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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RPR OF PCF11
 
Authors :  C. G. Noble, D. Hollingworth, S. R. Martin, V. E. Adeniran, S. J. Smerdon, G. Kelly, I. A. Taylor, A. Ramos
Date :  02 Dec 04  (Deposition) - 18 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  X
Keywords :  Transcription, Rna, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. G. Noble, D. Hollingworth, S. R. Martin, V. E. Adeniran, S. J. Smerdon, G. Kelly, I. A. Taylor, A. Ramos
Key Features Of The Interaction Between Pcf11 Cid And Rna Polymerase Ii Ctd.
Nat. Struct. Mol. Biol. V. 12 144 2005
PubMed-ID: 15665873  |  Reference-DOI: 10.1038/NSMB887

(-) Compounds

Molecule 1 - PCF11
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: CID, RESIDUES 1-138
    Organism Common: BAKERS YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU X:135 , ALA X:138BINDING SITE FOR RESIDUE CA X1139

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BF0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser X:76 -Pro X:77

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BF0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BF0)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR228C1YDR228C.1IV:923803-9219231881PCF11_YEAST1-6266261X:8-138131

(-) 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 X from PDB  Type:PROTEIN  Length:131
 aligned with PCF11_YEAST | P39081 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:131
                                    17        27        37        47        57        67        77        87        97       107       117       127       137 
          PCF11_YEAST     8 IVKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLIKA 138
               SCOP domains d2bf0x_ X: automated matches                                                                                                        SCOP domains
               CATH domains 2bf0X00 X:8-138  [code=1.25.40.90, no name defined]                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: X:8-138 UniProt: 1-626 [INCOMPLETE]                                                                                  Transcript 1
                 2bf0 X   8 IVKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCmPKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNTTRTKLINmFKLWLNPNDTGLPLFEGSALEKIEQFLIKA 138
                                    17        27        37        47        57        67        77        87        97       107|      117       127       137 
                                                                           56-MSE                                             108-MSE
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BF0)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (PCF11_YEAST | P39081)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000993    RNA polymerase II core binding    Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits.
    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).
biological process
    GO:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    GO:0006379    mRNA cleavage    Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
    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:0098789    pre-mRNA cleavage required for polyadenylation    The targeted, endonucleolytic cleavage of a pre-mRNA, required for polyadenylation of the 3' end. This cleavage is directed by binding sites near the 3' end of the mRNA and leaves a 3' hydoxyl end which then becomes a target for adenylation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005849    mRNA cleavage factor complex    Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
    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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  PCF11_YEAST | P39081
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 Related Entries

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

UniProtKB/Swiss-Prot
        PCF11_YEAST | P39081: 1sz9 1sza 2nax 2npi 4c0b 4c0h 4oi4

(-) Related Entries Specified in the PDB File

1sz9 THE RNA POLYMERASE II CTD IN MRNA PROCESSING: BETA-TURNRECOGNITION AND BETA- SPIRAL MODEL
1sza THE RNA POLYMERASE II CTD IN MRNA PROCESSING: BETA-TURNRECOGNITION AND BETA- SPIRAL MODEL