ADENOSINE)-5'-TETRAPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1B4P2Ligand/IonBIS(ADENOSINE)-5'-TETRAPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:63 , PHE A:103 , ARG A:150 , GLN A:157 , LYS A:172BINDING SITE FOR RESIDUE B4P A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BHO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BHO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BHO)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.CPSF5_HUMAN76-201  1A:76-201
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.CPSF5_HUMAN76-201  2A:76-201

(-) Exons   (7, 7)

Asymmetric Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003002911ENSE00001482691chr16:56485287-56484999289CPSF5_HUMAN1-39391A:20-3920
1.2ENST000003002912ENSE00001108683chr16:56481901-56481701201CPSF5_HUMAN39-106681A:39-10668
1.3ENST000003002913ENSE00001108681chr16:56480601-5648053864CPSF5_HUMAN106-127221A:106-12722
1.4ENST000003002914ENSE00001108678chr16:56473658-5647356990CPSF5_HUMAN128-157301A:128-157 (gaps)30
1.5ENST000003002915ENSE00001108686chr16:56468741-5646866676CPSF5_HUMAN158-183261A:158-18326
1.6ENST000003002916ENSE00001108677chr16:56468357-56468243115CPSF5_HUMAN183-221391A:183-22139
1.7ENST000003002917ENSE00001108679chr16:56466645-564630453601CPSF5_HUMAN221-22771A:221-2277

(-) Sequences/Alignments

Asymmetric 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:203
 aligned with CPSF5_HUMAN | O43809 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:208
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219        
          CPSF5_HUMAN    20 FGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeee.hhh.eeeeee........hhhhhhhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeee..eee..eee.....hhhhhhhhhhhhhhh.-----...eeeeeeeeeee...................eeeeeeeee....eeeeee...eeeeeehhhhh.hhhhhhhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------NUDIX  PDB: A:76-201 UniProt: 76-201                                                                                          -------------------------- PROSITE
           Transcript 1 (1) Exon 1.1            ------------------------------------------------------------------Exon 1.3              Exon 1.4  PDB: A:128-157 (gapsExon 1.5  PDB: A:158-183  -------------------------------------1.7     Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.2  PDB: A:39-106 UniProt: 39-106                             ----------------------------------------------------------------------------Exon 1.6  PDB: A:183-221               ------ Transcript 1 (2)
                 3bho A  20 FGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGR-----QDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
                                    29        39        49        59        69        79        89        99       109       119       129 |     139       149       159       169       179       189       199       209       219        
                                                                                                                                         131   137                                                                                          

   Legend:   → Mismatch (orange background)
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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 3BHO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BHO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BHO)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (CPSF5_HUMAN | O43809)
molecular function
    GO:0017091    AU-rich element binding    Interacting selectively and non-covalently with a region of RNA containing frequent adenine and uridine bases.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0031124    mRNA 3'-end processing    Any process involved in forming the mature 3' end of an mRNA molecule.
    GO:0006378    mRNA polyadenylation    The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
    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:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0006369    termination of RNA polymerase II transcription    The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
cellular component
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005849    mRNA cleavage factor complex    Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    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.
    GO:0042382    paraspeckles    Discrete subnuclear bodies in the interchromatin nucleoplasmic space, often located adjacent to nuclear specks. 10-20 paraspeckles are typically found in human cell nuclei.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CPSF5_HUMAN | O438092cl3 2j8q 3bap 3mdg 3mdi 3n9u 3p5t 3p6y 3q2s 3q2t

(-) Related Entries Specified in the PDB File

2cl3 CF IM 25KDA STRUCTURE
2j8q CF IM 25KDA STRUCTURE WITH SULFATE BOUND
3bap CF IM 25KDA STRUCTURE