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(-) Description

Title :  HUMAN ARGONAUTE2 BOUND TO T1-DAP 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 :  2.80
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*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*(N6G)P*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  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1IPH3Ligand/IonPHENOL
2MG3Ligand/IonMAGNESIUM ION
3N6G1Mod. Nucleotide((2R,3S,4R,5S)-5-(2,6-DIAMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGENPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:597 , VAL A:598 , HOH A:1003 , HOH A:1006 , HOH A:1007 , C B:10 , HOH B:204binding site for residue MG A 901
2AC2SOFTWARELYS A:660 , PRO A:661 , GLU A:695 , TYR A:698binding site for residue IPH A 902
3AC3SOFTWAREPHE A:587 , GLN A:589 , PRO A:590 , VAL A:591 , ALA A:620 , PHE A:653binding site for residue IPH A 903
4AC4SOFTWAREASP A:537 , MET A:542 , ALA A:543 , THR A:852 , THR A:855 , TYR A:857binding site for residue IPH A 904
5AC5SOFTWAREA B:13 , HOH B:201 , HOH B:202binding site for residue MG B 101
6AC6SOFTWAREU D:4 , HOH D:201 , HOH D:202 , HOH D:203 , HOH D:204 , HOH D:205binding site for residue MG D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z4F)

(-) 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 4Z4F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z4F)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z4F)

(-) 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:801
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.eeeee.....eeee.eeee..hhhhhhhhhhhhhhhh..........ee.....eee..........eeeee....eeeee...eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhheee..eeee.......eee..eeeeeeeeeeee.....eeeeeeeeeeeee...hhhhhhhhhhh..hhhhh....hhhhhhhhhhhhh..eee...eeeeeeeeeee....ee..eehhhhhhhh..........eeeee.......eee....ee..........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhh..ee....eeeeeee.....ee.......ee......................eeeee.......hhhhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhhh.....eeeeehhhhhh.hhhhhhhhhhhhhhhh.....ee.hhhhhhhhhh.eeeeeeeee..........eeeeeeee.......eeeeeeee........hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee......eee.hhhhh..........eee..........eeeee...........eeeeeeee....hhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z4f A  22 AFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEIKRKYRVCNVTRRPASHQTFPECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEGRDHQALAKAVQVHQDTLRTMYFA 859
                                    31        41        51        61 ||     73        83        93       103       113      |129       139       149       159       169       179       189       199       209       219       229       239       249       259       269|      285       295|      314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814      |838       848       858 
                                                                    63|                                                   120|                                                                                                                                           269|                295|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 821|                       
                                                                     66                                                    127                                                                                                                                            276                 305                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  836                       


Chain B from PDB  Type:RNA  Length:18
                                                  
                 4z4f B   1 UUCACAUUGCCCAAGUUU  21
                                    10     || 
                                          16| 
                                           20 


Chain D from PDB  Type:DNA/RNA  Length:10
                                          
                 4z4f D   1 CAAUGUGAxA  10
                                    10
                                    9-N6G
   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 4Z4F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z4F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z4F)

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

4z4c 4z4d 4z4e 4z4g 4z4h 4z4i