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(-) Description

Title :  SOLUTION STRUCTURE OF RNA BINDING DOMAIN 4 IN POLYADENYLATION BINDING PROTEIN 3
 
Authors :  K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  12 Dec 05  (Deposition) - 12 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rrm Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYADENYLATE-BINDING PROTEIN 3
    ChainsA
    EngineeredYES
    Expression System PlasmidP050516-01
    Expression System Vector TypePLASMID
    FragmentRNA RECOGNITION MOTIF
    GenePABP3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymPOLYA, -BINDING PROTEIN 3, PABP 3, TESTIS- SPECIFIC POLYA, -BINDING 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 2D9P)

(-) Sites  (0, 0)

(no "Site" information available for 2D9P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D9P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D9P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D9P)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.PABP3_HUMAN11-89
99-175
191-268
294-370
  1-
-
-
A:294-370

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002815891ENSE00001425120chr13:25670276-256727052430PABP3_HUMAN1-6526521A:279-381 (gaps)177

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:103
 aligned with PABP3_HUMAN | Q9H361 from UniProtKB/Swiss-Prot  Length:631

    Alignment length:177
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       
          PABP3_HUMAN   225 DESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRTFEQMKQDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAYLTNEYMQRMASVRAVPNQRAPPSG 401
               SCOP domains d2d9pa                      _                                 A: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......----------------------.--------------------------------..........eeee......hhhhhhhh......eeeeeeee....eeeeeeeee.hhhhhhhhhhhhh.........eeee.........--------------------..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM  PDB: - UniProt: 191-268                -------------------------RRM  PDB: A:294-370 UniProt: 294-370                                         ------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:279-381 (gaps) UniProt: 1-652 [INCOMPLETE]                                                                                                                       Transcript 1
                 2d9p A 279 GSSGSS----------------------G--------------------------------DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQS--------------------GPSSG 381
                                 |   -         -        |-         -         -         - |     294       304       314       324       334       344       354       364       374 |       -         -  |    
                               284                    285                              286                                                                                       376                  377    

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  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 2D9P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D9P)

(-) Gene Ontology  (7, 11)

NMR Structure(hide GO term definitions)
Chain A   (PABP3_HUMAN | Q9H361)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008143    poly(A) binding    Interacting selectively and non-covalently with a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA.
biological process
    GO:0016071    mRNA metabolic process    The chemical reactions and pathways involving mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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        PABP3_HUMAN | Q9H3614ive

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