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(-) 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
    ChainsA
    Organism CommonBACTERIA
    Organism ScientificAQUIFEX 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'
    ChainsG
    EngineeredYES
    Other DetailsDNA
    SyntheticYES
 
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'
    ChainsM
    EngineeredYES
    Other DetailsRNA
    SyntheticYES

 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    
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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 

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  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)
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 Related Entries

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(-) 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