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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF MARINITOGA PIEZOPHILA ARGONAUTE IN COMPLEX WITH 5' OH GUIDE RNA AND TARGET DNA
 
Authors :  K. W. Doxzen, J. A. Doudna
Date :  21 Feb 17  (Deposition) - 03 May 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Argonaute, Rnai, Rna, Dna, Hydrolase-Rna-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. W. Doxzen, J. A. Doudna
Dna Recognition By An Rna-Guided Bacterial Argonaute.
Plos One V. 12 77097 2017
PubMed-ID: 28520746  |  Reference-DOI: 10.1371/JOURNAL.PONE.0177097

(-) Compounds

Molecule 1 - ARGONAUTE PROTEIN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: MARINITOGA PIEZOPHILA
    Organism Taxid: 149715
 
Molecule 2 - RNA (5'- R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3')
    Chains: B, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*AP*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*CP*C)-3')
    Chains: C, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5UX0)

(-) Sites  (0, 0)

(no "Site" information available for 5UX0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UX0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:60 -Pro A:61
2Thr D:60 -Pro D:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UX0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UX0)

(-) Exons   (0, 0)

(no "Exon" information available for 5UX0)

(-) 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:632
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.eee......eeeeee.....hhhhhhhhhhhhhh...ee....eeeeee.......hhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeee...eeeeeeeeee......eeeeeeeeeeeeee..eeeeeeeeeeeeee..hhhhh.....eeee.....eeeeeehhhhh.eeee..eeee......eee..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee.....eee....eee..eee....hhhhhh......eeeeeeee.hhhhhhhhhhhhhhhhh...hhhhhhhhhh...eeee.........eee..........hhhhhh.....eeeeee......hhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhh......ee..hhhhh.eeeeeeeeee...eeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhh...eeeeeeee.............eeee....eeeee.........eeeeeeee....hhhhhhhhhhhhh.............hhhhhhhhhhhhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ux0 A   0 NAYLNLYKIDIPKKIKRLYFYNPDMEPKLFARNLSRVNNFKFQDSNDLVWIEIPDIDFQITPKNVFQYKVEKEEIIKEEEDKKLFVKTLYKYIKKLFLDNDFYFKKGNNFISNSEVFSLDSNENVNAHLTYKIKIHNISNEYYLSILPKFTFLSKEPALESAIKSGYLYNIKSGKSFPYISGLDGILKIDINNQIVEVAYPENYLFNFTTRDAEKYGFSKEVHEIYKNKVFEGFKKIPKTLGFLNKITNLNENYQLKDGYKIFINVIYKFKNGESRYAKDVFKYSFYKNEQPLKAIFFFSSKKQFFEVQKSLKELFHNKHSVFYRAAAELGFSKVEFLRDSKTKSSAFLYNPEEFTVKNTEFINQIEDNVMAIVLLDKYIGNIDPLVRNFPDNLILQPILKEKLIKPFIIKSYVYKMGNFIPECKPFILKKMEDKEKNLYIGIDLSHDRKTNLCIAAVDNTGDILYIGKHKNLEEKMNLDILEKEYIKAFEKYIEKFNVSPENVFILRAGRFIEDIEIIKNFISYNDTKYTLVEVNKNTNINSYDDLKEWIIKLDENTYIYYPKTFLNQKGVEVKILENNTDYTIEEIIEQIYLLTRVAHSTPYTNYKLPYPLHIANKVALTDYEWKLYIPY 639
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189||     200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400   ||  412       422       432       442       455       465       475   ||  487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637  
                                                                                                                                                                                                                        190|                                                                                                                                                                                                                 404|                                        450|                      479|                                                                                                                                                             
                                                                                                                                                                                                                         192                                                                                                                                                                                                                  407                                         454                       482                                                                                                                                                             


Chain B from PDB  Type:RNA  Length:20
                                                    
                 5ux0 B   1 GGUACAACCUACUACCUCAU  20
                                    10        20


Chain C from PDB  Type:DNA  Length:20
                                                    
                 5ux0 C   2 ATGAGGTAGTAGGTTGTACC  21
                                    11        21


Chain D from PDB  Type:PROTEIN  Length:639
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.....eeeeeee.....hhhhhhhhhhhhhh...ee....eeeeee.......hhhhhh.eeeeeeeee...hhhhhhhhhhhhhhhhhhhh.eeee...eeeeeeeeee......eeeeeeeeeeeeee..eeeeeeeeeeeeee............eeee.....eeeeeehhhhh.eeeehhheeee..hhh.eee..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eee....eee..eee....hhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhh...hhhhhhhhhh....eee.........eee..........hhhhhh.....eeeeee......hhhhhhhh....eeeeeehhhhhh.hhhhhhhhhhhhhhhh......ee.hhhhhh.eeeeeeeeee.....eeeeeeeee.....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhh.eeeeeeee.............eeee....eeeee.........eeeeeeee....hhhhhhhhhhhhh.............hhhhhhhhhhhhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ux0 D   1 AYLNLYKIDIPKKIKRLYFYNPDMEPKLFARNLSRVNNFKFQDSNDLVWIEIPDIDFQITPKNVFQYKVEKEEIIKEEEDKKLFVKTLYKYIKKLFLDNDFYFKKGNNFISNSEVFSLDSNENVNAHLTYKIKIHNISNEYYLSILPKFTFLSKEPALESAIKSGYLYNIKSGKSFPYISGLDGILKIDIGNNQIVEVAYPENYLFNFTTRDAEKYGFSKEVHEIYKNKVFEGFKKIPKTLGFLNKITNLNENYQLKDGYKIFINVIYKFKNGESRYAKDVFKYSFYKNEQPLKAIFFFSSKKQFFEVQKSLKELFHNKHSVFYRAAAELGFSKVEFLRDSKTKSSAFLYNPEEFTVKNTEFINQIEDNVMAIVLLDKYIGNIDPLVRNFPDNLILQPILKEKLEDIKPFIIKSYVYKMGNFIPECKPFILKKMEDKEKNLYIGIDLSHDTYARKTNLCIAAVDNTGDILYIGKHKNLELNEKMNLDILEKEYIKAFEKYIEKFNVSPENVFILRAGRFIEDIEIIKNFISYNDTKYTLVEVNKNTNINSYDDLKEWIIKLDENTYIYYPKTFLNQKGVEVKILENNTDYTIEEIIEQIYLLTRVAHSTPYTNYKLPYPLHIANKVALTDYEWKLYIPY 639
                                    10        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       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630         


Chain E from PDB  Type:RNA  Length:18
                                                  
                 5ux0 E   1 GGUACAACCUACUACCUC  18
                                    10        


Chain F from PDB  Type:DNA  Length:16
                                                
                 5ux0 F   6 GGTAGTAGGTTGTACC  21
                                    15
   Legend:   → Mismatch (orange background)
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  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 5UX0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UX0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UX0)

(-) Gene Ontology  (1, 1)

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