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(-) Description

Title :  HUMAN ARGONAUTE2 BOUND TO T1-G TARGET RNA
 
Authors :  N. T. Schirle, I. J. Macrae
Date :  02 Apr 15  (Deposition) - 23 Sep 15  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,D
Keywords :  Argonaute2, Mirna, Gene Regulation-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. T. Schirle, J. Sheu-Gruttadauria, S. D. Chandradoss, C. Joo, I. J. Macrae
Water-Mediated Recognition Of T1-Adenosine Anchors Argonaute2 To Microrna Targets.
Elife V. 4 2015
PubMed-ID: 26359634  |  Reference-DOI: 10.7554/ELIFE.07646

(-) Compounds

Molecule 1 - PROTEIN ARGONAUTE-2
    ChainsA
    EC Number3.1.26.-
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF-9
    Expression System Taxid7108
    GeneAGO2, EIF2C2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHAGO2,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*UP*UP*U)-3')
    ChainsB
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - RNA (5'-R(*CP*AP*AP*UP*GP*UP*GP*AP*G)-3')
    ChainsD
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1IPA5Ligand/IonISOPROPYL ALCOHOL
2IPH4Ligand/IonPHENOL
3MG3Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:597 , VAL A:598 , HOH A:1017 , HOH A:1118 , HOH A:1286 , HOH B:227binding site for residue MG A 901
02AC2SOFTWAREARG A:688 , CYS A:691 , ILE A:692 , TYR A:698 , GLN A:699 , PRO A:700 , ASP A:771 , HOH A:1110binding site for residue IPH A 902
03AC3SOFTWARELEU A:650 , TYR A:654 , LYS A:660 , TYR A:698 , HOH A:1157binding site for residue IPH A 903
04AC4SOFTWAREPHE A:587 , GLN A:589 , PRO A:590 , VAL A:591 , ALA A:620binding site for residue IPH A 904
05AC5SOFTWAREGLY A:541 , MET A:542 , ALA A:543 , LYS A:570 , THR A:852 , THR A:855 , TYR A:857 , HOH A:1229 , HOH A:1293binding site for residue IPH A 905
06AC6SOFTWAREALA A:184 , GLU A:197 , ALA A:227 , TYR A:654 , ARG A:658 , HOH A:1457binding site for residue IPA A 906
07AC7SOFTWARETHR A:183 , PHE A:200binding site for residue IPA A 907
08AC8SOFTWARETHR A:37 , ALA A:530 , ARG A:534 , VAL A:818 , LYS A:820 , HOH A:1211 , HOH A:1410binding site for residue IPA A 908
09AC9SOFTWAREA B:13 , HOH B:218 , HOH B:219 , HOH B:220 , HOH B:222 , HOH B:239binding site for residue MG B 101
10AD1SOFTWARELYS A:525 , U B:1 , A D:2 , A D:3binding site for residue IPA B 102
11AD2SOFTWARETHR A:599 , HIS A:600 , PRO A:601 , PRO A:602 , G B:9 , C B:10binding site for residue IPA B 103
12AD3SOFTWAREU D:4 , HOH D:209 , HOH D:219 , HOH D:227 , HOH D:229 , HOH D:235binding site for residue MG D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z4D)

(-) 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 4Z4D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z4D)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z4D)

(-) 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......hhhhhhhhhhhhhhhhhhhheee..eeee.......eee..eeeeeeeeeeee.....eeeeeeeeeeeee...hhhhhhhhhhh..hhhhh....hhhhhhhhhhhhh..eee...eeeeeeeeeee....ee..eehhhhhhhhhh........eeeee......eeee.hhhee..........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eeeeeee.....ee.......ee......................eeeee.......hhhhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhh.....eeeeehhhhhh.hhhhhhhhhhhhhhhh.....ee.hhhhhhhhhh.eeeeeeeee..........eeeeeeee.......eeeeeeee........hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee......eee.hhhhh..........eee..........eeeee...........eeeeeeee....hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z4d A  22 AFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEIKRKYRVCNVTRRPASHQTFPECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEGRDHQALAKAVQVHQDTLRTMYFA 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 ||    312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       836       846       856   
                                                                                                                            120|                                                                                                                                           269|                295|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 821|                       
                                                                                                                             127                                                                                                                                            276                 305                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  836                       

Chain B from PDB  Type:RNA  Length:20
                                                    
                 4z4d B   1 UUCACAUUGCCCAAGUCUUU  21
                                    10       |21
                                            18| 
                                             20 

Chain D from PDB  Type:DNA/RNA  Length:9
                                         
                 4z4d D   1 CAAUGUGAG   9

   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 4Z4D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z4D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z4D)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        AGO2_HUMAN | Q9UKV83luc 3lud 3lug 3luh 3luj 3luk 3qx8 3qx9 4f3t 4ola 4olb 4w5n 4w5o 4w5q 4w5r 4w5t 4z4c 4z4e 4z4f 4z4g 4z4h 4z4i 5js1 5js2 5ki6 5t7b

(-) Related Entries Specified in the PDB File

4z4c 4z4e 4z4f 4z4g 4z4h 4z4i