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(-) Description

Title :  THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS.
 
Authors :  J. S. Parker, S. M. Roe, D. Barford
Date :  13 Oct 04  (Deposition) - 13 Jan 05  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Argonaute, Piwi Domain, Rnai, Risc, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Parker, S. M. Roe, D. Barford
Crystal Structure Of A Piwi Protein Suggests Mechanisms For Sirna Recognition And Slicer Activity
Embo J. V. 23 4727 2004
PubMed-ID: 15565169  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600488

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN AF1318
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-17B
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: PIWI

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION
2CL4Ligand/IonCHLORIDE ION
3NI5Ligand/IonNICKEL (II) ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:159 , LEU A:427 , CL A:1435 , CL A:1436 , HOH A:2080BINDING SITE FOR RESIDUE CD A1428
02AC2SOFTWAREGLN A:99 , SER A:357 , GLU A:358 , CL A:1437 , CL A:1438BINDING SITE FOR RESIDUE CD A1429
03AC3SOFTWAREASP A:73 , ASP A:245 , HOH A:2037 , HOH A:2146BINDING SITE FOR RESIDUE NI A1430
04AC4SOFTWAREHIS A:79 , GLU A:247 , ASP A:284 , HOH A:2043BINDING SITE FOR RESIDUE NI A1431
05AC5SOFTWAREHIS A:291 , GLU A:349 , HOH A:2168 , HOH A:2189 , HOH A:2190BINDING SITE FOR RESIDUE NI A1432
06AC6SOFTWAREHIS A:365 , ASP A:369 , HOH A:2177 , HOH A:2205BINDING SITE FOR RESIDUE NI A1433
07AC7SOFTWAREASP A:105 , HOH A:2056 , HOH A:2140BINDING SITE FOR RESIDUE NI A1434
08AC8SOFTWAREGLN A:159 , ARG A:380 , CD A:1428BINDING SITE FOR RESIDUE CL A1435
09AC9SOFTWARELYS A:127 , GLN A:137 , PHE A:138 , LYS A:163 , CD A:1428BINDING SITE FOR RESIDUE CL A1436
10BC1SOFTWAREGLN A:99 , SER A:357 , CD A:1429 , CL A:1438BINDING SITE FOR RESIDUE CL A1437
11BC2SOFTWAREPHE A:86 , ASN A:102 , GLU A:358 , CD A:1429 , CL A:1437BINDING SITE FOR RESIDUE CL A1438

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W9H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W9H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W9H)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIWIPS50822 Piwi domain profile.PIWI_ARCFU110-406  1A:110-406

(-) Exons   (0, 0)

(no "Exon" information available for 1W9H)

(-) 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:398
 aligned with PIWI_ARCFU | O28951 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:417
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       
           PIWI_ARCFU    11 LTYRIGNGASVPISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQFSSLINQLKSQISSKIDEVWHIHNINISEFIYDSPHFDSIKSQVDNAIDTGVDGIMLVLPEYNTPLYYKLKSYLINSIPSQFMRYDILSNRNLTFYVDNLLVQFVSKLGGKPWILNVDPEKGSDIIIGTGATRIDNVNLFCFAMVFKKDGTMLWNEISPIVTSSEYLTYLKSTIKKVVYGFKKSNPDWDVEKLTLHVSGKRPKMKDGETKILKETVEELKKQEMVSRDVKYAILHLNETHPFWVMGDPNNRFHPYEGTKVKLSSKRYLLTLLQPYLKRNGLEMVTPIKPLSVEIVSDNWTSEEYYHNVHEILDEIYYLSKMNWRGFRSRNLPVTVNYPKLVAGIIANVNRYGGYPINPEGNRSLQTNPWFL 427
               SCOP domains ----------------------------------------------------------------------------------d1w9ha1 A:93-408 Hypothetical protein AF1318                                                                                                                                                                                                                                                                                ------------------- SCOP domains
               CATH domains 1w9hA01 A:11-172  [code=3.40.50.2300, no name defined]                                                                                                            1w9hA02 A:173-427  [code=3.30.420.10, no name defined]                                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------Piwi-1w9hA01 A:110-406                                                                                                                                                                                                                                                                                   --------------------- Pfam domains
         Sec.struct. author .eee.hhh.eee..hhhhhhhhhhhhh..........eeeeee...hhhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh...eeeee...-----hhhhhhhhhhhhhhhh.....ee..hhhhh..eeeeeeeee....eeeeeeeeee....eeeeee...ee..hhhhhhhhhhhhhhhhhhhhh......eeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeeeeeee...eee.-------......eee....eeee.......-------.eee..eeeeeeee.....hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh........hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------PIWI  PDB: A:110-406 UniProt: 110-406                                                                                                                                                                                                                                                                    --------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w9h A  11 LTYRIGNGASVPISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQFSSLINQLKSQISSKIDEVWHIHNINISEFIYDSPHFDSIKSQVDNAIDTGVDGIMLVLPEYNTPLYYKLKSYLINSIPSQFMRYDI-----LTFYVDNLLVQFVSKLGGKPWILNVDPEKGSDIIIGTGATRIDNVNLFCFAMVFKKDGTMLWNEISPIVTSSEYLTYLKSTIKKVVYGFKKSNPDWDVEKLTLHVSGKRPKMKDGETKILKETVEELKKQEMVSRDVKYAILHLNETHPFWVM-------HPYEGTKVKLSSKRYLLTLLQPYL-------VTPIKPLSVEIVSDNWTSEEYYHNVHEILDEIYYLSKMNWRGFRSRNLPVTVNYPKLVAGIIANVNRYGGYPINPEGNRSLQTNPWFL 427
                                    20        30        40        50        60        70        80        90       100       110       120       130       140  |    150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300|      310       320       330 |     340       350       360       370       380       390       400       410       420       
                                                                                                                                                              143   149                                                                                                                                                     301     309                    332     340
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PIWI_ARCFU | O28951)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
cellular component
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.

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  1w9h
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 Related Entries

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

UniProtKB/Swiss-Prot
        PIWI_ARCFU | O28951: 1ytu 2bgg 2w42

(-) Related Entries Specified in the PDB File

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