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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5 (CPSF5) IN COMPLEX WITH A SULPHATE ION.
 
Authors :  M. Moche, P. Stenmark, D. Ogg, C. Arrowsmith, H. Berglund, R. Busam, R. C A. Edwards, U. B. Ericsson, S. Flodin, A. Flores, S. Graslund, M. Hamma B. M. Hallberg, S. L. Holmberg, M. Hogbom, I. Johansson, T. Karlberg, U. Kosinska, T. Kotenyova, A. Magnusdottir, M. E. Nilsson, P. Nilsson T. Nyman, C. Persson, J. Sagemark, M. Sundstrom, J. Uppenberg, M. Upst A. G. Thorsell, S. Van Den Berg, K. Wallden, J. Weigelt, M. Welin, P. N
Date :  27 Oct 06  (Deposition) - 13 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nuclear Protein, Rna-Binding, Mrna Processing, Phosphorylation, 3'Mrna Cleavage And Polyadenylation Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Tresaugues, P. Stenmark, H. Schuler, S. Flodin, M. Welin, T. Nyman, M. Hammarstrom, M. Moche, S. Graslund, P. Nordlund
The Crystal Structure Of Human Cleavage And Polyadenylation Specific Factor-5 Reveals A Dimeric Nudix Protein With A Conserved Catalytic Site.
Proteins V. 73 1047 2008
PubMed-ID: 18767156  |  Reference-DOI: 10.1002/PROT.22198

(-) Compounds

Molecule 1 - CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 24-227
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CLEAVAGE 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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:63 , ARG A:150 , GLN A:157 , LYS A:172 , HOH A:2071BINDING SITE FOR RESIDUE SO4 A1228
2AC2SOFTWAREARG B:63 , ARG B:150 , GLN B:157 , LYS B:172BINDING SITE FOR RESIDUE SO4 B1228

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J8Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J8Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J8Q)

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (7, 14)

Asymmetric/Biological Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003002911ENSE00001482691chr16:56485287-56484999289CPSF5_HUMAN1-39392A:22-39
B:29-39		18
11
1.2ENST000003002912ENSE00001108683chr16:56481901-56481701201CPSF5_HUMAN39-106682A:39-106
B:39-106		68
68
1.3ENST000003002913ENSE00001108681chr16:56480601-5648053864CPSF5_HUMAN106-127222A:106-127
B:106-127		22
22
1.4ENST000003002914ENSE00001108678chr16:56473658-5647356990CPSF5_HUMAN128-157302A:128-157 (gaps)
B:128-157 (gaps)		30
30
1.5ENST000003002915ENSE00001108686chr16:56468741-5646866676CPSF5_HUMAN158-183262A:158-183
B:158-183		26
26
1.6ENST000003002916ENSE00001108677chr16:56468357-56468243115CPSF5_HUMAN183-221392A:183-221
B:183-221		39
39
1.7ENST000003002917ENSE00001108679chr16:56466645-564630453601CPSF5_HUMAN221-22772A:221-227
B:221-227		7
7

(-) Sequences/Alignments

Asymmetric/Biological 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:206
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221      
          CPSF5_HUMAN    22 NKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee.....eeeeee........hhhhhhhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeee...eee..........hhhhhhhhhhhhhhh...---..............................................eeeeee..eeeeeeehhhhh.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)
                 2j8q A  22 SMYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQD---QDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
                                    31        41        51        61        71        81        91       101       111       121       131 |   | 141       151       161       171       181       191       201       211       221      
                                                                                                                                         133 137                                                                                          


Chain B from PDB  Type:PROTEIN  Length:195
 aligned with CPSF5_HUMAN | O43809 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:199
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218         
          CPSF5_HUMAN    29 KPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....eeeeee........hhhhhhhhhhhhhhhh..eeeeeeeeeee....eeeeeee.....ee..........hhhhhhhhhhhhhhh...----.............................................eeeeee...eeeeeehhhhh.hhhhhhhhhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------NUDIX  PDB: B:76-201 UniProt: 76-201                                                                                          -------------------------- PROSITE
           Transcript 1 (1) Exon 1.1   ------------------------------------------------------------------Exon 1.3              Exon 1.4  PDB: B:128-157 (gapsExon 1.5  PDB: B:158-183  -------------------------------------1.7     Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2  PDB: B:39-106 UniProt: 39-106                             ----------------------------------------------------------------------------Exon 1.6  PDB: B:183-221               ------ Transcript 1 (2)
                 2j8q B  29 KPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQD----DWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
                                    38        48        58        68        78        88        98       108       118       128    |  138       148       158       168       178       188       198       208       218         
                                                                                                                                  133  138
   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  (0, 0)

(no "SCOP Domain" information available for 2J8Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J8Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J8Q)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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 | O43809: 2cl3 3bap 3bho 3mdg 3mdi 3n9u 3p5t 3p6y 3q2s 3q2t

(-) Related Entries Specified in the PDB File

2cl3 CRYSTAL STRUCTURE OF HUMAN CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5 (CPSF5)