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(-) Description

Title :  HUMAN ARGONAUTE2 BOUND TO T1-U 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 :  1.80
Chains :  Asym./Biol. Unit :  A,B,D
Keywords :  Argonaute2, 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
    Chains: A
    EC Number: 3.1.26.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF-9
    Expression System Taxid: 7108
    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*UP*U)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(*CP*AP*AP*UP*GP*UP*GP*AP*U)-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  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1IPA2Ligand/IonISOPROPYL ALCOHOL
2IPH4Ligand/IonPHENOL
3MG3Ligand/IonMAGNESIUM ION
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:597 , VAL A:598 , HOH A:1047 , HOH A:1080 , HOH A:1243 , HOH B:229binding site for residue MG A 901
2AC2SOFTWAREALA A:184 , GLU A:197 , ALA A:227 , ALA A:348 , TYR A:654 , ARG A:658binding site for residue IPA A 902
3AC3SOFTWAREPRO A:580 , GLN A:581 , ARG A:583 , PRO A:584binding site for residue IPA A 903
4AC4SOFTWAREARG A:688 , CYS A:691 , ILE A:692 , TYR A:698 , GLN A:699 , PRO A:700 , ASP A:771 , HOH A:1107 , HOH A:1352binding site for residue IPH A 904
5AC5SOFTWARELEU A:650 , TYR A:654 , LYS A:660 , TYR A:698 , HOH A:1071binding site for residue IPH A 905
6AC6SOFTWAREPHE A:587 , GLN A:589 , PRO A:590 , VAL A:591 , ALA A:620 , PHE A:653binding site for residue IPH A 906
7AC7SOFTWAREGLY A:541 , MET A:542 , ALA A:543 , LYS A:570 , THR A:852 , THR A:855 , TYR A:857 , HOH A:1058binding site for residue IPH A 907
8AC8SOFTWAREA B:13 , HOH B:207 , HOH B:216 , HOH B:222 , HOH B:230 , HOH B:239binding site for residue MG B 101
9AC9SOFTWAREU D:4 , HOH D:207 , HOH D:211 , HOH D:226 , HOH D:228 , HOH D:233binding site for residue MG D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z4E)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:62 -Pro A:63
2Glu A:245 -Gln A:246
3His A:621 -Pro A:622

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z4E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z4E)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z4E)

(-) 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..........eeeeee...eeeeeeeeeeeeehhhhhhhhh......hhhhhhhhhhhhhhhhhhhheee..eeee.......eee..eeeeeeeeeeee.....eeeeeeeeeeeee...hhhhhhhhhhh...........hhhhhhhhhhhhh..eee..eeeeeeeeee.........hhhhhhhhh..........eeeee.......eee.hhhee..........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eeeeeee.....ee.......ee......................eeeee.......hhhhhhhhhhhhhhhhhhhh........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
                 4z4e A  22 AFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEIKYRVCNVTRRPASHQTFPLCTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEGRDHQALAKAVQVHQDTLRTMYFA 859
                                    31        41        51        61        71        81        91       101       111       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266  ||   284       294 ||    313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       837       847       857  
                                                                                                                            120|                                                                                                                                            269|               296|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                821|                       
                                                                                                                             126                                                                                                                                             278                306                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 836                       


Chain B from PDB  Type:DNA/RNA  Length:19
                                                   
                 4z4e B   1 UUCACAUUGCCCAAGUCUU  21
                                    10       ||
                                            18|
                                             21


Chain D from PDB  Type:DNA/RNA  Length:9
                                         
                 4z4e D   1 CAAUGUGAU   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 4Z4E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z4E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z4E)

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:245 - Gln A:246   [ RasMol ]  
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  4z4e
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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 4z4f 4z4g 4z4h 4z4i 5js1 5js2 5ki6 5t7b

(-) Related Entries Specified in the PDB File

4z4c 4z4d 4z4f 4z4g 4z4h 4z4i