Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Theor.Model - manually
(-)Theoretical Model
collapse expand < >
Image Theor.Model - manually
Theor.Model - manually  (Jmol Viewer)
Image Theoretical Model
Theoretical Model  (Jmol Viewer)

(-) Description

Title :  THEORETICAL MODEL OF DNA-MEDIATED RNA CLEAVAGE BY A.AEOLICUS ARGONAUTE PROTEIN.
 
Authors :  Y. R. Yuan, Y. Pei, J. B. Ma, V. Kuryavyi, M. Zhadina, G. Meister, H. Y. Cheng, Z. Dauter, T. Tuschl, D. J. Patel
Date :  20 Jul 05  (Deposition) - 13 Sep 05  (Release) - 13 Sep 05  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,G,M,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Si-Rna, Si-Dna, A. Aeolicus Argonaute, Dna-Mediated Rna Cleavage, Theoretical Model. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. R. Yuan, Y. Pei, J. B. Ma, V. Kuryavyi, M. Zhadina, G. Meister, H. Y. Cheng, Z. Dauter, T. Tuschl, D. J. Patel
Crystal Structure Of A. Aeolicus Argonaute, A Site-Specific Dna-Guided Endoribonuclease, Provides Insights Into Risc-Mediated Mrna Cleavage.
Mol. Cell V. 19 405 2005
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARGONAUTE PROTEIN
    Chains: A
    Organism Common: BACTERIA
    Organism Scientific: AQUIFEX AEOLICUS
 
Molecule 2 - 5'- D(P*AP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C P*CP*C)-3'
    Chains: G
    Engineered: YES
    Other Details: DNA
    Synthetic: YES
 
Molecule 3 - 5'- R(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G P*GP*G)-3'
    Chains: M
    Engineered: YES
    Other Details: RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
Theoretical Model : 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Theoretical Model (2, 7)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2ADS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ADS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ADS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ADS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ADS)

(-) Exons   (0, 0)

(no "Exon" information available for 2ADS)

(-) Sequences/Alignments

Theoretical Model
   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:703
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeeee.....eeeeeee....hhhhhhhhhhhhhhhhh..eeee..eeee.........eeee.....eeeee..eee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhheeee..eeeeeeeeeeeeeee.....eeeeeeeeeeeeee..hhhhhhhh.......eeee......eeeeeeee.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhheeeee....eee...eee........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...eee....ee..ee.....eee......ee....hhhhhhhh.......eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhh.......eeeeee.......hhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhh....ee........eeeeeeeeeeee..eeeeeeeeeeeee....eeeeeeeeee...hhhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhh.eeeeeee.......ee........eeee.....eee.............ee..eee...hhhhhhhhhhhhhh................hhhhhhhhhhhh....eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ads A   4 EALLNLYRIEYRPKDTTFTVFKPTHEIQKEKLNKVRWRVFLQTGLPTFRREDEFWCAGKVEKDTLYLTLSNGEIVELKRVGEEEFRGFQNERECQELFRDFLTKTKVKDKFISDFYKKFRDKITVQGKNRKIALIPEVNEKVLKSEEGYFLLHLDLKFRIQPFETLQTLLERNDFNPKRIRVKPIGIDFVGRVQDVFKAKEKGEEFFRLCmERSTHKSSKKAWEELLKNRELREKAFLVVLEKGYTYPATILKPVLTYENLEDEERNEVADIVRmEPGKRLNLIRYILRRYVKALRDYGWYISPEEERAKGKLNFKDTVLDAKGKNTKVITNLRKFLELCRPFVKKDVLSVEIISVSVYKKLEWRKEEFLKELINFLKNKGIKLKIKGKSLILAQTREEAKEKLIPVINKIKDVDLVIVFLEEYPKVDPYKSFLLYDFVKRELLKKmIPSQVILNRTLKNENLKFVLLNVAEQVLAKTGNIPYKLKEIEGKVDAFVGIDISRITRDGKTVNAVAFTKIFNSKGELVRYYLTSYPAFGEKLTEKAIGDVFSLLEKLGFKKGSKIVVHRDGRLYRDEVAAFKKYGELYGYSLELLEIIKRNNPRFFSNEKFIKGYFYKLSEDSVILATYNQVYEGTHQPIKVRKVYGELPVEVLCSQILSLTLmNYSSFQPIKLPATVHYSDKITKLmLRGIEPIKKEGDImYWL 706
                                    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     | 693       703   
                                                                                                                                                                                                                                            214-MSE                                                         278-MSE                                                                                                                                                                     450-MSE                                                                                                                                                                                                                665-MSE                 689-MSE       703-MSE


Chain G from PDB  Type:DNA  Length:21
                                                     
                 2ads G   1 ACCCCCCCCCCCCCCCCCCCC  21
                                    10        20 


Chain M from PDB  Type:RNA  Length:21
                                                     
                 2ads M   1 GGGGGGGGGGGGGGGGGGGGG  21
                                    10        20
   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 2ADS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ADS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ADS)

(-) Gene Ontology  (0, 0)

Theoretical Model(hide GO term definitions)
    (no "Gene Ontology" information available for 2ADS)

 Visualization

(-) Interactive Views

Theoretical Model
  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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2ads)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ads)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Theoretical Model 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
  2ads
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2ADS)

(-) Related Entries Specified in the PDB File

1ytu FRAGMENT OF DS-RNA BOUND WITH 5'-END TO PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS
1yvu FREE A.AEOLICUS ARGONAUTE PROTEIN
2bgg FRAGMENT OF DS-RNA BOUND WITH 5'-END TO PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS