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(-) Description

Title :  SOLUTION STRUCTURE OF RNA-BINDING DOMAIN 3 OF CUGBP1 IN COMPLEX WITH RNA (UG)3
 
Authors :  K. Tsuda, K. Kuwasako, M. Takahashi, T. Someya, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  09 Apr 09  (Deposition) - 04 Aug 09  (Release) - 01 Sep 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Rrm Domain, Rbd, Protein-Rna Complex, Transcription/Rna Complex, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Activator, Alternative Splicing, Cytoplasm, Mrna Processing, Nucleus, Phosphoprotein, Rna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Tsuda, K. Kuwasako, M. Takahashi, T. Someya, M. Inoue, T. Terada, N. Kobayashi, M. Shirouzu, T. Kigawa, A. Tanaka, S. Sugano, P. Guntert, Y. Muto, S. Yokoyama
Structural Basis For The Sequence-Specific Rna-Recognition Mechanism Of Human Cug-Bp1 Rrm3
Nucleic Acids Res. V. 37 5151 2009
PubMed-ID: 19553194  |  Reference-DOI: 10.1093/NAR/GKP546
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CUG-BP- AND ETR-3-LIKE FACTOR 1
    ChainsA
    EngineeredYES
    Expression SystemFREE PROTEIN SYNTHESIS
    Expression System VectorP040329-21
    Expression System Vector TypeVECTOR
    FragmentRNA RECOGNITION MOTIF, RESIDUES 383-484
    GeneCUGBP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsE. COLI - CELL-FREE PROTEIN SYNTHESIS
    SynonymCELF-1, BRUNO-LIKE PROTEIN 2, RNA-BINDING PROTEIN BRUNOL-2, CUG TRIPLET REPEAT RNA-BINDING PROTEIN 1, CUG- BP1, DEADENYLATION FACTOR CUG-BP, 50 KDA NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN, EMBRYO DEADENYLATION ELEMENT-BINDING PROTEIN HOMOLOG, EDEN-BP HOMOLOG
 
Molecule 2 - 5'-R(*UP*GP*UP*GP*UP*G)-3'
    ChainsB
    EngineeredYES
    Other DetailsRNA WAS PREPARED BY IN VITRO TRANSCRIPTION
    SyntheticYES

 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 2RQC)

(-) Sites  (0, 0)

(no "Site" information available for 2RQC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.CELF1_HUMAN16-99
108-188
401-479
  1-
-
A:401-479

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.10dENST0000035859710dENSE00001601316chr11:47510576-47510389188CELF1_HUMAN1-60600--
1.11ENST0000035859711ENSE00002154815chr11:47508793-4750871183CELF1_HUMAN60-87280--
1.12bENST0000035859712bENSE00001704133chr11:47508350-4750830249CELF1_HUMAN88-104170--
1.13aENST0000035859713aENSE00001658663chr11:47506075-47505941135CELF1_HUMAN104-149460--
1.14aENST0000035859714aENSE00001624279chr11:47505084-4750500580CELF1_HUMAN149-175270--
1.15aENST0000035859715aENSE00001271006chr11:47504408-47504247162CELF1_HUMAN176-229540--
1.16aENST0000035859716aENSE00001404953chr11:47500504-4750042976CELF1_HUMAN230-255260--
1.17bENST0000035859717bENSE00001098102chr11:47498977-47498849129CELF1_HUMAN255-298441A:376-3761
1.18bENST0000035859718bENSE00001098106chr11:47498508-47498398111CELF1_HUMAN298-335381A:376-3783
1.19bENST0000035859719bENSE00001098105chr11:47497073-47496888186CELF1_HUMAN335-397631A:379-397 (gaps)54
1.20ENST0000035859720ENSE00001098104chr11:47494783-47494640144CELF1_HUMAN397-445491A:397-44549
1.21aENST0000035859721aENSE00001271057chr11:47493909-47493743167CELF1_HUMAN445-486421A:445-48844
1.23aENST0000035859723aENSE00001270964chr11:47490443-47489946498CELF1_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:115
 aligned with CELF1_HUMAN | Q92879 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:193
                                                                                                                                                                                                                        486  
                                                                                                                                                                                                                       485|  
                                                                                                                                                                                                                    484  ||  
                                   307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477      |485|  
          CELF1_HUMAN   298 GSSPSSSSSNSVNPIASLGALQTLAGATAGLNVGSLAGMAALNGGLGSSGLSNGTGSTMEALTQAYSGIQQYAAAALPTLYNQNLLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK--PY--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------RRM_1-2rqcA01 A:403-473                                                ----------------- Pfam domains
         Sec.struct. author ...-------------------------------------------....-----------------------------------...................eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------RRM  PDB: A:401-479 UniProt: 401-479                                           ----------- PROSITE
           Transcript 1 (1) 1------------------------------------Exon 1.19b  PDB: A:379-397 (gaps) UniProt: 335-397 [INCOMPLETE]-----------------------------------------------Exon 1.21a  PDB: A:445-488 UniProt: 445-486 -- Transcript 1 (1)
           Transcript 1 (2) Exon 1.18b  PDB: A:376-378            -------------------------------------------------------------Exon 1.20  PDB: A:397-445 UniProt: 397-445       --------------------------------------------- Transcript 1 (2)
                 2rqc A 376 GSS-------------------------------------------GSSG-----------------------------------LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSSG 490
                              |      -         -         -         -      |382         -         -         -     | 387       397       407       417       427       437       447       457       467       477       487   
                              |                                         379  |                                 383                                                                                                           
                            378                                            382                                                                                                                                               

Chain B from PDB  Type:RNA  Length:6
                                      
                 2rqc B 491 UGUGUG 496

   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  (0, 0)

(no "SCOP Domain" information available for 2RQC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RQC)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RRM (206)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (CELF1_HUMAN | Q92879)
molecular function
    GO:0042835    BRE binding    Interacting selectively and non-covalently with the RNA element BRE (Bruno response element).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    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:0031369    translation initiation factor binding    Interacting selectively and non-covalently with a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation.
    GO:0000900    translation repressor activity, nucleic acid binding    Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid.
biological process
    GO:0016246    RNA interference    The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes.
    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:0009790    embryo development    The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
    GO:0007281    germ cell development    The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
    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:0006376    mRNA splice site selection    Selection of a splice site by components of the assembling spliceosome.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0040018    positive regulation of multicellular organism growth    Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size.
    GO:0043484    regulation of RNA splicing    Any process that modulates the frequency, rate or extent of 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:0007286    spermatid development    The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CELF1_HUMAN | Q928792cpz 2dhs 2rq4 3nmr 3nna 3nnc 3nnh

(-) Related Entries Specified in the PDB File

2cpz THE SAME PROTEIN WITHOUT RNA RELATED ID: HSS001001546.2 RELATED DB: TARGETDB