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(-) Description

Title :  CRYSTAL STRUCTURE OF RNA POLYMERASE I TRANSCRIPTION INITIATION FACTOR RRN3
 
Authors :  C. Blattner, S. Jennebach, F. Herzog, A. Mayer, A. C. M. Cheung, G. Witte K. Lorenzen, K-P. Hopfner, A. J. R. Heck, R. Aebersold, P. Cramer
Date :  23 Aug 11  (Deposition) - 28 Sep 11  (Release) - 19 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heat Repeat, Transcription Factor, Nucleus, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Blattner, S. Jennebach, F. Herzog, A. Mayer, A. C. Cheung, G. Witte, K. Lorenzen, K. P. Hopfner, A. J. Heck, R. Aebersold, P. Cramer
Molecular Basis Of Rrn3-Regulated Rna Polymerase I Initiation And Cell Growth.
Genes Dev. V. 25 2093 2011
PubMed-ID: 21940764  |  Reference-DOI: 10.1101/GAD.17363311

(-) Compounds

Molecule 1 - RNA POLYMERASE I-SPECIFIC TRANSCRIPTION INITIATION FACTOR RRN3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RRN3, YKL125W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3TJ1)

(-) Sites  (0, 0)

(no "Site" information available for 3TJ1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TJ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TJ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 3TJ1)

(-) 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:483
 aligned with RRN3_YEAST | P36070 from UniProtKB/Swiss-Prot  Length:627

    Alignment length:572
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615  
           RRN3_YEAST    46 VFSAAMYSRFVKSALDDLDKNDSTQIGIIANQVALPSKNPERINDKNLNILLDILSSNINRIESSRGTFLIQSIINFEKWWELPPHTLSKYIYFIKILCSSIPKWWQDVSMILVSCFILPIKQTVCHHDMLKYFLRMIPSSMGFIDTYLAKFFPNKNDTRRKLVNYTSNLLKLRGYCSELGFQIWSLLIEKIISIDVELQNELDELDDDVDDDDLEEVDLEDDDDLDDDSGDDDDENCGNSNEELRSGAADGSQSDSEDMDIIEGMDGTEEYNVELTQGIKELSTKLDSILTLVSTHVEEQVTPESLESGEGVGVFNTLTTLFKTHVLPTYYTRSIQYIMFHVSQQQLELMDSFLVTLIDISFAVNEAAEKKIKSLQYLGSYIARAKKLSRTQIIFVASYLTSWLNRYVIEREEEVDQRGGMERFKHFYAAFQALCYIFCFRHNIFRDTDGNWECELDKFFQRMVISKFNPLKFCNENVMLMFARIAQQESVAYCFSIIENNNNERLRGIIGKADSDKKENSAQANTTSSSWSLATRQQFIDLQSYFPYDPLFLKNYKILMKEYYIEWSEAS 617
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh---------------------------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..........hhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh--------------------...hhhhhhhhhhhhhh.......hhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tj1 A  46 VFSAAMYSRFVKSALDDLDKNDSTQIGIIANQVALPSKNPERINDKNLNILLDILSSNINRIESSRGTFLIQSIINFEKWWELPPHTLSKYIYFIKILCSSIPKWWQDVSMILVSCFILPIKQTVCHHDMLKYFLRMIPSSMGFIDTYLAKFFPNKNDTRRKLVNYTSNLLKLRGYCSELGFQIWSLLIEKIISIDVELQNELDELD---------------------------------------------------------------------TQGIKELSTKLDSILTLVSTHVEEQVTPESLESGEGVGVFNTLTTLFKTHVLPTYYTRSIQYIMFHVSQQQLELMDSFLVTLIDISFAVNEAAEKKIKSLQYLGSYIARAKKLSRTQIIFVASYLTSWLNRYVIEREEEVDQRGGMERFKHFYAAFQALCYIFCFRHNIFRDTDGNWECELDKFFQRMVISKFNPLKFCNENVMLMFARIAQQESVAYCFSIIENNNNERLRG--------------------SSWSLATRQQFIDLQSYFPYDPLFLKNYKILMKEYYIEWSEAS 617
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245      |  -         -         -         -         -         -         -      |325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545        |-         -       575       585       595       605       615  
                                                                                                                                                                                                                                        252                                                                   322                                                                                                                                                                                                                                     554                  575                                          


