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(-) Description

Title :  STRUCTURE OF THERMUS THERMOPHILUS ARGONAUTE BOUND TO GUIDE DNA AND 12-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 :  2.82
Chains :  Asym./Biol. Unit :  A,C,D
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
    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(*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 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
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:685 , DT C:1 , DA C:3BINDING SITE FOR RESIDUE MG A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N47)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:34 -Pro A:35
2Val A:437 -Pro A:438
3Gly A:488 -Gly A:489

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N47)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N47)

(-) Exons   (0, 0)

(no "Exon" information available for 4N47)

(-) Sequences/Alignments

Asymmetric/Biological 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:666
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.hhhhhh.eeeeeeee......hhhhhhhhhhhhhh..eeee..eeee..hhhhh..eeeee....eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh....eee..eeeeeeeeee..eeeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhhh.......eeee.....eeeeeeee..hhhhh......hhhhhhhhh..........eeeee........eeee...eee.........hhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....ee.........hhhhhh......eeeeeee.......hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhh.....ee.......eeeeeee.........eeeeee...eeee......hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhh....eeeeeeee......eee........eeee....eeeee............eeeee.....hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4n47 A   5 GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKDPRKPIPHLTGLLVPVLTLEDLSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGHLLWTLPEAERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV 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    || 283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493 ||    506 ||    519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679      
                                                                                                                                                                                                                                                                                                  269|                                                                                                                                                                                                                     495|      508|                                                                                                                                                                             
                                                                                                                                                                                                                                                                                                   279                                                                                                                                                                                                                      499       512                                                                                                                                                                             


Chain C from PDB  Type:DNA  Length:14
                                              
                 4n47 C   1 TGAGGTAGTAGGGT  21
                                    10 || 
                                      12| 
                                       20 


Chain D from PDB  Type:DNA  Length:12
                                            
                 4n47 D   1 CCTACTACCTCG  12
                                    10
   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 4N47)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N47)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N47)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:34 - Pro A:35   [ RasMol ]  
    Gly A:488 - Gly A:489   [ RasMol ]  
    Val A:437 - Pro A:438   [ RasMol ]  
 

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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 4n76 4nca 4ncb

(-) Related Entries Specified in the PDB File

4n41 4n76 4nca 4ncb