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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CUGBP1 RRM1 WITH GUUGUUUUGUUU RNA
 
Authors :  M. Teplova, J. Song, H. Gaw, A. Teplov, D. J. Patel
Date :  23 Jun 10  (Deposition) - 27 Oct 10  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E  (1x)
Biol. Unit 2:  B,D,F  (1x)
Keywords :  Rna Recognition Motif, Pre-Mrna Splicing, Rna, Rna Binding Protein- Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Teplova, J. Song, H. Y. Gaw, A. Teplov, D. J. Patel
Structural Insights Into Rna Recognition By The Alternate-Splicing Regulator Cug-Binding Protein 1.
Structure V. 18 1364 2010
PubMed-ID: 20947024  |  Reference-DOI: 10.1016/J.STR.2010.06.018

(-) Compounds

Molecule 1 - CUGBP ELAV-LIKE FAMILY MEMBER 1
    ChainsA, C, B, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRRM1 DOMAIN (UNP RESIDUES 14-100)
    GeneBRUNOL2, CELF1, CUGBP, CUGBP1, NAB50
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCELF-1, CUG-BP- AND ETR-3-LIKE FACTOR 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 - RNA (5'-R(*GP*UP*UP*GP*UP*UP*UP*UP*GP*UP*UP*U)-3')
    ChainsE, F
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A C E 
Biological Unit 2 (1x) B D F

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3NNH)

(-) Sites  (0, 0)

(no "Site" information available for 3NNH)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NNH)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:54 -Pro A:55
2Asn C:54 -Pro C:55
3Asn B:54 -Pro B:55
4Asn D:54 -Pro D:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NNH)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.CELF1_HUMAN16-99
 
 
 
108-188
401-479
  4A:16-99
B:16-99
C:16-98
D:16-99
-
-
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.CELF1_HUMAN16-99
 
 
 
108-188
401-479
  2A:16-99
-
C:16-98
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.CELF1_HUMAN16-99
 
 
 
108-188
401-479
  2-
B:16-99
-
D:16-99
-
-

(-) Exons   (3, 12)

Asymmetric Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.10dENST0000035859710dENSE00001601316chr11:47510576-47510389188CELF1_HUMAN1-60604A:14-60
B:14-60
C:14-60
D:14-60
47
47
47
47
1.11ENST0000035859711ENSE00002154815chr11:47508793-4750871183CELF1_HUMAN60-87284A:60-87
B:60-87
C:60-87
D:60-87
28
28
28
28
1.12bENST0000035859712bENSE00001704133chr11:47508350-4750830249CELF1_HUMAN88-104174A:88-99
B:88-99
C:88-98
D:88-100
12
12
11
13
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_HUMAN255-298440--
1.18bENST0000035859718bENSE00001098106chr11:47498508-47498398111CELF1_HUMAN298-335380--
1.19bENST0000035859719bENSE00001098105chr11:47497073-47496888186CELF1_HUMAN335-397630--
1.20ENST0000035859720ENSE00001098104chr11:47494783-47494640144CELF1_HUMAN397-445490--
1.21aENST0000035859721aENSE00001271057chr11:47493909-47493743167CELF1_HUMAN445-486420--
1.23aENST0000035859723aENSE00001270964chr11:47490443-47489946498CELF1_HUMAN-00--

(-) Sequences/Alignments

Asymmetric 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:86
 aligned with CELF1_HUMAN | Q92879 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:86
                                    23        33        43        53        63        73        83        93      
          CELF1_HUMAN    14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADS  99
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhh....eeeeeeeee......eeeeeeeeee.hhhhhhhhhhhhh............eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: A:16-99 UniProt: 16-99                                                     PROSITE
           Transcript 1 (1) Exon 1.10d  PDB: A:14-60 UniProt: 1-60         ---------------------------Exon 1.12b   Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.11  PDB: A:60-87     ------------ Transcript 1 (2)
                 3nnh A  14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADS  99
                                    23        33        43        53        63        73        83        93      

Chain B from PDB  Type:PROTEIN  Length:86
 aligned with CELF1_HUMAN | Q92879 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:86
                                    23        33        43        53        63        73        83        93      
          CELF1_HUMAN    14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADS  99
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhh....eeeeeeeee......eeeeeeeeee.hhhhhhhhhhhhh............eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: B:16-99 UniProt: 16-99                                                     PROSITE
           Transcript 1 (1) Exon 1.10d  PDB: B:14-60 UniProt: 1-60         ---------------------------Exon 1.12b   Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.11  PDB: B:60-87     ------------ Transcript 1 (2)
                 3nnh B  14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADS  99
                                    23        33        43        53        63        73        83        93      

Chain C from PDB  Type:PROTEIN  Length:85
 aligned with CELF1_HUMAN | Q92879 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:85
                                    23        33        43        53        63        73        83        93     
          CELF1_HUMAN    14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPAD  98
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhh....eeeeeeeee......eeeeeeeeee.hhhhhhhhhhhhh............eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: C:16-98 UniProt: 16-99                                                    PROSITE
           Transcript 1 (1) Exon 1.10d  PDB: C:14-60 UniProt: 1-60         ---------------------------Exon 1.12b  Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.11  PDB: C:60-87     ----------- Transcript 1 (2)
                 3nnh C  14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPAD  98
                                    23        33        43        53        63        73        83        93     

Chain D from PDB  Type:PROTEIN  Length:87
 aligned with CELF1_HUMAN | Q92879 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:87
                                    23        33        43        53        63        73        83        93       
          CELF1_HUMAN    14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSE 100
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----RRM_1-3nnhD01 D:18-88                                                  ------------ Pfam domains (1)
           Pfam domains (2) ----RRM_1-3nnhD02 D:18-88                                                  ------------ Pfam domains (2)
           Pfam domains (3) ----RRM_1-3nnhD03 D:18-88                                                  ------------ Pfam domains (3)
           Pfam domains (4) ----RRM_1-3nnhD04 D:18-88                                                  ------------ Pfam domains (4)
         Sec.struct. author ...eeeee......hhhhhhhhhhhhh.eeeeeeeee......eeeeeeeeee.hhhhhhhhhhhhh............eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: D:16-99 UniProt: 16-99                                                    - PROSITE
           Transcript 1 (1) Exon 1.10d  PDB: D:14-60 UniProt: 1-60         ---------------------------Exon 1.12b    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.11  PDB: D:60-87     ------------- Transcript 1 (2)
                 3nnh D  14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSE 100
                                    23        33        43        53        63        73        83        93       

Chain E from PDB  Type:DNA/RNA  Length:11
                                           
                 3nnh E   2 UUGUUUUGUUU  12
                                    11 

Chain F from PDB  Type:DNA/RNA  Length:11
                                           
                 3nnh F   1 GUUGUUUUGUU  11
                                    10 

   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 3NNH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NNH)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: RRM (206)
(-)
Family: RRM_1 (131)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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 2rqc 3nmr 3nna 3nnc

(-) Related Entries Specified in the PDB File

3nmr THE SAME PROTEIN RRM1-RRM2 DOMAIN COMPLEXED WITH GUUGUUUUGUUU.
3nna THE SAME PROTEIN RRM1-RRM2 DOMAIN COMPLEXED WITH GUUGUUUUUGUU.
3nnc THE SAME PROTEIN RRM1-RRM2 DOMAIN COMPLEXED WITH UGUGUGUUGUGUG.