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(-) Description

Title :  SOLUTION STRUCTURE OF THE S1 RNA BINDING DOMAIN FROM HUMAN HYPOTHETICAL PROTEIN BAA11502
 
Authors :  S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  S1 Domain, Ob-Fold, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The S1 Rna Binding Domain From Human Hypothetical Protein Baa11502
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RRP5 PROTEIN HOMOLOG
    ChainsA
    EngineeredYES
    Expression System PlasmidP030512-28
    Expression System Vector TypePLASMID
    FragmentS1 DOMAIN
    GeneRIKEN CDNA HA02717
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymPROGRAMMED CELL DEATH PROTEIN 11

 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 1WI5)

(-) Sites  (0, 0)

(no "Site" information available for 1WI5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WI5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WI5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WI5)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S1PS50126 S1 domain profile.RRP5_HUMAN83-171
187-258
281-346
453-522
365-436
542-611
729-798
636-707
1036-1109
1149-1222
1230-1298
1324-1396
  2-
A:200-271
A:294-297
-
-
-
-
-
-
-
-
-

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003697971aENSE00001889304chr10:105156405-10515648783RRP5_HUMAN-00--
1.2ENST000003697972ENSE00002198293chr10:105158173-105158285113RRP5_HUMAN1-34340--
1.4ENST000003697974ENSE00000987736chr10:105160154-105160285132RRP5_HUMAN35-78440--
1.5aENST000003697975aENSE00000987737chr10:105162875-105163042168RRP5_HUMAN79-134560--
1.6aENST000003697976aENSE00000987738chr10:105164779-105164940162RRP5_HUMAN135-188541A:179-201 (gaps)35
1.7ENST000003697977ENSE00000987739chr10:105165742-105165865124RRP5_HUMAN189-230421A:202-24342
1.8ENST000003697978ENSE00000987740chr10:105166366-105166547182RRP5_HUMAN230-290611A:243-29250
1.9ENST000003697979ENSE00000987741chr10:105169456-105169563108RRP5_HUMAN291-326361A:293-297 (gaps)6
1.10ENST0000036979710ENSE00000987742chr10:105172873-105173079207RRP5_HUMAN327-395690--
1.11ENST0000036979711ENSE00000987743chr10:105173723-105173847125RRP5_HUMAN396-437420--
1.12ENST0000036979712ENSE00000987744chr10:105174027-10517408761RRP5_HUMAN437-457210--
1.13ENST0000036979713ENSE00000987745chr10:105174762-105174908147RRP5_HUMAN458-506490--
1.14ENST0000036979714ENSE00000987746chr10:105176248-105176499252RRP5_HUMAN507-590840--
1.15ENST0000036979715ENSE00000987747chr10:105177549-105177689141RRP5_HUMAN591-637470--
1.16ENST0000036979716ENSE00001025997chr10:105178197-105178391195RRP5_HUMAN638-702650--
1.17ENST0000036979717ENSE00000987749chr10:105179295-105179465171RRP5_HUMAN703-759570--
1.18ENST0000036979718ENSE00001092404chr10:105181105-105181324220RRP5_HUMAN760-833740--
1.19ENST0000036979719ENSE00001092406chr10:105182745-105182894150RRP5_HUMAN833-883510--
1.20ENST0000036979720ENSE00001092405chr10:105183300-105183415116RRP5_HUMAN883-921390--
1.21bENST0000036979721bENSE00001026013chr10:105184741-105185282542RRP5_HUMAN922-11021810--
1.22ENST0000036979722ENSE00001025995chr10:105187086-10518714863RRP5_HUMAN1102-1123220--
1.23ENST0000036979723ENSE00001026002chr10:105191886-105191991106RRP5_HUMAN1123-1158360--
1.24aENST0000036979724aENSE00001026016chr10:105193705-10519379490RRP5_HUMAN1159-1188300--
1.25aENST0000036979725aENSE00001026007chr10:105194005-105194107103RRP5_HUMAN1189-1223350--
1.26ENST0000036979726ENSE00001026009chr10:105194555-105194732178RRP5_HUMAN1223-1282600--
1.27ENST0000036979727ENSE00001026012chr10:105197772-10519782857RRP5_HUMAN1282-1301200--
1.28ENST0000036979728ENSE00001026008chr10:105198443-105198565123RRP5_HUMAN1301-1342420--
1.29ENST0000036979729ENSE00001025998chr10:105199503-105199625123RRP5_HUMAN1342-1383420--
1.30ENST0000036979730ENSE00001026011chr10:105200047-105200338292RRP5_HUMAN1383-1480980--
1.31ENST0000036979731ENSE00001026014chr10:105200491-105200607117RRP5_HUMAN1481-1519390--
1.32ENST0000036979732ENSE00001026006chr10:105201583-105201732150RRP5_HUMAN1520-1569500--
1.33ENST0000036979733ENSE00001026005chr10:105201970-105202217248RRP5_HUMAN1570-1652830--
1.34ENST0000036979734ENSE00001026000chr10:105202922-105203090169RRP5_HUMAN1652-1708570--
1.35ENST0000036979735ENSE00001026003chr10:105203672-105203825154RRP5_HUMAN1709-1760520--
1.36bENST0000036979736bENSE00001025994chr10:105204274-105204439166RRP5_HUMAN1760-1815560--
1.37bENST0000036979737bENSE00001450934chr10:105205135-105206049915RRP5_HUMAN1815-1871570--

(-) 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:119
 aligned with RRP5_HUMAN | Q14690 from UniProtKB/Swiss-Prot  Length:1871

    Alignment length:166
                                   163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313      
           RRP5_HUMAN   154 SSLGITDRGKKSVKLSLNPKNVNRVLSAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEVSTAIATEQQSWNLNNLLPGLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKAG 319
               SCOP domains d1wi5a  _           A: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------S1-1wi5A01 A:196-271                                                        ------------------------------------------------------------- Pfam domains
         Sec.struct. author ......--..----------...............eeeeeeeeee..eeeee......eeeeehhhhhhhhhh..........eeeeeeeeeee....eeeee.......................----------------------------------...-.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE S1  PDB: -        ---------------S1  PDB: A:200-271 UniProt: 187-258                                     ----------------------S1  PDB: A:294-297 UniProt: 281-346     PROSITE
           Transcript 1 (1) Exon 1.6a  PDB: A:179-201 (gaps)   Exon 1.7  PDB: A:202-243 UniProt: 189-230 ------------------------------------------------------------Exon 1.9 UniProt: 291-326     Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------Exon 1.8  PDB: A:243-292 UniProt: 230-290 [INCOMPLETE]       ----------------------------- Transcript 1 (2)
                 1wi5 A 179 GSSGSS--GK----------NVNRVLSAEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEVSTAIATEQQSWNLNNLS----------------------------------GPS-SG 297
                                 | 186         -|      196       206       216       226       236       246       256       266       276       286     |   -         -         -         -| | | 
                               184  ||        187                                                                                                      292                                293 | | 
                                  185|                                                                                                                                                      295 | 
                                   186                                                                                                                                                        296 

   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)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WI5)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: OB (224)
(-)
Family: S1 (23)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (RRP5_HUMAN | Q14690)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
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:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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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