Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THERMUS THERMOPHILUS ARGONAUTE BOUND TO GUIDE DNA AND 19-MER TARGET DNA WITH MG2+
 
Authors :  G. Sheng, H. Zhao, J. Wang, Y. Rao, Y. Wang
Date :  24 Oct 13  (Deposition) - 15 Jan 14  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B,C,D,E,F,H,P
Biol. Unit 1:  A,C,D,P  (1x)
Biol. Unit 2:  B,E,F,H  (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(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3'
    Chains: P, H
    Engineered: YES
    Fragment: SEE REMARK 999
    Synthetic: YES
 
Molecule 4 - 5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP *G)-3'
    Chains: D
    Engineered: YES
    Fragment: SEE REMARK 999
    Synthetic: YES
 
Molecule 5 - 5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3'
    Chains: F
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFHP
Biological Unit 1 (1x): A CD   P
Biological Unit 2 (1x):  B  EFH 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1DT2Ligand/IonTHYMIDINE-5'-MONOPHOSPHATE
2MG6Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1DT-1Ligand/IonTHYMIDINE-5'-MONOPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1DT-1Ligand/IonTHYMIDINE-5'-MONOPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:195 , TYR A:197 , ARG A:200 , LEU A:217 , PRO A:218 , LEU A:223 , TYR A:226 , HIS A:227 , ARG A:232 , ILE A:254 , PRO A:255 , HIS A:256 , PRO B:37 , ARG B:39BINDING SITE FOR RESIDUE DT A 701
2AC2SOFTWAREASP A:478 , ASP A:660 , DT D:10 , HOH D:201 , HOH D:202 , HOH D:203BINDING SITE FOR RESIDUE MG A 702
3AC3SOFTWAREPRO A:37 , ARG A:39 , VAL A:42 , ASN B:195 , TYR B:197 , ARG B:200 , TRP B:202 , LEU B:217 , PRO B:218 , LEU B:223 , TYR B:226 , HIS B:227 , ARG B:232 , ILE B:254 , PRO B:255 , HIS B:256BINDING SITE FOR RESIDUE DT B 701
4AC4SOFTWAREASP B:478 , ASP B:660 , MG B:703 , HOH B:802 , HOH B:958 , DT F:10BINDING SITE FOR RESIDUE MG B 702
5AC5SOFTWAREASP B:478 , ASP B:546 , MG B:702 , HOH B:803 , HOH B:804 , DT F:10 , DC H:9BINDING SITE FOR RESIDUE MG B 703
6AC6SOFTWAREVAL A:685 , HOH A:803 , DT C:1 , DA C:3 , HOH C:221BINDING SITE FOR RESIDUE MG C 101
7AC7SOFTWAREASP A:478 , ASP A:546 , HOH A:801 , HOH A:802 , DC D:9 , DT D:10 , DC P:9BINDING SITE FOR RESIDUE MG D 101
8AC8SOFTWAREVAL B:685 , DT E:1 , DA E:3 , HOH E:202 , HOH E:208BINDING SITE FOR RESIDUE MG E 101

(-) SS Bonds  (0, 0)

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

(-) 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
4Val B:437 -Pro B:438

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NCB)

(-) 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:676
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........eeeeeeee......hhhhhhhhhhhhh...eeee..eeee..hhhhh..eeeee....eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhh.....eee..eeeeeeeeee..eeeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhhhh......eeee.....eeeeee...............hhhhhhhhh..........eeeeee..eeeeeeeee...eee..hhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.............hhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhh..............eeeeeeee.....eeeeeeeee.....eeee...eee.....hhhhhhhhhhhhhhhhhhhhh....eeeeeee.......hhhhhhhhhhh..eeeeeeee......eee........eeee....eeeee............eeeeeee...hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ncb A   5 GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKDPRKPIPHLTGLLVPVLTLEDLSLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV 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     ||279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679      
                                                                                                                                                                                                                                                                                                   270|                                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                    276                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:672
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........eeeeeeee......hhhhhhhhhhhhhh..eeee..eeee.........eeeeee..eeeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh....eee..eeeeeeeeee..eeeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhhhh......eeee.....eeeeeeee.............hhhhhhhh...........eeeee..eeee...eee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....ee...ee.hhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhh.....ee.......eeeeeeee.....eeeeeeeee.hhhheeee...eee.....hhhhhhhhhhhhhhhhhhh......eeeeeee.......hhhhhhhhhhh..eeeeeeee......eee........eeee....eeeee............eeeeeee...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ncb B   5 GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPIPHLTGLLVPVLTLEDLHESLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV 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 ||    260       270 ||    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  
                                                                                                                                                                                                                                                                           246|                272|                                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                            253                 276                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain C from PDB  Type:DNA  Length:16
                                                
                 4ncb C   1 TGAGGTAGTAGGTTGT  16
                                    10      


Chain D from PDB  Type:DNA  Length:15
                                               
                 4ncb D   5 CAACCTACTACCTCG  19
                                    14     


Chain E from PDB  Type:DNA  Length:17
                                                 
                 4ncb E   1 TGAGGTAGTAGGTTGTA  17
                                    10       


Chain F from PDB  Type:DNA  Length:10
                                          
                 4ncb F  10 TACTACCTCG  19
                                    19


Chain H from PDB  Type:DNA  Length:6
                                      
                 4ncb H   4 ACAACC   9


Chain P from PDB  Type:DNA  Length:5
                                     
                 4ncb P   5 CAACC   9
   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 4NCB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    DT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:34 - Pro A:35   [ RasMol ]  
    Asp B:34 - Pro B:35   [ RasMol ]  
    Glu A:125 - Gly A:126   [ RasMol ]  
    Val B:437 - Pro B:438   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ncb
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q746M7_THET2 | Q746M7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q746M7_THET2 | Q746M7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4n76 4nca

(-) Related Entries Specified in the PDB File

4n41 4n47 4n76 4nca