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(-) Description

Title :  CRYSTAL STRUCTURE OF A CBF5-NOP10-GAR1 COMPLEX FROM SACCHAROMYCES CEREVISIAE
 
Authors :  K. Ye, S. Li
Date :  02 Oct 11  (Deposition) - 14 Dec 11  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Pseudouridine Synthase, Pseudouridylation, H/Aca Rna, Nucleolus, Isomerase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Li, J. Duan, D. Li, B. Yang, M. Dong, K. Ye
Reconstitution And Structural Analysis Of The Yeast Box H/Aca Rna-Guided Pseudouridine Synthase
Genes Dev. V. 25 2409 2011
PubMed-ID: 22085967  |  Reference-DOI: 10.1101/GAD.175299.111

(-) Compounds

Molecule 1 - H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT 4
    Chains: A
    EC Number: 5.4.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 3-394
    Gene: CBF5
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: CENTROMERE-BINDING FACTOR 5, CENTROMERE/MICROTUBULE-BINDING PROTEIN CBF5, H/ACA SNORNP PROTEIN CBF5, SMALL NUCLEOLAR RNP PROTEIN CBF5, P64'
 
Molecule 2 - H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT 3
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET-1
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NOP10
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: NUCLEOLAR PROTEIN 10, NUCLEOLAR PROTEIN FAMILY A MEMBER 3, SNORNP PROTEIN NOP10
 
Molecule 3 - H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT 1
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 32-124
    Gene: GAR1
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: SNORNP PROTEIN GAR1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3U28)

(-) Sites  (0, 0)

(no "Site" information available for 3U28)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U28)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U28)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U28)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.CBF5_YEAST266-341  1A:266-341

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YHR072W-A1YHR072W-A.1VIII:241666-241842177NOP10_YEAST1-58581B:1-4848

(-) 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:335
 aligned with CBF5_YEAST | P33322 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:346
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344      
           CBF5_YEAST     5 DFVIKPEAAGASTDTSEWPLLLKNFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSGVINLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQGAGKEYVCIVRLHDALKDEKDLGRSLENLTGALFQRPPLISAVKRQLRVRTIYESNLIEFDNKRNLGVFWASCEAGTYMRTLCVHLGMLLGVGGHMQELRRVRSGALSENDNMVTLHDVMDAQWVYDNTRDESYLRSIIQPLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGVVASVKRCIMERDLYPRRW 350
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......------.....hhhhhhhhhhee............hhhhhhhhhhhhheeeeeee....hhhhhhhhhhhhhh...eee........eeeeeeee.hhhhhhhhhhhh.eeeeeeeee.......hhhhhhhhhh.eeeee...-----....eeeeeeeeeeeeee....eeeeeeee....hhhhhhhhhhhhhh..eeeeeeeeeee..ee......hhhhhhhhhhhhhhhh.hhhhhhhhee.hhhhh...eeee...hhhhhhhhheee...eeee........eeeee.....eeeeeee..hhhhhhhh...eeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: A:266-341 UniProt: 266-341                                        --------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u28 A   5 DFVIKPE------DTSEWPLLLKNFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSGVINLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQGAGKEYVCIVRLHDALKDEKDLGRSLENLTGALFQRPP-----KRQLRVRTIYESNLIEFDNKRNLGVFWASCEAGTYMRTLCVHLGMLLGVGGHMQELRRVRSGALSENDNMVTLHDVMDAQWVYDNTRDESYLRSIIQPLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGVVASVKRCIMERDLYPRRW 350
                                  |  -   |    24        34        44        54        64        74        84        94       104       114       124       134       144       154|     |164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344      
                                 11     18                                                                                                                                      155   161                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:48
 aligned with NOP10_YEAST | Q6Q547 from UniProtKB/Swiss-Prot  Length:58

