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(-) Description

Title :  SOLUTION STRUCTURE OF RRM DOMAIN IN HETEROGENEOUS NUCLEAR RIBONUCLEAOPROTEINS A2/B1
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 May 05  (Deposition) - 14 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structure Genomics, Rrm Domain, Heterogeneous Nuclear Ribonucleoproteins A2/B1, 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 :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2/B1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEINS A2/B1
    ChainsA
    EngineeredYES
    Expression System PlasmidP040510-06
    Expression System Vector TypePLASMID
    FragmentRRM DOMAIN
    GeneHNRPA2B1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymHNRNP A2 / HNRNP B1

 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 1X4B)

(-) Sites  (0, 0)

(no "Site" information available for 1X4B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X4B)

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Arg A:89 -Pro A:90

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X4B)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.ROA2_HUMAN21-104
112-191
  2A:28-110
A:111-116

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003607871cENSE00001524804chr7:26240366-26240192175ROA2_HUMAN1-221A:8-92
1.1dENST000003607871dENSE00001423216chr7:26237486-2623745136ROA2_HUMAN3-14121A:10-2112
1.1eENST000003607871eENSE00001390055chr7:26237352-26237242111ROA2_HUMAN15-51371A:22-5837
1.2ENST000003607872ENSE00000832055chr7:26237081-26236935147ROA2_HUMAN52-100491A:59-10749
1.3aENST000003607873aENSE00000832054chr7:26236637-26236427211ROA2_HUMAN101-171711A:108-116 (gaps)54
1.4ENST000003607874ENSE00000832052chr7:26236278-26236177102ROA2_HUMAN171-205350--
1.5ENST000003607875ENSE00001223366chr7:26236101-2623602181ROA2_HUMAN205-232280--
1.6aENST000003607876aENSE00000832049chr7:26235529-2623546763ROA2_HUMAN232-253220--
1.7aENST000003607877aENSE00001738745chr7:26233314-26233195120ROA2_HUMAN253-293410--
1.8ENST000003607878ENSE00001671571chr7:26232993-26232871123ROA2_HUMAN293-334420--
1.9aENST000003607879aENSE00001631417chr7:26232197-2623211583ROA2_HUMAN334-353200--
1.9gENST000003607879gENSE00001656664chr7:26230748-26230613136ROA2_HUMAN-00--
1.9hENST000003607879hENSE00001661340chr7:26230080-26229745336ROA2_HUMAN-00--

(-) 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:116
 aligned with ROA2_HUMAN | P22626 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:161
                                   1                                                                                                                                                         
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153 
           ROA2_HUMAN     - -------MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRG 154
               SCOP domains -------d1x4ba1 A:8-110 Heterogeneous nuclear ribonucleoproteins A2/B1                                         --------------------------------------------------- SCOP domains
               CATH domains --------------------1x4bA01 A:21-102  [code=3.30.70.330, no name defined]                             ----------------------------------------------------------- CATH domains
               Pfam domains -----------------------------RRM_6-1x4bA01 A:30-99                                                 -------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhh.eeeee.......hhhhhhhh.......eeeee..........eeeee...hhhhhhhh....eee..eeeeee.........---------------------------------------------...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------RRM  PDB: A:28-110 UniProt: 21-104                                                  -------RRM  PDB: A:111-116 UniProt: 112-191        PROSITE
               Transcript 1 -------1.Exon 1.1d   Exon 1.1e  PDB: A:22-58              Exon 1.2  PDB: A:59-107 UniProt: 52-100          Exon 1.3a  PDB: A:108-116 (gaps) UniProt: 101-171      Transcript 1
                 1x4b A   1 GSSGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESG---------------------------------------------SGPSSG 116
                                    10        20        30        40        50        60        70        80        90       100       110         -         -         -         -     | 115 
                                                                                                                                       110                                           111     

   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  (1, 1)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RRM (206)

(-) Gene Ontology  (30, 30)

NMR Structure(hide GO term definitions)
Chain A   (ROA2_HUMAN | P22626)
molecular function
    GO:1990247    N6-methyladenosine-containing RNA binding    Interacting selectively and non-covalently with an RNA molecule modified by N6-methyladenosine (m6A), a modification present at internal sites of mRNAs and some non-coding RNAs.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003730    mRNA 3'-UTR binding    Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
    GO:0035198    miRNA binding    Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes.
    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:0097157    pre-mRNA intronic binding    Interacting selectively and non-covalently with an intronic sequence of a pre-messenger RNA (pre-mRNA).
    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:0043047    single-stranded telomeric DNA binding    Interacting selectively and non-covalently with single-stranded telomere-associated DNA.
biological process
    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:0050658    RNA transport    The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    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:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:1990428    miRNA transport    The directed movement of microRNA (miRNA) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.
    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:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0031053    primary miRNA processing    Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0071013    catalytic step 2 spliceosome    A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
    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.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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    Arg A:89 - Pro A:90   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        ROA2_HUMAN | P226265en1 5ho4

(-) Related Entries Specified in the PDB File

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