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(-) Description

Title :  CRYSTAL STRUCTURE OF UP1 COMPLEXED WITH D(TAGG(6MI)TTAGGG): A HUMAN TELOMERIC REPEAT CONTAINING 6-METHYL-8-(2-DEOXY-BETA-RIBOFURANOSYL)ISOXANTHOPTERIDINE (6MI)
 
Authors :  J. C. Myers, S. A. Moore, Y. Shamoo
Date :  13 Jun 03  (Deposition) - 11 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Dna Complex, Up1, Human Telomeric Repeat, Htr, Tr2- 6F, Rrm, Rna Recognition Motif, 6Mi, 6-Methyl-8-(2-Deoxy- Beta-Ribofuranosyl)Isoxanthopteridine, Hnrnp A1, Rna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. C. Myers, S. A. Moore, Y. Shamoo
Structure-Based Incorporation Of 6-Methyl-8-(2-Deoxy-Beta-Ribofuranosyl) Isoxanthopteridine Into The Human Telomeric Repeat Dna As A Probe For Up1 Binding And Destabilization Of G-Tetrad Structures
J. Biol. Chem. V. 278 42300 2003
PubMed-ID: 12904298  |  Reference-DOI: 10.1074/JBC.M306147200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*T*AP*GP*GP*(6MI)P*TP*TP*AP*GP*GP*G)-3'
    ChainsB
    EngineeredYES
    Other DetailsOLIGONUCLEOTIDE D(TAGG(6MI)TTAGGG) BASED ON HUMAN TELOMERIC REPEAT D(TTAGGG)N
    SyntheticYES
 
Molecule 2 - HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPYS45
    Expression System StrainBL21DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 8-190
    GeneHNRPA1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHELIX-DESTABILIZING PROTEIN, SINGLE-STRAND BINDING PROTEIN, HNRNP CORE PROTEIN A1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
16MI1Mod. Nucleotide6-METHYL-8-(2-DEOXY-RIBOFURANOSYL)ISOXANTHOPTERIDINE

(-) Sites  (0, 0)

(no "Site" information available for 1PO6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PO6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:75 -Pro A:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014711N73SROA1_HUMANPolymorphism6533AN73S

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.ROA1_HUMAN14-97
105-184
  2A:14-97
A:105-184

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003409131aENSE00001482313chr12:54674488-54674606119ROA1_HUMAN1-550--
1.2ENST000003409132ENSE00000920024chr12:54675170-54675286117ROA1_HUMAN6-44391A:8-4437
1.3ENST000003409133ENSE00000920026chr12:54675579-54675725147ROA1_HUMAN45-93491A:45-9349
1.4ENST000003409134ENSE00000920027chr12:54675874-54676084211ROA1_HUMAN94-164711A:94-16471
1.5ENST000003409135ENSE00000920030chr12:54676178-5467627093ROA1_HUMAN164-195321A:164-19027
1.6ENST000003409136ENSE00000920032chr12:54676357-5467644993ROA1_HUMAN195-226320--
1.7ENST000003409137ENSE00000920033chr12:54676584-5467665875ROA1_HUMAN226-251260--
1.8aENST000003409138aENSE00001690592chr12:54676863-54677018156ROA1_HUMAN251-303530--
1.9aENST000003409139aENSE00001532273chr12:54677596-54677751156ROA1_HUMAN303-355530--
1.10ENST0000034091310ENSE00001378946chr12:54678042-5467810160ROA1_HUMAN355-372180--
1.11ENST0000034091311ENSE00001532276chr12:54678333-54679028696ROA1_HUMAN-00--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:183
 aligned with ROA1_HUMAN | P09651 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:183
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187   
           ROA1_HUMAN     8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS 190
               SCOP domains d1po6a1 A:8-98 Nuclear ribonucleoprotein A1 (RNP A1, UP1)                                  d1po6a2 A:99-190 Nuclear ribonucleoprotein A1 (RNP A1, UP1)                                  SCOP domains
               CATH domains -1po6A01 A:9-93  [code=3.30.70.330, no name defined]                                  ------1po6A02 A:100-180  [code=3.30.70.330, no name defined]                           ---------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------RRM_1-1po6A01 A:107-176                                               -------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------RRM_1-1po6A02 A:107-176                                               -------------- Pfam domains (2)
         Sec.struct. author ..hhhh.eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhh...ee..ee.eeee....hhhhh........eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhh....ee..ee.eeee..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------S--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------RRM  PDB: A:14-97 UniProt: 14-97                                                    -------RRM  PDB: A:105-184 UniProt: 105-184                                            ------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:8-44 UniProt: 6-44  Exon 1.3  PDB: A:45-93 UniProt: 45-93            Exon 1.4  PDB: A:94-164 UniProt: 94-164                                -------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:164-190    Transcript 1 (2)
                 1po6 A   8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS 190
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187   

Chain B from PDB  Type:DNA  Length:11
                                           
                 1po6 B 202 TAGGxTTAGGG 212
                                |  211 
                              206-6MI  

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: RRM (206)
(-)
Family: RRM_1 (131)
1aRRM_1-1po6A01A:107-176
1bRRM_1-1po6A02A:107-176

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ROA1_HUMAN | P09651)
molecular function
    GO:0098505    G-rich strand telomeric DNA binding    Interacting selectively and non-covalently with G-rich, single-stranded, telomere-associated DNA.
    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: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:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
    GO:0061752    telomeric repeat-containing RNA binding    Interacting selectively and non-covalently with long non-coding RNA molecules transcribed from subtelomeric regions in most eukaryotes. Telomeric repeat-containing RNA (TERRA) molecules consist of subtelomeric-derived sequences and G-rich telomeric repeats.
biological process
    GO:0006405    RNA export from nucleus    The directed movement of RNA from the nucleus to the cytoplasm.
    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: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:0032211    negative regulation of telomere maintenance via telomerase    Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0051168    nuclear export    The directed movement of substances out of the nucleus.
    GO:0051170    nuclear import    The directed movement of substances into the nucleus.
    GO:0032212    positive regulation of telomere maintenance via telomerase    Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        ROA1_HUMAN | P096511ha1 1l3k 1pgz 1u1k 1u1l 1u1m 1u1n 1u1o 1u1p 1u1q 1u1r 1up1 2h4m 2lyv 2up1 4yoe 5mpg 5mpl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1PO6)