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(-) Description

Title :  STRUCTURE OF THERMUS THERMOPHILUS ARGONAUTE BOUND TO GUIDE DNA AND CLEAVED TARGET DNA WITH MN2+
 
Authors :  G. Sheng, H. Zhao, J. Wang, Y. Rao, Y. Wang
Date :  15 Oct 13  (Deposition) - 15 Jan 14  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
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, Rna Interference, Dna Interference, Piwi, Nuclear Protein- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Sheng, H. Zhao, J. Wang, Y. Rao, W. Tian, D. C. Swarts, J. Van Der Oost, D. J. Patel, Y. Wang
Structure-Based Cleavage Mechanism Of Thermus Thermophilus Argonaute Dna Guide Strand-Mediated Dna Target Cleavage.
Proc. Natl. Acad. Sci. Usa V. 111 652 2014
PubMed-ID: 24374628  |  Reference-DOI: 10.1073/PNAS.1321032111

(-) Compounds

Molecule 1 - ARGONAUTE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO
    Expression System Strain: ROSETTA
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: ARGONAUTE, TT_P0026
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Strain: THERMOPHILUS
 
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'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
    Chains: D, F
    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  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1DT1Ligand/IonTHYMIDINE-5'-MONOPHOSPHATE
2MN4Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1DT-1Ligand/IonTHYMIDINE-5'-MONOPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1DT-1Ligand/IonTHYMIDINE-5'-MONOPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:433 , LYS B:457 , VAL B:685 , DT E:1 , DA E:3BINDING SITE FOR RESIDUE MN B 701
2AC2SOFTWAREASP B:478 , ALA B:479 , GLU B:512 , ASP B:546 , MN B:703 , DT F:10BINDING SITE FOR RESIDUE MN B 702
3AC3SOFTWAREASP B:478 , ASP B:660 , MN B:702 , DT F:10BINDING SITE FOR RESIDUE MN B 703
4AC4SOFTWAREPRO A:37 , ARG A:39 , VAL A:42 , ASN B:195 , TYR B:197 , PRO B:218 , TYR B:226 , HIS B:227 , ARG B:232 , PRO B:255 , HIS B:256BINDING SITE FOR RESIDUE DT B 704
5AC5SOFTWARELYS A:457 , VAL A:685 , DT C:1 , DA C:3 , HOH C:201BINDING SITE FOR RESIDUE MN C 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N76)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:34 -Pro A:35
2Glu A:125 -Gly A:126
3Asp B:34 -Pro B:35
4Glu B:125 -Gly B:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N76)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N76)

(-) Exons   (0, 0)

(no "Exon" information available for 4N76)

(-) 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:641
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeee........eeeeee.....hhhhhhhhhhhhhhhh...eeee..eeee..hhhhh..eeeee....eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh....eee..eeeeeeee....eeeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhhh........ee.......hhhhhhhh................ee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....ee......hhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh.....ee.......eeeeeeee.....eeeeeeeee......eee...eee.....hhhhhhhhhhhhhhhhhhhhh....eeeeeee.......hhhhhhhhhhhh.eeeeeeee......eee........eeee....eeeee...hhhhh....eeeeeeee..hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n76 A   3 HLGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNALPGGLSLLDYHASKGRLQGREGGHLTGLLVPVLTLEDSLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV 685
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192   ||  222       232      |258       268||     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 
                                                                                                                                                                                                                           196|                   239|          269|                                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                            217                    256           276                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:667
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeee........eeeeeeee......hhhhhhhhhhh...eeee..eeee..hhhhh..eeee....eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh....ee...eeeeeeeee...eeeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhhh.......eeee.....eee.....hhhhh......hhhhhhhhh..........eeee....eeee...eee..hhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....ee......hhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhh....ee.......eeeeeeee.....eeeeeeeee......eee...eee.....hhhhhhhhhhhhhhhhhhhhh....eeeeeee.......hhhhhhhhhhhh.eeeeeeee......eee........eeee....eeeee............eeeeeeee..hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n76 B   3 HLGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGRVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVARKPIPHLTGLLVPVLTLEDLSLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV 685
                                    12        22        32      ||44        54        64        74      ||86        96       106       116       126       136       146       156       166       176       186       196       206||     218       228       238      |253       263      |278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       
                                                               39|                                     81|                                                                                                                        207|                                245|                270|                                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                42                                      84                                                                                                                         210                                 251                 276                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain C from PDB  Type:DNA  Length:10
                                          
                 4n76 C   1 TGAGGTAGTA  10
                                    10


Chain D from PDB  Type:DNA  Length:10
                                          
                 4n76 D  10 TACTACCTCG  19
                                    19


Chain E from PDB  Type:DNA  Length:11
                                           
                 4n76 E   1 TGAGGTAGTAG  11
                                    10 


Chain F from PDB  Type:DNA  Length:10
                                          
                 4n76 F  10 TACTACCTCG  19
                                    19
   Legend:   → Mismatch (orange background)
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    → 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 4N76)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N76)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N76)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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  4n76
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 Related Entries

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

UniProtKB/TrEMBL
        Q746M7_THET2 | Q746M7: 3dlb 3dlh 3f73 3hjf 3hk2 3hm9 3ho1 3hvr 3hxm 4kpy 4n41 4n47 4nca 4ncb

(-) Related Entries Specified in the PDB File

4n41 4n47 4nca 4ncb