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(-) Description

Title :  CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS NOP5 (1-262) AND FIBRILLARIN COMPLEX
 
Authors :  K. Ye
Date :  20 Jul 09  (Deposition) - 25 Aug 09  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
Keywords :  C/D Guide Rna, 2'-O-Methylation, Coiled-Coil, Methyltransferase, Rna- Binding, Rrna Processing, Transferase, Trna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ye, R. Jia, J. Lin, M. Ju, J. Peng, A. Xu, L. Zhang
Structural Organization Of Box C/D Rna-Guided Rna Methyltransferase.
Proc. Natl. Acad. Sci. Usa V. 106 13808 2009
PubMed-ID: 19666563  |  Reference-DOI: 10.1073/PNAS.0905128106

(-) Compounds

Molecule 1 - PRE MRNA SPLICING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)/RIL+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NTD AND COILED-COIL DOMAIN (RESIDUES 1-262)
    Gene: SSO0939
    Mutation: YES
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: NOP5
 
Molecule 2 - FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE
    Chains: C
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)/RIL+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FLPA, SSO0940, C33_014
    Mutation: YES
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: FIBRILLARIN, FIB

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (2x): AC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR C:82 , GLY C:84 , ALA C:85 , ALA C:86 , THR C:90 , GLU C:108 , PHE C:109 , SER C:110 , ASP C:133 , ALA C:134 , ASP C:153 , ILE C:154 , GLN C:156BINDING SITE FOR RESIDUE SAM C 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ID6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp C:217 -Pro C:218

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ID6)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRILLARINPS00566 Fibrillarin signature.FLPA_SULSO102-116  1C:102-116
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRILLARINPS00566 Fibrillarin signature.FLPA_SULSO102-116  2C:102-116

(-) Exons   (0, 0)

(no "Exon" information available for 3ID6)

(-) 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:258
 aligned with Q97ZH3_SULSO | Q97ZH3 from UniProtKB/TrEMBL  Length:412

    Alignment length:258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251        
         Q97ZH3_SULSO     2 MKIYLIEHVIGAVAYDENGNIVDYITNPRDLGKITEELLNNEKGIPFSATVELLKKVNPQEVVVENEAEVPKLQALGYRVSYEPYSKVSRIFRESLPKVAIDIKFASNEEDYYNFLHELSLEYTRRKLRSAAQKRDLLAIQAVRAMDDIDKTINLFSERLREWYSIHFPELDKLIEDHEEYATIVSRFGDRGFLTIDSLKELGFNEQRINRILDAAKKSIGADISEDDLSAMRMIANTILDLYNIRRNLNNYLEGVMK 259
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..eeeee.....eeeeee...hhhhhhhhhhhhhhh..hhhhhhhhhhh...eeee...hhhhhhh....eeee...hhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3id6 A   2 VKIYLIEHVIGAVAYDENGNIVDYITNPRDLGKITEELLNNEKGIPFSATVELLKKVNPQEVVVENEAEVPKLQALGYRVSYEPYSKVSRIFRESLPKVAIDIKFASNEEDYYNFLHELSLEYTRRKLRSAAQKRDLLAIQAVRAMDDIDKTINLFSERLREWYSIHFPELDKLIEDHEEYATIVSRFGDRGFLTIDSLKELGFNEQRINRILDAAKKSIGADISEDDLSAMRMIANTILDLYNIRRNLNNYLEGVMK 259
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251        


Chain C from PDB  Type:PROTEIN  Length:220
 aligned with FLPA_SULSO | P58032 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:227
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       
           FLPA_SULSO     5 ITVKQTNMENIYECEFNDGSFRLCTRNLVPNFNVYGERLIKYEGVEYREWNAFRSKLAGAILKGLKTNPIRKGTKVLYLGAASGTTISHVSDIIELNGKAYGVEFSPRVVRELLLVAQRRPNIFPLLADARFPQSYKSVVENVDVLYVDIAQPDQTDIAIYNAKFFLKVNGDMLLVIKARSIDVTKDPKEIYKTEVEKLENSNFETIQIINLDPYDKDHAIVLSKYK 231
               SCOP domains d3id6c_ C: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains 3id6C01 C:5-54 Phosphorylase Kinase; domain 1     3id6C02 C:55-231 Vaccinia Virus protein VP39                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee.....eeeeee............eeee..eeeee.....hhhhhhhhh...........eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh..eeeee....hhhhh......eeeeee.....hhhhhhhhhhhhheeeeeeeeeee.-------.......hhhhhhhhhh.eeeeeeee........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------FIBRILLARIN    ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3id6 C   5 ITVKQTNMENIYECEFNDGSFRLCTRNLVPNFNVYGERLIKYEGVEYREWNAFRSKLAGAILKGLKTNPIRKGTKVLYLGAASGTTISHVSDIIELNGKAYGVEFSPRVVRELLLVAQRRPNIFPLLADARFPQSYKSVVENVDVLYVDIAQPDQTDIAIYNAKFFLKVNGDMLLVIK-------KDPKEIYKTEVEKLENSNFETIQIINLDPYDKDHAIVLSKYK 231
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       | -     | 194       204       214       224       
                                                                                                                                                                                                           182     190
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ID6)

(-) Gene Ontology  (16, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q97ZH3_SULSO | Q97ZH3)
molecular function
    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:0030515    snoRNA binding    Interacting selectively and non-covalently with small nucleolar RNA.
biological process
    GO:0000154    rRNA modification    The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.
cellular component
    GO:0031428    box C/D snoRNP complex    A ribonucleoprotein complex containing small nucleolar RNA of the box C/D type that can carry out ribose-2'-O-methylation of target RNAs.
    GO:0032040    small-subunit processome    A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S 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.

Chain C   (FLPA_SULSO | P58032)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:1990259    histone-glutamine methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-glutamine = S-adenosyl-L-homocysteine + (histone)-N5-methyl-glutamine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0008649    rRNA methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0000494    box C/D snoRNA 3'-end processing    Any process involved in forming the mature 3' end of a box C/D snoRNA molecule.
    GO:1990258    histone glutamine methylation    The modification of a histone by addition of a methyl group to an glutamine residue.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0031428    box C/D snoRNP complex    A ribonucleoprotein complex containing small nucleolar RNA of the box C/D type that can carry out ribose-2'-O-methylation of target RNAs.
    GO:0032040    small-subunit processome    A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S 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.

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  Q97ZH3_SULSO | Q97ZH3
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 Related Entries

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

UniProtKB/Swiss-Prot
        FLPA_SULSO | P58032: 3id5 3pla 5jpq
UniProtKB/TrEMBL
        Q97ZH3_SULSO | Q97ZH3: 3icx 3id5 3pla 5gin 5gio 5gip 5jpq

(-) Related Entries Specified in the PDB File

3id5