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(-) Description

Title :  STRUCTURE OF THERMUS THERMOPHILUS ARGONAUTE BOUND TO GUIDE DNA AND 15-MER TARGET DNA
 
Authors :  G. Sheng, H. Zhao, J. Wang, Y. Rao, Y. Wang
Date :  08 Oct 13  (Deposition) - 15 Jan 14  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
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, 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*T*GP*TP*AP*TP *AP*GP*T)-3'
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(P*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - 5'-D(*AP*AP*CP*CP*TP*AP*CP*TP*GP*CP*CP*TP*CP*G)-3'
    Chains: 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  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1MG3Ligand/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  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:478 , ALA B:479 , ASP B:660 , HOH B:808 , DT F:6BINDING SITE FOR RESIDUE MG B 701
2AC2SOFTWAREVAL A:685 , HOH A:735 , DT C:1 , DA C:3 , HOH C:205BINDING SITE FOR RESIDUE MG C 101
3AC3SOFTWAREVAL B:685 , DT E:1 , DA E:3 , HOH E:203BINDING SITE FOR RESIDUE MG E 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N41)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Asp A:34 -Pro A:35
2Gly A:142 -Pro A:143
3Val A:437 -Pro A:438
4Asp B:34 -Pro B:35
5Gly B:142 -Pro B:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N41)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N41)

(-) Exons   (0, 0)

(no "Exon" information available for 4N41)

(-) 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:658
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.hhhhhh.eeeeee....hhhhhhhhhh..eeee..eeee..hhhhh...............eeeeeee......hhhhhhhhhhhhhhhhhhhhhh....eee..eeeeeeeee...eeeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhhh.......eeee.....eeeeeeee.......hhhhhh........eeeee.......eeeee...eee...............hhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....ee......hhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhh.....ee.......eeeeee...........eeeeee....eeee.........hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh..eeeeeeee......eee........eeee....eeeee...hhhhh....eeeeeee...hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n41 A   5 GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELLDYHASKQGREGGRVAWVADPKDPRKPIPHLTGLLVPVLTLEDLHEELALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV 685
                                    14        24        34||      52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212 ||    230|      243       253       263       273|      286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496|      507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677        
                                                         35|                                                                                                                                                                       214|    230|                                    273|                                                                                                                                                                                                                        496|                                                                                                                                                                                           
                                                          44                                                                                                                                                                        223     234                                     277                                                                                                                                                                                                                         498                                                                                                                                                                                           


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......hhhhhhhhhhhhhh..eeee..eeee..hhhhh..eeeeee..eeeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh....eee..eeeeeeeee...eeeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhhhh......eeee.....eeeeeeee.............hhhhhhhh...........eeeeee..eeeeeeeee...eeee.............hhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....ee......hhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhh.....ee.......eeeeee.....hhhhh.eeeee..eee.........hhhhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhh..eeeeeeee......eee........eeee....eeeee............eeeeeee...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n41 B   5 GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKDPRKPIPHLTGLLVPVLTLEDLHSLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIVDREKLFFV 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      |278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488     ||503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       678       
                                                                                                                                                                                                                                                                                                    271|                                                                                                                                                                                                                       494|                                                                                                                                                                        671|        
                                                                                                                                                                                                                                                                                                     276                                                                                                                                                                                                                        500                                                                                                                                                                         677        


Chain C from PDB  Type:DNA  Length:15
                                               
                 4n41 C   1 TGAGGTAGTAGGTGT  21
                                    10  || 
                                       13| 
                                        20 


Chain D from PDB  Type:DNA  Length:13
                                             
                 4n41 D   3 ACCTACTACCTCG  15
                                    12   


Chain E from PDB  Type:DNA  Length:16
                                                
                 4n41 E   1 TGAGGTAGTAGGTTGT  21
                                    10   || 
                                        14| 
                                         20 


Chain F from PDB  Type:DNA  Length:14
                                              
                 4n41 F   2 AACCTACTACCTCG  15
                                    11
   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 4N41)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N41)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N41)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:34 - Pro A:35   [ RasMol ]  
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    Val A:437 - Pro A:438   [ RasMol ]  
 
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  4n41
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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 4n47 4n76 4nca 4ncb

(-) Related Entries Specified in the PDB File

3dlh 3hm9 3hvr 4n47 4n76 4nca 4ncb