    Alignment length:48
                                    10        20        30        40        
          NOP10_YEAST     1 MHLMYTLGPDGKRIYTLKKVTESGEITKSAHPARFSPDDKYSRQRVTL  48
               SCOP domains d3u28b_ B:                                       SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.....eeee...........ee...........hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-48 UniProt: 1-58 [INCOMPLETE] Transcript 1
                 3u28 B   1 MHLMYTLGPDGKRIYTLKKVTESGEITKSAHPARFSPDDKYSRQRVTL  48
                                    10        20        30        40        


Chain C from PDB  Type:PROTEIN  Length:92
 aligned with GAR1_YEAST | P28007 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:92
                                    42        52        62        72        82        92       102       112       122  
           GAR1_YEAST    33 PPDTVLEMGAFLHPCEGDIVCRSINTKIPYFNAPIYLENKTQVGKVDEILGPLNEVFFTIKCGDGVQATSFKEGDKFYIAADKLLPIERFLP 124
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee..eeeeee....ee....eee.....eeeeeeeee......eeeeee....hhhhh....eeeee...eehhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 3u28 C  33 PPDTVLEMGAFLHPCEGDIVCRSINTKIPYFNAPIYLENKTQVGKVDEILGPLNEVFFTIKCGDGVQATSFKEGDKFYIAADKLLPIERFLP 124
                                    42        52        62        72        82        92       102       112       122
   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
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U28)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U28)

(-) Gene Ontology  (30, 51)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBF5_YEAST | P33322)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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:0009982    pseudouridine synthase activity    Catalysis of the reaction: RNA uridine = RNA pseudouridine. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
biological process
    GO:0009451    RNA modification    The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
    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:0000495    box H/ACA snoRNA 3'-end processing    Any process involved in forming the mature 3' end of a box H/ACA snoRNA molecule.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:1990481    mRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in an mRNA molecule.
    GO:0001522    pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
    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.
    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:0031118    rRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine 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.
    GO:0031120    snRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in an snRNA molecule.
cellular component
    GO:0031429    box H/ACA snoRNP complex    A box H/ACA RNP complex that is located in the nucleolus.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    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.

Chain B   (NOP10_YEAST | Q6Q547)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0030515    snoRNA binding    Interacting selectively and non-covalently with small nucleolar RNA.
biological process
    GO:0000469    cleavage involved in rRNA processing    Any phosphodiester bond hydrolysis involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule.
    GO:0001522    pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
    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:0031118    rRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine 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.
    GO:0031120    snRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in an snRNA molecule.
cellular component
    GO:0031429    box H/ACA snoRNP complex    A box H/ACA RNP complex that is located in the nucleolus.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    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.
    GO:0005732    small nucleolar ribonucleoprotein complex    A ribonucleoprotein complex that contains an RNA molecule of the small nucleolar RNA (snoRNA) family and associated proteins. Most are involved in a step of processing of rRNA: cleavage, 2'-O-methylation, or pseudouridylation. The majority, though not all, fall into one of two classes, box C/D type or box H/ACA type.

Chain C   (GAR1_YEAST | P28007)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0034513    box H/ACA snoRNA binding    Interacting selectively and non-covalently with box H/ACA small nucleolar RNA.
    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:0001522    pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
    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.
    GO:0031120    snRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in an snRNA molecule.
cellular component
    GO:0031429    box H/ACA snoRNP complex    A box H/ACA RNP complex that is located in the nucleolus.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    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.
    GO:0005732    small nucleolar ribonucleoprotein complex    A ribonucleoprotein complex that contains an RNA molecule of the small nucleolar RNA (snoRNA) family and associated proteins. Most are involved in a step of processing of rRNA: cleavage, 2'-O-methylation, or pseudouridylation. The majority, though not all, fall into one of two classes, box C/D type or box H/ACA type.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBF5_YEAST | P33322: 3uai 3zv0
        GAR1_YEAST | P28007: 3uai
        NOP10_YEAST | Q6Q547: 1y2y 2aqa 3uai

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3U28)