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(-) Description

Title :  ARGONAUTE-2 - 5'-(E)-VINYLPHOSPHONATE 2'-O-METHYL-URIDINE MODIFIED MRTTR GUIDE RNA COMPLEX
 
Authors :  E. Elkayam, L. Joshua-Tor
Date :  02 Sep 16  (Deposition) - 14 Dec 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.53
Chains :  Asym./Biol. Unit :  A,R
Keywords :  Rnai, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Elkayam, L. Joshua-Tor
Protein Structure
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RNA (UVP)UAUAGAGCAAGAACACUGUU
    Chains: R
    Engineered: YES
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synthetic: YES
 
Molecule 2 - PROTEIN ARGONAUTE-2
    Chains: A
    EC Number: 3.1.26.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1IPH2Ligand/IonPHENOL
2UVP1Mod. Nucleotide1-[(5E)-5,6-DIDEOXY-2-O-METHYL-6-PHOSPHONO-BETA-D-RIBO-HEX-5-ENOFURANOSYL]-2,4-DIHYDROXYPYRIMIDIN-1-IUM

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:589 , PRO A:590 , VAL A:591 , ASP A:619 , ALA A:620 , PHE A:653binding site for residue IPH A 901
2AC2SOFTWARELEU A:650 , TYR A:654 , LYS A:660 , TYR A:698binding site for residue IPH A 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5T7B)

(-) 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 5T7B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T7B)

(-) Exons   (0, 0)

(no "Exon" information available for 5T7B)

(-) 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:802
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.eeeee....eeeeeeeeee....hhhhhhhhhhhhhhhh..........ee....eeee..........eeeee....eeeeeeeeeeeehhhhhhhhh......hhhhhhhhhhhhhhhhhhhheee..eee.....eee..eeeeeeeeeeeeee..eeeeeeeeeeeeee...hhhhhhhhhhh........hhhhhhhhhhhhh..eeee.....eeeeeeeeeee....eeeee.....eeeeehhhhhhhh..........eeeee......eeee...eee..........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eeeeeee.....ee.......ee......................eeeee.......hhhhhhhhhhhhhhhhhhh.........eeee.....hhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhh...eeeeeehhhhhh.hhhhhhhhhhhhhhhh.....ee.....hhhhhh.eeeeeeeee......eeeeeeee.......eeeeeeee........hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee......eee.hhhhh..........eee.........eeeeee...........eeeeeeee....hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t7b A  23 FKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEKPLTDSQRVKFTKEIKGLKVEITHCKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSASFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGANVTHPPKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRNGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKRDHQALAKAVQVHQDTLRTMYFA 859
                                    32        42        52        62        72        82        92       102       112       128       138       148       158       168       178      |191       201       211       221       231       241  ||   254       264       277       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       837       847       857  
                                                                                                                           120|                                                       185|                                                    244|                     272|                                                                                                                                                                                                                                                                                                                                   602|                                                                                                                                                                                                                  820|                      
                                                                                                                            127                                                        189                                                     248                      276                                                                                                                                                                                                                                                                                                                                    607                                                                                                                                                                                                                   837                      


Chain R from PDB  Type:RNA  Length:11
                                           
                 5t7b R   1 xUAUAGAGCAU  21
                            |       10|
                            1-UVP   10|
                                     21
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 5T7B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T7B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T7B)

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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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 5ki6

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5T7B)