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(-) Description

Title :  STRUCTURE OF THE ARGONAUTE PROTEIN FROM METHANOCALDCOCCUS JANASCHII IN COMPLEX WITH GUIDE DNA
 
Authors :  S. Schneider, C. A. Oellig, R. Keegan, D. Grohmann, A. Zander, S. Willko
Date :  03 Jun 16  (Deposition) - 08 Feb 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Hydrolase-Dna Complex, Argonaute, Bacterial Defense (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Willkomm, C. A. Oellig, A. Zander, T. Restle, R. Keegan, D. Grohmann S. Schneider
Structural And Mechanistic Insights Into An Archaeal Dna-Guided Argonaute Protein.
Nat Microbiol V. 2 17035 2017
PubMed-ID: 28319084  |  Reference-DOI: 10.1038/NMICROBIOL.2017.35

(-) Compounds

Molecule 1 - ARGONAUTE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
 
Molecule 2 - GUIDE DNA
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2SO47Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:457 , GLN A:479 , LYS A:483 , DT D:1 , DA D:3BINDING SITE FOR RESIDUE MG A 1714
2AC2SOFTWAREASP A:504 , THR A:505 , ARG A:569 , ASP A:570 , GLY A:571BINDING SITE FOR RESIDUE SO4 A 1715
3AC3SOFTWAREHIS A:145 , PHE A:616 , GLY A:617 , ASN A:618 , LYS A:651BINDING SITE FOR RESIDUE SO4 A 1716
4AC4SOFTWARELYS A:163 , THR A:607 , SER A:608BINDING SITE FOR RESIDUE SO4 A 1717
5AC5SOFTWAREGLU A:18 , PHE A:19 , HIS A:110 , ARG A:293BINDING SITE FOR RESIDUE SO4 A 1718
6AC6SOFTWAREASP A:296 , ASN A:297 , THR A:298BINDING SITE FOR RESIDUE SO4 A 1719
7AC7SOFTWAREHIS A:126 , LYS A:133 , LYS A:187BINDING SITE FOR RESIDUE SO4 A 1720
8AC8SOFTWAREGLU A:349 , LYS A:487 , ARG A:529 , HIS A:707BINDING SITE FOR RESIDUE SO4 A 1721

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5G5T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5G5T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5G5T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G5T)

(-) Exons   (0, 0)

(no "Exon" information available for 5G5T)

(-) 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:670
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.eee.hhhhh..eeeeeee..........eee.....eeee.......ee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eee..eeeeeeeeeeeee....eeeeeeeeeeeee..hhhhhh..hhhhhhhhh..eeee..eeeeeeeeeeee..hhhhhhhhhhhhhhh...hhhhhhhhh........eeee.....ee....eee..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......eeeeeee.....eeee.....eeee.hhhhh...................eeeeeeeee.hhh.hhhhhhhhhhhhhhhhhhhhh.....eee....eeee.....hhhhhhhhh......eeeeeee..hhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.....ee.......eeeeeee....eeeeeeee.....eeeeeeee.....hhhhhhhhhhhh........eeeeee.......hhhhhhhhhhhhh.eeeeeeee.............eeeee..eeeee..........eeeeeeeeee...eeee...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhh....hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g5t A   1 MVLNKVTYKINAYKIKEEFIPKEVHFYRIKSRFVNFYGGMIINKKDKSFVLPYKVDNKVLKPIDIEYIKSLKLEYVKPEIAEKLVRGYLKSVHKIEPELSRIIKNIRKHKVVENIKVESYCEYEVKKHDGDYYLILNFRHTASITKHLWDFVNRDKALLEEYVGKKIIFKPNPKVRYTISLVDAPNPQKIEEIMSHIIKYYKWSEDMVKSTFGEIDYNQPIMYCEEILEPFAPQFCNLVFYMDELDSYILKELQSYWRLSNENKGKIINEIAKKLRFIDNTPKELEFMKFNNTPLLVKDVNKNPTKIYSTNTLFTWIKIYLPYDVPEIIRNKNLLTYILIDEEIKDELKAIKDKVNKMFRNYNKIANKTELPKFNYANRWKYFSTDDIRGIIKEIKSEFNDEICFALIIGKEYEILKKQLFDLKIISQNILWENWRKDDKGYMTNNLLIQIMGKLGIKYFILDSKTPYDYIMGLDTGNHRVGGCTVVYDSEGKIRRIQPIETPERLHLPYVIEYLENKANIDMENKNILFLRDGFIQNSERNDLKEISKELNSNIEVISIRKNNKYKVFTSDYRIGSVFGNDGIFLPHKTPFGSNPVKLSTWLRFNCGNEEGLKINESIMQLLYDLTKMNYSAYLRIPAPIHYADKFVKALGKNWKIDEELLKHGFLYFI 713
                                    10        20        30||      49        59        69||      87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327      |342       352       362       372       382       392       402       412       422       432 ||    449       459       469       479       489       499      |514       524       534  ||   547       557       567       577       587       597       607       617       627       637       647       657       667  ||   683       693       703       713
                                                         31|                           70|                                                                                                                                                                                                                                                            334|                                                                                           434|                                                             506|                      537|                                                                                                                              670|                                    
                                                          41                            79                                                                                                                                                                                                                                                             340                                                                                            442                                                              512                       541                                                                                                                               677                                    


Chain D from PDB  Type:DNA  Length:11
                                           
                 5g5t D   1 TGAGGTAGAGT  21
                                   |20 
                                   8|  
                                   19
   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 5G5T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G5T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G5T)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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  Y1321_METJA | Q58717
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 Related Entries

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UniProtKB/Swiss-Prot
        Y1321_METJA | Q58717: 5g5s

(-) Related Entries Specified in the PDB File

5g5s STRUCTURE OF THE ARGONAUTE PROTEIN FROM METHANOCALDCOCCUS JANASCHII