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(-) Description

Title :  ALIGNMENT OF GUIDE-TARGET SEED DUPLEX WITHIN AN ARGONAUTE SILENCING COMPLEX
 
Authors :  Y. Wang, H. Li, G. Sheng, S. Juranek, T. Tuschl, D. J. Patel
Date :  07 Nov 08  (Deposition) - 16 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,H,X,Y
Biol. Unit 1:  A,C,H  (1x)
Biol. Unit 2:  B,X,Y  (1x)
Keywords :  Argonaute, Protein-Dna-Rna-Complex, Nucleic Acid Binding Protein-Dna- Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wang, S. Juranek, H. Li, G. Sheng, T. Tuschl, D. J. Patel
Structure Of An Argonaute Silencing Complex With A Seed-Containing Guide Dna And Target Rna Duplex.
Nature V. 456 921 2008
PubMed-ID: 19092929  |  Reference-DOI: 10.1038/NATURE07666

(-) Compounds

Molecule 1 - ARGONAUTE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Gene: TT_P0026
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27
 
Molecule 2 - DNA (5'- D(P*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*D A*DTP*DAP*DGP*DT)-3')
    Chains: C, X
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - RNA (5'- R(*UP*AP*UP*AP*CP*AP*A*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3')
    Chains: H, Y
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCHXY
Biological Unit 1 (1x): A CH  
Biological Unit 2 (1x):  B  XY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:478 , ASP A:546 , ARG A:548 , ASP A:660BINDING SITE FOR RESIDUE MG A 686
2AC2SOFTWAREVAL A:685 , DT C:1 , DG C:2 , DA C:3BINDING SITE FOR RESIDUE MG C 22
3AC3SOFTWAREVAL B:685 , DT X:1 , DA X:3BINDING SITE FOR RESIDUE MG X 22

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F73)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:34 -Pro A:35
2Asp B:34 -Pro B:35

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F73)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F73)

(-) Exons   (0, 0)

(no "Exon" information available for 3F73)

(-) 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:678
 aligned with Q746M7_THET2 | Q746M7 from UniProtKB/TrEMBL  Length:685

    Alignment length:681
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684 
         Q746M7_THET2     5 GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKDPRKPIPHLTGLLVPVLTLEDLHEEEGSLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV 685
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.hhhhhh.eeeeeeee.......hhhhhhhhhhhhh..eeee..eeee.........eee........eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh....eee..eeeeee......eeeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhhh.......eeee.....eeeeeee..............hhhhhhhhh..........eeeee........eeee...eee..................hhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....ee...ee.hhhhhhhhh.......eeeeee.......hhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh....ee.......eeeeeee.........eeeeee..-....eeee........hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh..eeeeeeee......eee........eeee....eeeee....--......eeeeeee...hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f73 A   5 GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKDPRKPIPHLTGLLVPVLTLEDLHEEEGSLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGG-GGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHR--RGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV 685
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494 | |   504       514       524       534       544       554       564       574       584       594       604   |  |614       624       634       644       654       664       674       684 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     496 |                                                                                                           608  |                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       498                                                                                                              611                                                                          


Chain B from PDB  Type:PROTEIN  Length:670
 aligned with Q746M7_THET2 | Q746M7 from UniProtKB/TrEMBL  Length:685

    Alignment length:682
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683  
         Q746M7_THET2     4 LGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKDPRKPIPHLTGLLVPVLTLEDLHEEEGSLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV 685
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee........eeeeeeee......hhhhhhhhhhhhhh..eeee..eeee.........eeeeee..eeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh....eee..eeeeeeeeee..eeeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhhhh......eeee.....eeeeeee..............hhhhhhhhh...........eeee...........hhh.eee........---.......hhhhhhhhhhhhhhhhhhh......eeeeeeeee.....ee...ee.hhhhhhhhh.......eeeeee.......hhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhh.....ee..-....eeeeeee.........eeeeee..--...eeee.....---hhhhhhhhhhhhhhhhhhh-......eeeeee....hhhhhhhhhhhhhhhh.eeeeeeee......eee........eeee....eeeee....--......eeeeeee...hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f73 B   4 LGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKDPRKPIPHLTGLLVPVLTLEDLH---GSLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSG-YPAELAVGFDAGGRESFRFGGAACAVGG--GHLLWTLPEAQA---IPQEVVWDLLEETLWAFRR-AGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHR--RGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV 685
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       | - |     283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463   | | 473       483       493  |  | 503      |  -|      523        |-|      543       553       563       573       583       593       603    |  613       623       633       643       653       663       673       683  
                                                                                                                                                                                                                                                                                                     271 275                                                                                                                                                                                             467 |                        496  |        510 514               532 |                                                                       608  |                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           469                           499                                534                                                                          611                                                                          


Chain C from PDB  Type:DNA  Length:16
                                                
                 3f73 C   1 TGAGGTAGTAGGTAGT  21
                                    10 ||   
                                      12|   
                                       18   


Chain H from PDB  Type:DNA/RNA  Length:12
                                            
                 3f73 H   8 CUCACUACCUCG  19
                                    17  


Chain X from PDB  Type:DNA  Length:15
                                               
                 3f73 X   1 TGAGGTAGTAATAGT  21
                                    10|    
                                    10|    
                                     17    


Chain Y from PDB  Type:DNA/RNA  Length:11
                                           
                 3f73 Y   9 UCACUACCUCG  19
                                    18
   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 3F73)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F73)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F73)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q746M7_THET2 | Q746M7)
molecular function
    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.

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  3f73
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  Q746M7_THET2 | Q746M7
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 Related Entries

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

UniProtKB/TrEMBL
        Q746M7_THET2 | Q746M7: 3dlb 3dlh 3hjf 3hk2 3hm9 3ho1 3hvr 3hxm 4kpy 4n41 4n47 4n76 4nca 4ncb

(-) Related Entries Specified in the PDB File

3dlb SAME PROTEIN WITH DIFFERENT LIGAND
3dlh SAME PROTEIN WITH DIFFERENT LIGAND