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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HUMAN ARGONAUTE2 BOUND TO A GUIDE AND TARGET RNA CONTAINING SEED PAIRING FROM 2-8
 
Authors :  N. T. Schirle, I. J. Macrae
Date :  18 Aug 14  (Deposition) - 12 Nov 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,D
Keywords :  Ago2, Guide, Target, Rnase, Rnai, Hydrolase-Rna Complex (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*GP*CP*CP*CP*AP*AP*GP*UP*CP*U)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(*AP*AP*AP*UP*GP*UP*GP*AP*AP*A)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1IPH4Ligand/IonPHENOL
2MG3Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:597 , VAL A:598binding site for residue MG A 901
2AC2SOFTWAREARG A:688 , GLN A:699 , PRO A:700 , ILE A:702 , ASP A:771binding site for residue IPH A 902
3AC3SOFTWARELEU A:650 , TYR A:654 , LYS A:660 , TYR A:698binding site for residue IPH A 903
4AC4SOFTWAREPHE A:587 , GLN A:589 , VAL A:591 , ALA A:620binding site for residue IPH A 904
5AC5SOFTWAREASP A:537 , GLY A:541 , MET A:542 , ALA A:543 , LYS A:570 , THR A:852 , TYR A:857binding site for residue IPH A 905
6AC6SOFTWAREC B:12 , A B:13binding site for residue MG B 101
7AC7SOFTWAREU D:4binding site for residue MG D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W5Q)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Lys A:62 -Pro A:63
2Gly A:109 -Arg A:110
3Glu A:245 -Gln A:246
4His A:621 -Pro A:622
5Lys A:696 -Asp A:697

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W5Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W5Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4W5Q)

(-) 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:803
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.eeeee....eeeeeeeeee....hhhhhhhhhhhhhhhh..........ee....eeee..........eeeee....eeeeeeeeeeeehhhhhhhhh......hhhhhhhhhhhhh.hhhhhheee..eeee.......eee..eeeeeeeeeeee.....eeeeeeeeeeeee...hhhhhhhhhh.............hhhhhhhhhhhh..eee...eeeeeee........ee....eehhhhhhhh...........eeee.......eee.hhhee..........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eeeeeee.....ee.......ee......................eeeee.......hhhhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhh.....eeeeehhhhhh.hhhhhhhhhhhhhhhh.....ee.....hhhhhh.eeeeeeeee..........eeeeeeee.......eeeeeeee........hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee......eee.hhhhh..........eee..........eeeee...........eeeeeeee....hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.....hhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w5q A  22 AFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEIKRKYRVCNVTRRPASHQTFPLVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEDHQALAKAVQVHQDTLRTMYFA 859
                                    31        41        51        61        71        81        91       101       111       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267 ||    283       293  ||   310       320       330       340       350       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       820||     846       856   
                                                                                                                            120|                                                                                                                                           269|                 296|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  821|                     
                                                                                                                             127                                                                                                                                            276                  304                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   838                     


Chain B from PDB  Type:RNA  Length:18
                                                  
                 4w5q B   1 UUCACAUUGCCCAAGUCU  18
                                    10        


Chain D from PDB  Type:DNA/RNA  Length:10
                                          
                 4w5q D   1 AAAUGUGAAA  10
                                    10
   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 4W5Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W5Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W5Q)

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys A:62 - Pro A:63   [ RasMol ]  
    Lys A:696 - Asp A:697   [ RasMol ]  
 

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  4w5q
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  AGO2_HUMAN | Q9UKV8
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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 4w5r 4w5t 4z4c 4z4d 4z4e 4z4f 4z4g 4z4h 4z4i 5js1 5js2 5ki6 5t7b

(-) Related Entries Specified in the PDB File

4w5n 4w5o 4w5r 4w5t