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(-) Description

Title :  CRYSTAL STRUCTURE OF DROSOPHILA HEXAMERIC C3PO FORMED BY TRUNCATED TRANSLIN AND TRAX
 
Authors :  Y. Tian, D. K. Simanshu, D. J. Patel
Date :  14 Apr 11  (Deposition) - 11 May 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Translin-Fold, Ribonuclease, Risc Activator, Nucleus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Tian, D. K. Simanshu, M. Ascano, R. Diaz-Avalos, A. Y. Park, S. A. Juranek, W. J. Rice, Q. Yin, C. V. Robinson, T. Tuschl, D. J. Patel
Multimeric Assembly And Biochemical Characterization Of The Trax-Translin Endonuclease Complex.
Nat. Struct. Mol. Biol. V. 18 658 2011
PubMed-ID: 21552261  |  Reference-DOI: 10.1038/NSMB.2069

(-) Compounds

Molecule 1 - TRANSLIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PRSFDUET-1 VECTOR WITH N- TERMINAL 6XHIS AND YEAST SUMO AS FUSION TAG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-217
    Gene: CG11761, DMEL_CG11761, TRANSLIN, TRSN
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: GM27569P
 
Molecule 2 - TRANSLIN ASSOCIATED FACTOR X, ISOFORM B
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PRSFDUET-1 VECTOR WITH N- TERMINAL 6XHIS AND YEAST SUMO AS FUSION TAG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 30-298
    Gene: DMEL_CG5063, TRAX
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: TRAX

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3RIU)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1C:229 -C:268

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser C:147 -Val C:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RIU)

(-) Exons   (0, 0)

(no "Exon" information available for 3RIU)

(-) 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:206
 aligned with Q7JVK6_DROME | Q7JVK6 from UniProtKB/TrEMBL  Length:235

    Alignment length:208
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207        
         Q7JVK6_DROME     8 DIFSNYQKYIDNEQEVRENIRIVVREIEHLSKEAQIKLQIIHSDLSQISAACGLARKQVELCAQKYQKLAELVPAGQYYRYSDHWTFITQRLIFIIALVIYLEAGFLVTRETVAEMLGLKISQSEGFHLDVEDYLLGILQLASELSRFATNSVTMGDYERPLNISHFIGDLNTGFRLLNLKNDGLRKRFDALKYDVKKIEEVVYDVSI 215
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...--..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3riu A   8 DIFSNYQKYIDNEQEVRENIRIVVREIEHLSKEAQIKLQIIHSDLSQISAACGLARKQVELCAQKYQKLAELVPAGQYYRYSDHWTFITQRLIFIIALVIYLEAGFLVTRETVAEmLGLKISQSEGFHLDVEDYLLGILQLASELSRFATNSVTmGDYERPLNISHFIGDLNTGFRLLNL--DGLRKRFDALKYDVKKIEEVVYDVSI 215
                                    17        27        37        47        57        67        77        87        97       107       117     | 127       137       147       157    |  167       177       187  |    197       207        
                                                                                                                                             123-MSE                                162-MSE                  187  |                         
                                                                                                                                                                                                                190                         


Chain B from PDB  Type:PROTEIN  Length:203
 aligned with Q7JVK6_DROME | Q7JVK6 from UniProtKB/TrEMBL  Length:235

    Alignment length:207
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       
         Q7JVK6_DROME     7 LDIFSNYQKYIDNEQEVRENIRIVVREIEHLSKEAQIKLQIIHSDLSQISAACGLARKQVELCAQKYQKLAELVPAGQYYRYSDHWTFITQRLIFIIALVIYLEAGFLVTRETVAEMLGLKISQSEGFHLDVEDYLLGILQLASELSRFATNSVTMGDYERPLNISHFIGDLNTGFRLLNLKNDGLRKRFDALKYDVKKIEEVVYDV 213
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------Translin-3riuB01 B:21-213                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) --------------Translin-3riuB02 B:21-213                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....----hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3riu B   7 LDIFSNYQKYIDNEQEVRENIRIVVREIEHLSKEAQIKLQIIHSDLSQISAACGLARKQVELCAQKYQKLAELVPAGQYYRYSDHWTFITQRLIFIIALVIYLEAGFLVTRETVAEmLGLKISQSEGFHLDVEDYLLGILQLASELSRFATNSVTmGDYERPLNISHFIGDLNTGFRLLNLK----RKRFDALKYDVKKIEEVVYDV 213
                                    16        26        36        46        56        66        76        86        96       106       116      |126       136       146       156     | 166       176       186 |    |196       206       
                                                                                                                                              123-MSE                                162-MSE                   188  193                    


Chain C from PDB  Type:PROTEIN  Length:190
 aligned with Q9VF77_DROME | Q9VF77 from UniProtKB/TrEMBL  Length:298

    Alignment length:243
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
         Q9VF77_DROME    31 VQQFRIYSNELIMKHDRHERIVKLSRDITIESKRIIFLLHSIDSRKQNKEKVLEEARQRLNKLIAVNFRAVALELRDQDVYQFRSSYSPGLQEFIEAYTYMEYLCHEDAEGENETKSVSDWQAIQAVMQYVEESSQPKEEPTEGEDVQAIAQVESPKKFQFFVDPTEYILGLSDLTGELMRRCINSLGSGDTDTCLDTCKALQHFYSGYISLNCQRARELWRKITTMKQSVLKAENVCYNVKV 273
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...-----..hhhhhhhhhhhhhhhhhhhhhhhh..----hhhhhhhhhhhhhhhhhhhhhhhhh...-------.....hhhhhhhhhh...----------------------------....hhhhhhhhhhhhhhhhhhhhhh.-----.hhhhhhhhhhhhhhh......----.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3riu C  31 VQQFRIYSNELImKHDRHERIVKLSRDITIESKRIIFLLHSI-----NKEKVLEEARQRLNKLIAVNFRAVALEL----VYQFRSSYSPGLQEFIEAYTYmEYLCHE-------TKSVSDWQAIQAVmQYVE----------------------------FFVDPTEYILGLSDLTGELmRRCINSL-----DTCLDTCKALQHFYSGYISLNC----ELWRKITTmKQSVLKAENVCYNVKV 273
                                    40  |     50        60        70 |     |80        90       100    |  110       120       130|     |  -    |  150       160 |       -         -         -|      200       210      |  -  |    230       240   |   250      |260       270   
                                       43-MSE                       72    78                        105  110                  131-MSE37     145          158-MSE                          191                210-MSE217   223                  244  249     257-MSE
   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 3RIU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Translin] (5)

(-) Gene Ontology  (10, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7JVK6_DROME | Q7JVK6)
molecular function
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
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:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0007630    jump response    The sudden, usually upward, movement off the ground or other surface through sudden muscular effort in the legs, following exposure to an external stimulus.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

Chain C   (Q9VF77_DROME | Q9VF77)
molecular function
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/TrEMBL
        Q7JVK6_DROME | Q7JVK6: 2qrx 2qva 3axj 4dg7
        Q9VF77_DROME | Q9VF77: 3axj

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