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(-) Description

Authors :  J. Min, H. Wu, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)
Date :  12 Oct 06  (Deposition) - 24 Oct 06  (Release) - 24 Feb 09  (Revision)
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A
Keywords :  Fbl, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  H. Wu, J. Min, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov
The Crystal Structure Of Human Fibrillarin In Complex With Sah
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

    EC Number2.1.1.-
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneFBL, FIB1, FLRN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
1AC1SOFTWAREPHE A:141 , THR A:209 , GLU A:304 , HOH A:4005 , HOH A:4006 , HOH A:4027BINDING SITE FOR RESIDUE CA A 317
3AC3SOFTWAREGLY A:168 , ALA A:170 , GLU A:192 , PHE A:193 , GLU A:216 , ASP A:217 , ALA A:218 , ARG A:219 , ASP A:237 , VAL A:238 , GLN A:240 , HOH A:4112 , HOH A:4216 , HOH A:4234BINDING SITE FOR RESIDUE MTA A 4001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IPX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
1FIBRILLARINPS00566 Fibrillarin signature.FBRL_HUMAN185-199  1A:186-200

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4ENST000002218014ENSE00000706151chr19:40330967-4033087395FBRL_HUMAN95-126321A:96-127 (gaps)32

(-) 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:220
 aligned with FBRL_HUMAN | P22087 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:229
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306         
               SCOP domains d2ipxa_ A: aut     omated matches                                                                                                                                                                                                     SCOP domains
               CATH domains -2ipxA01 A:89-     138 Phosphorylase Kin    ase; do2ipxA02 A:139-316 Vaccinia Virus protein VP39                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------FIBRILLARIN    -------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3 -------------------------------Exon 1.5  PDB: A:132-184 UniProt: 127-183 [INCOMPLETE]   Exon 1.6  PDB: A:185-229 UniProt: 184-228    -------------------------------------Exon 1.8  PDB: A:267-315 UniProt: 266-314        - Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.4  PDB: A:96-127 (gaps)  -----------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:229-266              ------------------------------------------------1. Transcript 1 (2)
                            |       97   |   107       117       127    |  137       147       157       167       177       187       197       207       217       227  |    237       247       257       267       277       287    |  297       307         
                            |          101   107                 127  132                                                                                           226-MSE                                                      287-MSE|                        
                           88-MSE                                                                                                                                       230-MSE                                                       292-MSE                    

   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/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FBRL_HUMAN | P22087)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0001094    TFIID-class transcription factor binding    Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
    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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    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:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    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:0048254    snoRNA localization    Any process in which small nucleolar RNA is transported to, or maintained in, a specific location.
    GO:0016074    snoRNA metabolic process    The chemical reactions and pathways involving snoRNA, small nucleolar RNA, any of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.
    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:0015030    Cajal body    A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.
    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:0001651    dense fibrillar component    A structure found in the nucleolus, which contains newly synthesized preribosomal RNA (pre-rRNA) and a collection of proteins.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0001652    granular component    A structure found in the nucleolus, which contains nearly completed preribosomal particles destined for the cytoplasm.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    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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