Chain B from PDB  Type:PROTEIN  Length:482
 aligned with RRN3_YEAST | P36070 from UniProtKB/Swiss-Prot  Length:627

    Alignment length:572
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615  
           RRN3_YEAST    46 VFSAAMYSRFVKSALDDLDKNDSTQIGIIANQVALPSKNPERINDKNLNILLDILSSNINRIESSRGTFLIQSIINFEKWWELPPHTLSKYIYFIKILCSSIPKWWQDVSMILVSCFILPIKQTVCHHDMLKYFLRMIPSSMGFIDTYLAKFFPNKNDTRRKLVNYTSNLLKLRGYCSELGFQIWSLLIEKIISIDVELQNELDELDDDVDDDDLEEVDLEDDDDLDDDSGDDDDENCGNSNEELRSGAADGSQSDSEDMDIIEGMDGTEEYNVELTQGIKELSTKLDSILTLVSTHVEEQVTPESLESGEGVGVFNTLTTLFKTHVLPTYYTRSIQYIMFHVSQQQLELMDSFLVTLIDISFAVNEAAEKKIKSLQYLGSYIARAKKLSRTQIIFVASYLTSWLNRYVIEREEEVDQRGGMERFKHFYAAFQALCYIFCFRHNIFRDTDGNWECELDKFFQRMVISKFNPLKFCNENVMLMFARIAQQESVAYCFSIIENNNNERLRGIIGKADSDKKENSAQANTTSSSWSLATRQQFIDLQSYFPYDPLFLKNYKILMKEYYIEWSEAS 617
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------------------------------------------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh---------------------...hhhhhhhhhhhhhh.......hhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tj1 B  46 VFSAAMYSRFVKSALDDLDKNDSTQIGIIANQVALPSKNPERINDKNLNILLDILSSNINRIESSRGTFLIQSIINFEKWWELPPHTLSKYIYFIKILCSSIPKWWQDVSMILVSCFILPIKQTVCHHDMLKYFLRMIPSSMGFIDTYLAKFFPNKNDTRRKLVNYTSNLLKLRGYCSELGFQIWSLLIEKIISIDVELQNELDELD---------------------------------------------------------------------TQGIKELSTKLDSILTLVSTHVEEQVTPESLESGEGVGVFNTLTTLFKTHVLPTYYTRSIQYIMFHVSQQQLELMDSFLVTLIDISFAVNEAAEKKIKSLQYLGSYIARAKKLSRTQIIFVASYLTSWLNRYVIEREEEVDQRGGMERFKHFYAAFQALCYIFCFRHNIFRDTDGNWECELDKFFQRMVISKFNPLKFCNENVMLMFARIAQQESVAYCFSIIENNNNERLR---------------------SSWSLATRQQFIDLQSYFPYDPLFLKNYKILMKEYYIEWSEAS 617
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245      |  -         -         -         -         -         -         -      |325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       | -         -       575       585       595       605       615  
                                                                                                                                                                                                                                        252                                                                   322                                                                                                                                                                                                                                    553                   575
   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 3TJ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TJ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TJ1)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RRN3_YEAST | P36070)
molecular function
    GO:0001042    RNA polymerase I core binding    Interacting selectively and non-covalently with RNA polymerase I core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of seventeen subunits.
    GO:0001179    RNA polymerase I transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase I transcription factor, any protein required to initiate or regulate transcription by RNA polymerase I.
    GO:0000182    rDNA binding    Interacting selectively and non-covalently with DNA sequences encoding ribosomal RNA.
    GO:0001082    transcription factor activity, RNA polymerase I transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase I transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
    GO:0001181    transcription factor activity, core RNA polymerase I binding    Interacting selectively and non-covalently with an RNA polymerase I (RNAP I) complex, typically composed of fourteen subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
    GO:0006356    regulation of transcription from RNA polymerase I promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase I promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0001180    transcription initiation from RNA polymerase I promoter for nuclear large rRNA transcript    Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an polymerase I promoter for the nuclear large ribosomal RNA (rRNA) transcript, resulting in the subsequent synthesis of rRNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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

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

UniProtKB/Swiss-Prot
        RRN3_YEAST | P36070: 5g5l 5n5y 5n5z 5n60 5n61

(-) Related Entries Specified in the PDB File

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