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(-) Description

Title :  NMR, REPRESENTATIVE STRUCTURE
 
Authors :  M. R. Conte, T. Grune, S. Curry, S. Matthews
Date :  22 Sep 99  (Deposition) - 03 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Ribonucleoprotein, Polypyrimidine Tract Binding Protein, Rnp, Rna, Spicing, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Conte, T. Grune, G. Kelly, A. Ladas, S. Matthews, S. Curry
Structure Of Tandem Rna Recognition Motifs From Polypyrimidine Tract Binding Protein Reveals Novel Features Of The Rrm Fold
Embo J. V. 19 3132 2000
PubMed-ID: 10856256  |  Reference-DOI: 10.1093/EMBOJ/19.12.3132
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYPYRIMIDINE TRACT-BINDING PROTEIN
    Cellular Location: NUCLEUS/CYTOPLASM
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RNA BINDING FRAGMENT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PTB, PTB-C198, HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN I, HNRNP I, 57 KD RNA-BINDING PROTEIN PPTB-1

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1QM9)

(-) Sites  (0, 0)

(no "Site" information available for 1QM9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QM9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QM9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QM9)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.PTBP1_HUMAN59-143
184-260
337-411
454-529		  2-
-
A:4-78
A:121-196

(-) Exons   (6, 6)

NMR Structure (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003490381ENSE00001155026chr19:797392-797505114PTBP1_HUMAN1-330--
1.2ENST000003490382ENSE00001113327chr19:799413-79944331PTBP1_HUMAN3-13110--
1.3ENST000003490383ENSE00000892209chr19:803561-80363676PTBP1_HUMAN14-39260--
1.4ENST000003490384ENSE00000768682chr19:804036-804208173PTBP1_HUMAN39-96580--
1.5ENST000003490385ENSE00000892212chr19:804292-804438147PTBP1_HUMAN97-145490--
1.6ENST000003490386ENSE00000892214chr19:804532-804702171PTBP1_HUMAN146-202570--
1.7ENST000003490387ENSE00000892216chr19:804829-804939111PTBP1_HUMAN203-239370--
1.8ENST000003490388ENSE00000892217chr19:805013-805187175PTBP1_HUMAN240-298590--
1.10ENST0000034903810ENSE00000464365chr19:806408-806556149PTBP1_HUMAN298-347501A:1-1414
1.11ENST0000034903811ENSE00000892219chr19:807869-80790234PTBP1_HUMAN348-359121A:15-2612
1.12ENST0000034903812ENSE00000768789chr19:808360-80845293PTBP1_HUMAN359-390321A:26-5732
1.13ENST0000034903813ENSE00000768790chr19:808546-808762217PTBP1_HUMAN390-462731A:57-12973
1.14ENST0000034903814ENSE00000768792chr19:810543-81062078PTBP1_HUMAN462-488271A:129-15527
1.15ENST0000034903815ENSE00001155037chr19:810694-8123271634PTBP1_HUMAN488-531441A:155-19844

(-) 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:198
 aligned with PTBP1_HUMAN | P26599 from UniProtKB/Swiss-Prot  Length:531

    Alignment length:198
                                   343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523        
          PTBP1_HUMAN   334 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 531
               SCOP domains d1qm9a1 A:1-110 Polypyrimidine tract-binding protein                                                          d1qm9a2 A:111-198 Polypyrimidine tract-binding protein                                   SCOP domains
               CATH domains 1qm9A01 A:1-98  [code=3.30.70.330, no name defined]                                               -----------1qm9A02 A:110-198  [code=3.30.70.330, no name defined]                                    CATH domains
               Pfam domains --------------------RRM_5-1qm9A01 A:21-76                                   ----------------------------------------------RRM_6-1qm9A02 A:123-190                                             -------- Pfam domains
         Sec.struct. author ....eeeee........hhhhhhhhhhh....eee.........eee....hhhhhhhhhh..........eeee..................eee.........................eeee........hhhhhhhhhh......eeee.......eeee...hhhhhhhhhhh............eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---RRM  PDB: A:4-78 UniProt: 337-411                                          ------------------------------------------RRM  PDB: A:121-196 UniProt: 454-529                                        -- PROSITE
           Transcript 1 (1) Exon 1.10     Exon 1.11   ------------------------------Exon 1.13  PDB: A:57-129 UniProt: 390-462                                -------------------------Exon 1.15  PDB: A:155-198 UniProt: 488-531   Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.12  PDB: A:26-57         -----------------------------------------------------------------------Exon 1.14  PDB: A:129-155  ------------------------------------------- Transcript 1 (2)
                 1qm9 A   1 MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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, 2)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

NMR Structure
(-)
Clan: RRM (206)

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (PTBP1_HUMAN | P26599)
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:0008187    poly-pyrimidine tract binding    Interacting selectively and non-covalently with any stretch of pyrimidines (cytosine or uracil) in an RNA molecule.
    GO:0036002    pre-mRNA binding    Interacting selectively and non-covalently with pre-messenger RNA (pre-mRNA), an intermediate molecule between DNA and protein that may contain introns and, at least in part, encodes one or more proteins. Introns are removed from pre-mRNA to form a mRNA 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).
biological process
    GO:0075522    IRES-dependent viral translational initiation    Process by which viral mRNA translation is initiated, where a domain in the 5' untranslated region (UTR) of the viral mRNA called an internal ribosome entry site (IRES) binds the host 43S preinitiation complex, circumventing regular cap-dependent translation initiation.
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0008543    fibroblast growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
    GO:0010467    gene expression    The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    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:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0033119    negative regulation of RNA splicing    Any process that stops, prevents, or reduces the frequency, rate or extent of RNA splicing.
    GO:0048025    negative regulation of mRNA splicing, via spliceosome    Any process that stops, prevents or reduces the rate or extent of mRNA splicing via a spliceosomal mechanism.
    GO:0051148    negative regulation of muscle cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of muscle cell differentiation.
    GO:0000381    regulation of alternative mRNA splicing, via spliceosome    Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
cellular component
    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: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.

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 Related Entries

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UniProtKB/Swiss-Prot
        PTBP1_HUMAN | P26599: 1sjq 1sjr 2ad9 2adb 2adc 2evz 2n3o 3zzy 3zzz

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