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(-) Description

Title :  THE RNA POLYMERASE II CTD IN MRNA PROCESSING: BETA-TURN RECOGNITION AND BETA-SPIRAL MODEL
 
Authors :  A. Meinhart, P. Cramer
Date :  05 Apr 04  (Deposition) - 13 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,Z
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B,Z  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Pcf11, Rna Polymerase Ii Ctd Interacting Domain, Arm Repeats, Phosphoserine, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Meinhart, P. Cramer
Recognition Of Rna Polymerase Ii Carboxy-Terminal Domain By 3'-Rna-Processing Factors.
Nature V. 430 223 2004
PubMed-ID: 15241417  |  Reference-DOI: 10.1038/NATURE02679
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PCF11 PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CTD INTERACTING DOMAIN OF PCF11
    Gene: PCF11, YDR228C, YD9934.13C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 2 - CTD-PEPTIDE
    Chains: Z
    Engineered: YES
    Fragment: CTD REPEAT DERIVED PEPTIDE
    Other Details: PEPTIDE DERIVED FROM THE CONSERVED REPEAT SEQUENCE IN RNA POLYMERASE II CTD.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCZ
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B Z
Biological Unit 3 (1x):   C 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SEP-1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SEP-1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (0, 0)

(no "Site" information available for 1SZA)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SZA)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:76 -Pro A:77
2Ser B:76 -Pro B:77
3Ser C:76 -Pro C:77

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SZA)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CIDPS51391 CID domain profile.PCF11_YEAST4-139
 
 		  3A:4-139
B:4-139
C:4-139
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CIDPS51391 CID domain profile.PCF11_YEAST4-139
 
 		  1A:4-139
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CIDPS51391 CID domain profile.PCF11_YEAST4-139
 
 		  1-
B:4-139
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CIDPS51391 CID domain profile.PCF11_YEAST4-139
 
 		  1-
-
C:4-139

(-) Exons   (1, 3)

Asymmetric Unit (1, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR228C1YDR228C.1IV:923803-9219231881PCF11_YEAST1-6266263A:1-144
B:4-143
C:2-141		144
140
140

(-) 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:144
 aligned with PCF11_YEAST | P39081 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    
          PCF11_YEAST     1 MDHDTEVIVKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLIKASALHQK 144
               SCOP domains d1szaa_ A: PCF11 protein                                                                                                                         SCOP domains
               CATH domains 1szaA00 A:1-144  [code=1.25.40.90, no name defined]                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---CID  PDB: A:4-139 UniProt: 4-139                                                                                                        ----- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-144 UniProt: 1-626 [INCOMPLETE]                                                                                               Transcript 1
                 1sza A   1 MDHDTEVIVKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLIKASAAALE 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with PCF11_YEAST | P39081 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
          PCF11_YEAST     4 DTEVIVKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLIKASALHQ 143
               SCOP domains d1szab_ B: PCF11 protein                                                                                                                     SCOP domains
               CATH domains 1szaB00 B:4-143  [code=1.25.40.90, no name defined]                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CID  PDB: B:4-139 UniProt: 4-139                                                                                                        ---- PROSITE
               Transcript 1 Exon 1.1  PDB: B:4-143 UniProt: 1-626 [INCOMPLETE]                                                                                           Transcript 1
                 1sza B   4 DTEVIVKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLIKASAAAL 143
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143


Chain C from PDB  Type:PROTEIN  Length:140
 aligned with PCF11_YEAST | P39081 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:140
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
          PCF11_YEAST     2 DHDTEVIVKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLIKASAL 141
               SCOP domains d1szac_ C: PCF11 protein                                                                                                                     SCOP domains
               CATH domains 1szaC00 C:2-141  [code=1.25.40.90, no name defined]                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --CID  PDB: C:4-139 UniProt: 4-139                                                                                                        -- PROSITE
               Transcript 1 Exon 1.1  PDB: C:2-141 UniProt: 1-626 [INCOMPLETE]                                                                                           Transcript 1
                 1sza C   2 DHDTEVIVKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFKLWLNPNDTGLPLFEGSALEKIEQFLIKASAA 141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141


Chain Z from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 1sza Z   1 PSYsPTSPS   9
                               |     
                               4-SEP
   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  (1, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1SZA)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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 2bf0 2nax 2npi 4c0b 4c0h 4oi4

(-) Related Entries Specified in the PDB File

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