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(-) Description

Title :  HUMAN ARGONAUTE-2 BOUND TO A MODIFIED SIRNA
 
Authors :  N. T. Schirle, I. J. Macrae
Date :  07 May 16  (Deposition) - 20 Jul 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Argonaute, Sirna, Rnai, Nuclease, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. T. Schirle, G. A. Kinberger, H. F. Murray, W. F. Lima, T. P. Prakash, I. J. Macrae
Structural Analysis Of Human Argonaute-2 Bound To A Modifie Sirna Guide.
J. Am. Chem. Soc. V. 138 8694 2016
PubMed-ID: 27380263  |  Reference-DOI: 10.1021/JACS.6B04454

(-) Compounds

Molecule 1 - PROTEIN ARGONAUTE-2
    Chains: A
    EC Number: 3.1.26.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: AGO2, EIF2C2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HAGO2,ARGONAUTE RISC CATALYTIC COMPONENT 2,EUKARYOTIC TRANSLATION INITIATION FACTOR 2C 2,EIF2C 2,PAZ PIWI DOMAIN PROTEIN, PPD,PROTEIN SLICER
 
Molecule 2 - MODIFIED SIRNA
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 10)

Asymmetric/Biological Unit (8, 10)
No.NameCountTypeFull Name
16NW1OTHER2'-O-METHYL-5'-O-THIOPHOSPHONOADENOSINE
26OO1OTHER2'-O-METHYL-5'-O-THIOPHOSPHONOCYTIDINE
36OP1OTHER1-[(5E)-5,6-DIDEOXY-2-O-(2-METHOXYETHYL)-6-PHOSPHONO-BETA-D-RIBO-HEX-5-ENOFURANOSYL]-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE
4F2T1OTHER2'-DEOXY-2'-FLUORO-5'-O-THIOPHOSPHONOURIDINE
5IPH2Ligand/IonPHENOL
6MG1Ligand/IonMAGNESIUM ION
7PO41Ligand/IonPHOSPHATE ION
8UFT2OTHER2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:650 , TYR A:654 , LYS A:660 , LEU A:694 , GLU A:695 , TYR A:698binding site for residue IPH A 901
2AC2SOFTWAREPHE A:587 , GLN A:589 , PRO A:590 , VAL A:591 , ALA A:620 , PHE A:653binding site for residue IPH A 902
3AC3SOFTWAREGLY A:178 , ARG A:179binding site for residue PO4 A 903
4AC4SOFTWAREASP A:597 , VAL A:598binding site for residue MG A 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JS2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:62 -Pro A:63
2His A:621 -Pro A:622

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JS2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JS2)

(-) Exons   (0, 0)

(no "Exon" information available for 5JS2)

(-) 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:800
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.eeeee....eeeeeeeeee....hhhhhhhhhhhhhhhh..........ee....eeee..........eeeeeee..eeeeeeeeeeeeeehhhhhhhh.....hhhhhhhhhhhhhhhhhhhheee..eee..........eeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhhhh............hhhhhhhhhhhhh..eeee...eeeeee........eeeee.....eeeeehhhhhhhh...........eeee......eeee...eee..........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eeeeeee.....ee.......ee......................eeeee.......hhhhhhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhh....eeeeeehhhhhh.hhhhhhhhhhhhhhhh.....ee.....hhhhhh.eeeeeeeee......eeeeeeee.......eeeeeeee........hhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhhhhhh.....eeeeeeee......eee.hhhhh..........eee..........eeeee...........eeeeeeee....hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5js2 A  23 FKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPDRIFKVSIKWVSCVSLQALHDALSGRLVPFETIQALDVVMRHLPSMRYTPVGRSFFTASSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDDHQALAKAVQVHQDTLRTMYFA 859
                                    32        42        52        62        72        82        92       102       112       126       136       146    || 158       168       178      |191       201       211       221       231       241       251       261       271|      287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597    || 611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       839       849       859
                                                                                                                           120|                       151|                            185|                                                                               271|                                                                                                                                                                                                                                                                                                                                 602|                                                                                                                                                                                                                 819|                     
                                                                                                                            125                        154                             189                                                                                278                                                                                                                                                                                                                                                                                                                                  607                                                                                                                                                                                                                  838                     


Chain B from PDB  Type:OTHER  Length:6
                                      
                 5js2 B 901 xxxxxx 906
                            ||||||
                          901-6OP|
                           902-F2T
                            903-6NW
                             904-UFT
                              905-6OO
                               906-UFT
   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 5JS2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JS2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JS2)

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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  3.1.26.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        AGO2_HUMAN | Q9UKV8: 3luc 3lud 3lug 3luh 3luj 3luk 3qx8 3qx9 4f3t 4ola 4olb 4w5n 4w5o 4w5q 4w5r 4w5t 4z4c 4z4d 4z4e 4z4f 4z4g 4z4h 4z4i 5js1 5ki6 5t7b

(-) Related Entries Specified in the PDB File

5js1