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(-) Description

Title :  CRYSTAL STRUCTURE OF SILKWORM PIWI-CLADE ARGONAUTE SIWI BOUND TO PIRNA
 
Authors :  N. Matsumoto, H. Nishimasu, R. Ishitani, O. Nureki
Date :  29 Aug 16  (Deposition) - 19 Oct 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nuclease, Rnaseh, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Matsumoto, H. Nishimasu, K. Sakakibara, K. M. Nishida, T. Hirano, R. Ishitani, H. Siomi, M. C. Siomi, O. Nureki
Crystal Structure Of Silkworm Piwi-Clade Argonaute Siwi Bound To Pirna
Cell V. 167 484 2016
PubMed-ID: 27693359  |  Reference-DOI: 10.1016/J.CELL.2016.09.002

(-) Compounds

Molecule 1 - PIWI
    Chains: A
    Organism Common: SILK MOTH
    Organism Scientific: BOMBYX MORI
    Organism Taxid: 7091
    Other Details: THE N-TERMINAL REGION (RESIDUES 1-129) WAS TRUNCATED BY THERMOLYSIN TREATMENT.
    Synonym: PIWI,SIWI,UNCHARACTERIZED PROTEIN
 
Molecule 2 - RNA (28-MER)
    Chains: B
    Organism Scientific: BOMBYX MORI
    Organism Taxid: 7091
    Other Details: THE BOUND RNAS ARE CO-PURIFIED ENDOGENOUS PIRNAS, WHICH HAVE DIVERGENT SEQUENCES AND LENGTHS.

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2OMU1Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:645 , LEU A:899 , HOH A:1027 , U B:1 , U B:3binding site for residue MG A 901
2AC2SOFTWAREASP A:740 , LYS A:780binding site for residue MG A 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GUH)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:213 -Pro A:214

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GUH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GUH)

(-) Exons   (0, 0)

(no "Exon" information available for 5GUH)

(-) 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:759
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeeee.eeeeee.....eeeeeeee.....hhhhhhhhhhhhhhhhh.eee...eeee.........eeee........eeeeeeeeeee...hhhhhhhhhhhhhhhhhhh..eee..eee.hhhheeehhh.eeeeeeeeeeeee....eeeeeeeeeeeeeeeehhhhhhhhhhhh.hhhhhhh..eeee....eeee..eee......eeee..eeeehhhhhhhhh..........eeeeee..........eeeeehhh.eeee..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeeeeee....eee.hhh.eee.......hhhhhh............eeeeee..hhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh.....eeeeehhhhh..hhhhhhhhhhhhhhhhh.............eeeeeeeeee.......eeeeeeee.......eeeeeeee.hhhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee......eeeee..eee.....eee..........eeee............eeeeeeee....hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh.....hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5guh A 130 ISILRTRPEAVTSKKGTSGTPLDLLANYFTVETTPKWGLYQYHVDISPEEDSTGVRKALMRVHSKTLGGYLFDGTVLYTVNRLHPDPMELYSDRKTDNERMRILIKLTCEVSPGDYHYIQIFNIIIRKCFNLLKLQLMGRDYFDPEAKIDIPEFKLQIWPGYKTTINQYEDRLLLVTEIAHKVLRMDTVLQMLSEYAATKKIFLEDVVGKIVMTDYNKRTYRVDDVANVSPKSTFKMRDENITYIEYYYKKYNLRIQDPGQPLLISRSKPREIRAGLPELIYLVPELCRQTGLSDEMRANFKLMRSLDVHTKIGPDKRIEKLNNFNRRFTSTPEVVEELATWSLKLSKELVKIKGRQLPPENIIQANNVKYPAGDTTEGWTRDMRSKHLLAIAQLNSWVVITPERQRRDTESFIDLIIKTGGGVGFRMRSPDLVVIRHDGPIEYANMCEEVIARKNPALILCVLARNYADRYEAIKKKCTVDRAVPTQVVCARNMSSKSAMSIATKVAIQINCKLGGSPWTVDIPLPSLMVVGYDVCHDTRSKEKSFGAFVATLDKQMTQYYSIVNAHLSSHMGFNIASAVKKFREKNGTYPARIFIYRDGVGDGQIPYVHSHEVAEIKKKLAEIYAGVEIKLAFIIVSKRINTRIFVQRGRSGENPRPGTVIDDVVTLPERYDFYLVSQNVREGTIAPTSYNVIEDTTGLNPDRIQRLTYKLTHLYFNCSSQVRVPSVCQYAHKLAFLAANSLHNQPHYSLNETLYFL 899
                                   139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329|      344       354      |365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890         
                                                                                                                                                                                                                                 329|                       361|                                                                                                                                                                                                                                                                                                                                                 703|                                                                                                                                                                                              
                                                                                                                                                                                                                                  335                        363                                                                                                                                                                                                                                                                                                                                                  709                                                                                                                                                                                              


Chain B from PDB  Type:RNA  Length:8
                                        
                 5guh B   1 UAUUUUUx  28
                                || |
                                5| |
                                26 |
                                  28-OMU
   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 5GUH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GUH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GUH)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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