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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HUMAN ARGONAUTE2 BOUND TO A DEFINED GUIDE RNA
 
Authors :  N. T. Schirle, J. Sheu-Gruttadauria, I. J. Macrae
Date :  18 Aug 14  (Deposition) - 12 Nov 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ago2, Rnase, Rnai, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. T. Schirle, J. Sheu-Gruttadauria, I. J. Macrae
Gene Regulation. Structural Basis For Microrna Targeting.
Science V. 346 608 2014
PubMed-ID: 25359968  |  Reference-DOI: 10.1126/SCIENCE.1258040

(-) Compounds

Molecule 1 - PROTEIN ARGONAUTE-2
    Chains: A
    EC Number: 3.1.26.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector: PFASTBAC HT-A
    Expression System Vector Type: BACULOVIRUS
    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 - RNA (5'- R(P*UP*UP*CP*AP*CP*AP*UP*UP*CP*AP*AP*GP*UP*CP*UP*CP*UP*U)-3')
    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  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1IPH3Ligand/IonPHENOL
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:587 , GLN A:589 , VAL A:591 , ALA A:620 , PHE A:653binding site for residue IPH A 901
2AC2SOFTWARELEU A:650 , LYS A:660 , LEU A:694 , TYR A:698binding site for residue IPH A 902
3AC3SOFTWARETYR A:174 , PHE A:200 , GLY A:201 , LEU A:382binding site for residue IPH A 903
4AC4SOFTWAREASP A:597 , VAL A:598binding site for residue MG A 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W5N)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:62 -Pro A:63
2Glu A:186 -Gly A:187
3Gln A:334 -Lys A:335
4His A:621 -Pro A:622

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W5N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W5N)

(-) Exons   (0, 0)

(no "Exon" information available for 4W5N)

(-) 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:806
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.eeeee....eeeeeeeeee....hhhhhhhhhhhhhhhh..........ee....eeee..........eeeeeee......eeeeeeeeeeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhhheee..eeee......eeee..eeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhhhhh..........hhhhhhhhhhhhh..eeee......eeeeee........eeeee.....eeeeehhhhhhhh...........eeee.......eee...eee..........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eeeeeee.....ee.......ee......................eeeee.......hhhhhhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhh.....eeeeehhhhhh.hhhhhhhhhhhhhhhh.....ee.....hhhhhh.eeeeeeeee.......eeeeeeee.......eeeeeeee........hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee......eee................eee..........eeeee...........eeeeeeee....hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.....hhhhhhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w5n A  22 AFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQKPLTDSQRVKFTKEIKGLKVEITHCKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLHQALAKAVQVHQDTLRTMYFA 859
                                    31        41        51        61        71        81        91       101       111       121       131       141       155       165       175       185       195       205       215       225       235       245|      256       266     ||279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599  ||   612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812    || 843       853      
                                                                                                                                                         149|                                                                                        245|                      272|                                                                                                                                                                                                                                                                                                                                   602|                                                                                                                                                                                                                817|                    
                                                                                                                                                          154                                                                                         247                       276                                                                                                                                                                                                                                                                                                                                    606                                                                                                                                                                                                                 839                    


Chain B from PDB  Type:DNA/RNA  Length:18
                                                  
                 4w5n B   1 UUCACAUUCAAGUCUCUU  21
                                   |13        
                                   8|         
                                   12
   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 4W5N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W5N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W5N)

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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    Glu A:186 - Gly A:187   [ RasMol ]  
    His A:621 - Pro A:622   [ RasMol ]  
    Lys A:62 - Pro A:63   [ RasMol ]  
 

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  4w5n
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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 4w5o 4w5q 4w5r 4w5t 4z4c 4z4d 4z4e 4z4f 4z4g 4z4h 4z4i 5js1 5js2 5ki6 5t7b

(-) Related Entries Specified in the PDB File

4w5o 4w5q 4w5r 4w5t