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(-) Description

Title :  HUMAN ARGONAUTE-2 BOUND TO A GUIDE RNA WITH A NUCLEOBASE MODIFICATION AT POSITION 1
 
Authors :  N. T. Schirle, I. J. Macrae
Date :  16 Jun 16  (Deposition) - 20 Jul 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Argonaute, Mirna, Rnai, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Suter, J. Sheu-Gruttadauria, N. T. Schirle, R. Valenzuela, A. A. Ball-Jones, K. Onizuka, I. J. Macrae, P. A. Beal
Structure-Guided Control Of Sirna Off-Target Effects.
J. Am. Chem. Soc. V. 138 8667 2016
PubMed-ID: 27387838  |  Reference-DOI: 10.1021/JACS.6B06137

(-) Compounds

Molecule 1 - PROTEIN ARGONAUTE-2
    Chains: A
    EC Number: 3.1.26.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: AGO2, EIF2C2
    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 - MIR-122
    Chains: B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
16U01Mod. Nucleotide[(2~{R},3~{S},4~{R},5~{S})-3,4-BIS(OXIDANYL)-5-[1-[(2-PHENYL-1~{H}-IMIDAZOL-5-YL)METHYL]-1,2,3-TRIAZOL-4-YL]OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE
2IPH3Ligand/IonPHENOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:650 , LYS A:660 , LEU A:694 , TYR A:698 , HOH A:1057binding 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
3AC3SOFTWAREARG A:688 , GLN A:699 , PRO A:700binding site for residue IPH A 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KI6)

(-) 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 5KI6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KI6)

(-) Exons   (0, 0)

(no "Exon" information available for 5KI6)

(-) 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:798
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeeee.eeeee....eeeeeeeeee....hhhhhhhhhhhhhhhh..........ee....eeee..........eeeee....eeeeeeeeeeeehhhhhhhh.....hhhhhhhhhhhhhhhhhhhheee..eee.........eeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhhhhh..hhhhh....hhhhhhhhhhhhh..eeee..eeeeeeeeeee....eeeee.....eeeeehhhhhhhhhh........eeeee......eeee...eee.........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eeeeeee.....ee.......ee......................eeeee.......hhhhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhh....eeeeeehhhhhh.hhhhhhhhhhhhhhhh.....ee.hhhhhhhhhh.eeeeeeeee..........eeeeeeee.......eeeeeeee........hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee......eee.hhhhh..........eee..........eeeee...........eeeeeeee....hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ki6 A  22 AFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLRIFKVSIKWVSCVSLQALHDALSGRLVPFETIQALDVVMRHLPSMRYTPVGRSFFTASNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLHQALAKAVQVHQDTLRTMYFA 859
                                    31        41        51        61        71        81        91       101       111       127       137       147   ||  159       169       179     ||193       203       213       223       233       243       253       263      |279       289       299       309       319       329       339       349   ||  360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810      |841       851        
                                                                                                                           119|                      151|                            185|                                                                             270|                                                                         353|                                                                                                                                                                                                                                                                                                                                                                                                                                                                           817|                    
                                                                                                                            126                       154                             190                                                                              277                                                                          355                                                                                                                                                                                                                                                                                                                                                                                                                                                                            839                    


Chain B from PDB  Type:RNA  Length:10
                                          
                 5ki6 B   1 xGGAGUGUUU  21
                            |      |21
                            1-6U0  8| 
                                   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 5KI6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KI6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KI6)

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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    His A:621 - Pro A:622   [ RasMol ]  
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  AGO2_HUMAN | Q9UKV8
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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 5js2 5t7b

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5KI6)