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(-) Description

Title :  CRYSTAL STRUCTURE OF T. THERMOPHILUS ARGONAUTE N478 MUTANT PROTEIN COMPLEXED WITH DNA GUIDE STRAND AND 19-NT RNA TARGET STRAND
 
Authors :  Y. Wang, H. Li, G. Sheng, D. J. Patel
Date :  22 May 09  (Deposition) - 06 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (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, G. S. Wardle, T. Tuschl, D. J. Patel
Nucleation, Propagation And Cleavage Of Target Rnas In Ago Silencing Complexes.
Nature V. 461 754 2009
PubMed-ID: 19812667  |  Reference-DOI: 10.1038/NATURE08434

(-) Compounds

Molecule 1 - ARGONAUTE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO
    Expression System Strain: ROSETTA 2 (DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TT_P0026
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27
 
Molecule 2 - 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T P*AP*GP*T)-3'
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP *G)-3'
    Chains: F, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:433 , LYS A:457 , VAL A:685 , DT C:1 , DA C:3BINDING SITE FOR RESIDUE MG C 22
2AC2SOFTWAREASN A:478 , ALA A:479 , ASP A:546 , C D:9 , U D:10BINDING SITE FOR RESIDUE MG A 686
3AC3SOFTWARELYS B:457 , VAL B:685 , DT E:1 , DA E:3BINDING SITE FOR RESIDUE MG E 22
4AC4SOFTWAREASN B:478 , ALA B:479 , ASP B:546 , C F:9 , U F:10BINDING SITE FOR RESIDUE MG B 686

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HK2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HK2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HK2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HK2)

(-) Exons   (0, 0)

(no "Exon" information available for 3HK2)

(-) 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:664
 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 ..eeeeeeeeeeeee........eeee..........hhhhhhhhhhhhhh..eeee..eeee..hhhhh.....eee..eee....eeeee........hhhhhhhhhhhhhhhhhhhh.........ee..........eeee..eeeeee.....eeeeeeee..eeee....hhhhhh......eeee.....ee................---hhhhhhhh..............ee.......ee......eeee....------------.hhhhhhhhhhhhhhhhhhh......eeeeeeeee....eee......hhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhh....eee......eeeeeee......eeeeeeeee.....eeee...eee.....hhhhhhhhhhhhhhhhhhhh.....eeeeee........hhhhhhhhhhh..eeeeeeee......eee........eeee....eeeee...---......eeeeeee...hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hk2 A   4 LGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPLP---SLLDYHASKGRLQGREGGRVAWVADPKDPRKPIPHLTGLLVPVLTLE------------LPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFNAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVH---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       513       523       533       543       553       563       573       583       593       603   |   613       623       633       643       653       663       673       683  
                                                                                                                                                                                                                                                218 222                                           268          281                                                                                                                                                                                                                                                                                                                                   607 611                                                                          


Chain B from PDB  Type:PROTEIN  Length:666
 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 ..eeeeeeeeeeeee........eeee..........hhhhhhhhhhhhhh..eeee..eeee..hhhhh.....eee..eee....eeeee......hhhhhhhhhhhhhhhhhhhhhh.........ee..........eeee..eeeeee.....eeeeeeee..eeee....hhhhhh......eeee.....ee................---hhhhhhhh..............ee.......ee......eeee....-----------..hhhhhhhhhhhhhhhhhhh......eeeeeeeee....eee......hhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhh....eee......eeeeeee......eeeeeeeee.....eeee...eee.....hhhhhhhhhhhhhhhhhhhh.....eeeeee........hhhhhhhhhhh..eeeeeeee......eee........eeee....eeeee....--......eeeeeee...hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hk2 B   4 LGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPLP---SLLDYHASKGRLQGREGGRVAWVADPKDPRKPIPHLTGLLVPVLTLE-----------SLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFNAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHR--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       513       523       533       543       553       563       573       583       593       603    |  613       623       633       643       653       663       673       683  
                                                                                                                                                                                                                                                218 222                                           268         280                                                                                                                                                                                                                                                                                                                                     608  |                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         611                                                                          


Chain C from PDB  Type:DNA  Length:17
                                                 
                 3hk2 C   1 TGAGGTAGTAGGTTGTA  17
                                    10       


Chain D from PDB  Type:RNA  Length:15
                                               
                 3hk2 D   4 ACAACCUACUACCUC  18
                                    13     


Chain E from PDB  Type:DNA  Length:17
                                                 
                 3hk2 E   1 TGAGGTAGTAGGTTGTA  17
                                    10       


Chain F from PDB  Type:RNA  Length:15
                                               
                 3hk2 F   4 ACAACCUACUACCUC  18
                                    13
   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 3HK2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HK2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HK2)

(-) 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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  3hk2
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 Related Entries

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

UniProtKB/TrEMBL
        Q746M7_THET2 | Q746M7: 3dlb 3dlh 3f73 3hjf 3hm9 3ho1 3hvr 3hxm 4kpy 4n41 4n47 4n76 4nca 4ncb

(-) Related Entries Specified in the PDB File

3dlb WILD TYPE PROTEIN COMPLEXED WITH 10-NT DNA GUIDE STRAND
3dlh WILD TYPE PROTEIN COMPLEXED WITH SAME DNA GUIDE STRAND
3f73 WILD TYPE PROTEIN COMPLEXED WITH SAME DNA GUIDE STRAND AND 20-NT RNA TARGET WITH TWO MISMATCHES.
3hge DIFFERENT MUTANT PROTEIN COMPLEXED WITH SAME DNA GUIDE AND 20-NT RNA TAGET CONTAINING ONE NUCLEIC ACID BULGE
3hjf DIFFERENT MUTANT PROTEIN COMPLEXED WITH SAME DNA GUIDE AND 15-NT RNA GUIDE