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(-) Description

Title :  CRYSTAL STRUCTURE OF A. AEOLICUS ARGONAUTE
 
Authors :  Y. R. Yuan, Y. Pei, J. B. Ma, V. Kuryavyi, M. Zhadina, G. Meister, H. Y. Che Z. Dauter, T. Tuschl, D. J. Patel
Date :  16 Feb 05  (Deposition) - 09 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Rnase H Fold, Rna Binding Protein, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. R. Yuan, Y. Pei, J. B. Ma, V. Kuryavyi, M. Zhadina, G. Meister, H. Y. Chen, Z. Dauter, T. Tuschl, D. J. Patel
Crystal Structure Of A. Aeolicus Argonaute Provides Unique Perspectives Into The Mechanism Of Guide Strand-Mediated Mrna Cleavage
Mol. Cell V. 19 405 2005
PubMed-ID: 16061186  |  Reference-DOI: 10.1016/J.MOLCEL.2005.07.011

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN AQ_1447
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:502 , SER A:504 , ASP A:683BINDING SITE FOR RESIDUE CA A 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YVU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YVU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YVU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YVU)

(-) Exons   (0, 0)

(no "Exon" information available for 1YVU)

(-) 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:682
 aligned with O67434_AQUAE | O67434 from UniProtKB/TrEMBL  Length:706

    Alignment length:703
                                    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   
         O67434_AQUAE     4 EALLNLYRIEYRPKDTTFTVFKPTHEIQKEKLNKVRWRVFLQTGLPTFRREDEFWCAGKVEKDTLYLTLSNGEIVELKRVGEEEFRGFQNERECQELFRDFLTKTKVKDKFISDFYKKFRDKITVQGKNRKIALIPEVNEKVLKSEEGYFLLHLDLKFRIQPFETLQTLLERNDFNPKRIRVKPIGIDFVGRVQDVFKAKEKGEEFFRLCMERSTHKSSKKAWEELLKNRELREKAFLVVLEKGYTYPATILKPVLTYENLEDEERNEVADIVRMEPGKRLNLIRYILRRYVKALRDYGWYISPEEERAKGKLNFKDTVLDAKGKNTKVITNLRKFLELCRPFVKKDVLSVEIISVSVYKKLEWRKEEFLKELINFLKNKGIKLKIKGKSLILAQTREEAKEKLIPVINKIKDVDLVIVFLEEYPKVDPYKSFLLYDFVKRELLKKMIPSQVILNRTLKNENLKFVLLNVAEQVLAKTGNIPYKLKEIEGKVDAFVGIDISRITRDGKTVNAVAFTKIFNSKGELVRYYLTSYPAFGEKLTEKAIGDVFSLLEKLGFKKGSKIVVHRDGRLYRDEVAAFKKYGELYGYSLELLEIIKRNNPRFFSNEKFIKGYFYKLSEDSVILATYNQVYEGTHQPIKVRKVYGELPVEVLCSQILSLTLMNYSSFQPIKLPATVHYSDKITKLMLRGIEPIKKEGDIMYWL 706
               SCOP domains d1yvua1 A:4-314 Argonaute homologue Aq_1447                                                                                                                                                                                                                                                                            d1yvua2 A:315-706 Argonaute homologue Aq_1447                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      ----------------------------------------------------------------------------------------------     ----------------------------------------------------Piwi-1y          vuA01 A:419-694                                                                                                                                                                                                                                                    ------------ Pfam domains
         Sec.struct. author ..ee.eeeeee.....ee...ee....hhhhhhhhhhhhhhhhh..eeee..eeee.........eeee.....eeeee...ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee....eeeeeeeeeeeeee.....eeeeeeeeeeeee..hhhhhhhhh.......eeee......eeeeeeee....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhheeeee....eee...eee....------hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eee....ee..ee......ee.....ee.....hhhhhhhh.......eeeeeeeeee.-----hhhhhhhhhhhhhhhh...eeeeeeeeeee....hhhhhhhhhhhh......eeeeee.----------hhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhh.....ee........eeeee.eee.........eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhhhh.eeeeeeee......ee........eeee....eeee.............eeeeeee...hhhhhhhhhhhhhhhhh.............hhhhhhhhhhh.....eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yvu A   4 EALLNLYRIEYRPKDTTFTVFKPTHEIQKEKLNKVRWRVFLQTGLPTFRREDEFWCAGKVEKDTLYLTLSNGEIVELKRVGEEEFRGFQNERECQELFRDFLTKTKVKDKFISDFYKKFRDKITVQGKNRKIALIPEVNEKVLKSEEGYFLLHLDLKFRIQPFETLQTLLERNDFNPKRIRVKPIGIDFVGRVQDVFKAKEKGEEFFRLCmERSTHKSSKKAWEELLKNRELREKAFLVVLEKGYTYPATILKPVLTY------ERNEVADIVRmEPGKRLNLIRYILRRYVKALRDYGWYISPEEERAKGKLNFKDTVLDAKGKNTKVITNLRKFLELCRPFVKKDVLSVEIISVSV-----WRKEEFLKELINFLKNKGIKLKIKGKSLILAQTREEAKEKLIPVINKIKDVDLVIVFLE----------FLLYDFVKRELLKKmIPSQVILNRTLKNENLKFVLLNVAEQVLAKTGNIPYKLKEIEGKVDAFVGIDISRITRDGKTVNAVAFTKIFNSKGELVRYYLTSYPAFGEKLTEKAIGDVFSLLEKLGFKKGSKIVVHRDGRLYRDEVAAFKKYGELYGYSLELLEIIKRNNPRFFSNEKFIKGYFYKLSEDSVILATYNQVYEGTHQPIKVRKVYGELPVEVLCSQILSLTLmNYSSFQPIKLPATVHYSDKITKLmLRGIEPIKKEGDImYWL 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       | -    |  273    |  283       293       303       313       323       333       343       353       | -   |   373       383       393       403       413       423 |       -  |    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                                        261    268       278-MSE                                                                            361   367                                                       425        436           450-MSE                                                                                                                                                                                                                665-MSE                 689-MSE       703-MSE
   Legend:   → Mismatch (orange background)
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  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YVU)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: RNase_H (288)
(-)
Family: Piwi (16)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O67434_AQUAE | O67434)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.

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  1yvu
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 Related Entries

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

UniProtKB/TrEMBL
        O67434_AQUAE | O67434: 2f8s 2f8t 2nub

(-) Related Entries Specified in the PDB File

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