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(-) Description

Title :  STRUCTURE OF THE HUMAN SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN, SBDS
 
Authors :  J. F. De Oliveira, M. L. Sforca, T. Blumenschein, B. G. Guimaraes, N. I. T. Zanchin, A. C. Zeri
Date :  14 Jan 09  (Deposition) - 19 Jan 10  (Release) - 11 Aug 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sbds Protein, Nmr Protein Structure, Rna-Interacting Protein, Disease Mutation, Phosphoprotein, Ribosome Biogenesis, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. F. De Oliveira, M. L. Sforca, T. M. Blumenschein, M. B. Goldfeder, B. G. Guimaraes, C. C. Oliveira, N. I. Zanchin, A. C. Zeri
Structure, Dynamics, And Rna Interaction Analysis Of The Human Sbds Protein.
J. Mol. Biol. V. 396 1053 2010
PubMed-ID: 20053358  |  Reference-DOI: 10.1016/J.JMB.2009.12.039

(-) Compounds

Molecule 1 - RIBOSOME MATURATION PROTEIN SBDS
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET-TEV
    GeneSBDS, CGI-97
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KDO)

(-) Sites  (0, 0)

(no "Site" information available for 2KDO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

NMR Structure (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_015390N8KSBDS_HUMANDisease (SDS)28942099AN10K
2UniProtVAR_071673K33TSBDS_HUMANDisease (SDS)  ---AK35T
3UniProtVAR_015391E44GSBDS_HUMANDisease (SDS)  ---AE46G
4UniProtVAR_015392K67ESBDS_HUMANDisease (SDS)  ---AK69E
5UniProtVAR_015393I87SSBDS_HUMANDisease (SDS)  ---AI89S
6UniProtVAR_015394R126TSBDS_HUMANDisease (SDS)113993995AR128T
7UniProtVAR_015395R169CSBDS_HUMANDisease (SDS)113993996AR171C
8UniProtVAR_015396I212TSBDS_HUMANDisease (SDS)79344818AI214T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0023PS01267 Uncharacterized protein family UPF0023 signature.SBDS_HUMAN44-63  1A:46-65

(-) Exons   (0, 0)

(no "Exon" information available for 2KDO)

(-) Sequences/Alignments

NMR Structure
   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:252
 aligned with SBDS_HUMAN | Q9Y3A5 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:252
                              1                                                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248  
           SBDS_HUMAN     - --MSIFTPTNQIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQTEICKQILTKGEVQVSDKERHTQLEQMFRDIATIVADKCVNPETKRPYTVILIERAMKDIHYSVKTNKSTKQQALEVIKQLKEKMKIERAHMRLRFILPVNEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFREIDELIKKETKGKGSLEVLNLKDVEEGDEKFE 250
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------SBDS-2kdoA02 A:15-105                                                                      --SBDS_C-2kdoA01 A:108-229                                                                                                  ----------------------- Pfam domains
         Sec.struct. author ................eeeeeee....eeeeeee..hhhhhhh..............eeee....eeehhhhhhhhh...hhhhhhhhhhhh.ee............hhhhhhhhhhhh.ee........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..eee...eeee.hhhhhhhhh.hhhhhh.eeeee.......eee..hhhhhhhhhhhhhhhh....eeee.............. Sec.struct. author
                 SAPs(SNPs) ---------K------------------------T----------G----------------------E-------------------S--------------------------------------T------------------------------------------C------------------------------------------T-------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------UPF0023  PDB: A:46-6------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2kdo A   1 GHMSIFTPTNQIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQTEICKQILTKGEVQVSDKERHTQLEQMFRDIATIVADKCVNPETKRPYTVILIERAMKDIHYSVKTNKSTKQQALEVIKQLKEKMKIERAHMRLRFILPVNEGKKLKEKLKPLIKVIESEDYGQQLEIVCLIDPGCFREIDELIKKETKGKGSLEVLNLKDVEEGDEKFE 252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  

   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 2KDO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KDO)

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: EF-G_C (20)

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (SBDS_HUMAN | Q9Y3A5)
molecular function
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
biological process
    GO:0048539    bone marrow development    The process whose specific outcome is the progression of the bone marrow over time, from its formation to the mature structure.
    GO:0030282    bone mineralization    The deposition of hydroxyapatite, a form of calcium phosphate with the formula Ca10(PO4)6(OH)2, in bone tissue.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0001833    inner cell mass cell proliferation    The proliferation of cells in the inner cell mass.
    GO:0030595    leukocyte chemotaxis    The movement of a leukocyte in response to an external stimulus.
    GO:0042256    mature ribosome assembly    The aggregation, arrangement and bonding together of the large and small ribosomal subunits into a functional ribosome.
    GO:0007052    mitotic spindle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
    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: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: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:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
    GO:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SBDS_HUMAN | Q9Y3A52l9n 5an9 5anb 5anc

(-) Related Entries Specified in the PDB File

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