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(-) Description

Title :  STRUCTURE OF RCL1P - BMS1P COMPLEX
 
Authors :  S. Fribourg
Date :  15 Jan 14  (Deposition) - 26 Nov 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Delprato, Y. Al Kadri, N. Perebaskine, C. Monfoulet, Y. Henry, A. K. Henras, S. Fribourg
Crucial Role Of The Rcl1P-Bms1P Interaction For Yeast Pre- Ribosomal Rna Processing.
Nucleic Acids Res. V. 42 10161 2014
PubMed-ID: 25064857  |  Reference-DOI: 10.1093/NAR/GKU682

(-) Compounds

Molecule 1 - RNA 3'-TERMINAL PHOSPHATE CYCLASE-LIKE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-15B
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: RCL1P
 
Molecule 2 - RIBOSOME BIOGENESIS PROTEIN BMS1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-15B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 547-636
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: BMS1P

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4CLQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CLQ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:159 -Pro A:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CLQ)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RTCPS01287 RNA 3'-terminal phosphate cyclase signature.RCL1_YEAST156-166  1A:156-166

(-) Exons   (0, 0)

(no "Exon" information available for 4CLQ)

(-) 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:355
 aligned with RCL1_YEAST | Q08096 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:355
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356     
           RCL1_YEAST     7 KYTTFQGSQNFRLRIVLATLSGKPIKIEKIRSGDLNPGLKDYEVSFLRLIESVTNGSVIEISYTGTTVIYRPGIIVGGASTHICPSSKPVGYFVEPMLYLAPFSKKKFSILFKGITASHNDAGIEAIKWGLMPVMEKFGVRECALHTLKRGSPPLGGGEVHLVVDSLIAQPITMHEIDRPIISSITGVAYSTRVSPSLVNRMIDGAKKVLKNLQCEVNITADVWRGENSGKSPGWGITLVAQSKQKGWSYFAEDIGDAGSIPEELGEKVACQLLEEISKSAAVGRNQLPLAIVYMVIGKEDIGRLRINKEQIDERFIILLRDIKKIFNTEVFLKPVDEADNEDMIATIKGIGFTN 361
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhee..eeee......eeee..ee..eeeeee.....hhhhhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhhhhh.....eeeeee........eeeeeee..........ee.......eeeeeeeee...hhhhhhhhhhhhhhhh....eeeeeeeee.hhhhh...eeeeeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhh...eeee........eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------RTC        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4clq A   7 KYTTFQGSQNFRLRIVLATLSGKPIKIEKIRSGDLNPGLKDYEVSFLRLIESVTNGSVIEISYTGTTVIYRPGIIVGGASTHICPSSKPVGYFVEPmLYLAPFSKKKFSILFKGITASHNDAGIEAIKWGLmPVmEKFGVRECALHTLKRGSPPLGGGEVHLVVDSLIAQPITmHEIDRPIISSITGVAYSTRVSPSLVNRmIDGAKKVLKNLQCEVNITADVWRGENSGKSPGWGITLVAQSKQKGWSYFAEDIGDAGSIPEELGEKVACQLLEEISKSAAVGRNQLPLAIVYmVIGKEDIGRLRINKEQIDERFIILLRDIKKIFNTEVFLKPVDEADNEDmIATIKGIGFTN 361
                                    16        26        36        46        56        66        76        86        96      |106       116       126       136 |  |  146       156       166       176   |   186       196       206 |     216       226       236       246       256       266       276       286       296    |  306       316       326       336       346   |   356     
                                                                                                                          103-MSE                            138-MSE                                   180-MSE                     208-MSE                                                                                      301-MSE                                          350-MSE       
                                                                                                                                                                141-MSE                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:54
 aligned with BMS1_YEAST | Q08965 from UniProtKB/Swiss-Prot  Length:1183

    Alignment length:90
                                   556       566       576       586       596       606       616       626       636
           BMS1_YEAST   547 WNIGKLIYMDNISPEECIRRWRGEDDDSKDESDIEEDVDDDFFRKKDGTVTKEGNKDHAVDLEKFVPYFDTFEKLAKKWKSVDAIKERFL 636
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh....hhhhhhhhhh.------------------------------------...........hhhhhhhhh..hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4clq B  24 WNIGKLIYMDNISPEECIRRWRG------------------------------------VDLEKFVPYFDTFEKLAKKWKSVDAIKERFL 113
                                    33        43  |      -         -         -        83        93       103       113
                                                 46                                   83
   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 4CLQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CLQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CLQ)

(-) Gene Ontology  (24, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RCL1_YEAST | Q08096)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003963    RNA-3'-phosphate cyclase activity    Catalysis of the reaction: ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0000480    endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)    Endonucleolytic cleavage within the 5'-External Transcribed Spacer (ETS) of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript. Endonucleolytic cleavage within the 5'-ETS of the pre-RNA is conserved as one of the early steps of rRNA processing in all eukaryotes, but the specific position of cleavage is variable.
    GO:0000447    endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)    Endonucleolytic cleavage between the SSU-rRNA and the 5.8S rRNA of an rRNA molecule originally produced as a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript.
    GO:0000472    endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)    Endonucleolytic cleavage between the 5'-External Transcribed Spacer (5'-ETS) and the 5' end of the SSU-rRNA of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
    GO:0030686    90S preribosome    A large ribonucleoprotein complex considered to be the earliest preribosomal complex. In S. cerevisiae, it has a size of 90S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins.
    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: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.

Chain B   (BMS1_YEAST | Q08965)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0034511    U3 snoRNA binding    Interacting selectively and non-covalently with U3 small nucleolar RNA.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0000480    endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)    Endonucleolytic cleavage within the 5'-External Transcribed Spacer (ETS) of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript. Endonucleolytic cleavage within the 5'-ETS of the pre-RNA is conserved as one of the early steps of rRNA processing in all eukaryotes, but the specific position of cleavage is variable.
    GO:0000472    endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)    Endonucleolytic cleavage between the 5'-External Transcribed Spacer (5'-ETS) and the 5' end of the SSU-rRNA of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA.
    GO:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
    GO:0030686    90S preribosome    A large ribonucleoprotein complex considered to be the earliest preribosomal complex. In S. cerevisiae, it has a size of 90S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BMS1_YEAST | Q08965: 5jpq 5tzs 5wyj 5wyk
        RCL1_YEAST | Q08096: 5jpq 5tzs 5wyj 5wyk

(-) Related Entries Specified in the PDB File

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