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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 (LONG TARGET)
 
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 :  2.50
Chains :  Asym./Biol. Unit :  A,B,D
Keywords :  Ago2, Guide, Target, Seed, Rnase, Rnai, Microrna (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*UP*U)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(P*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  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1IPA2Ligand/IonISOPROPYL ALCOHOL
2IPH3Ligand/IonPHENOL
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:184 , GLU A:197 , ALA A:227 , ALA A:348 , TYR A:654 , ARG A:658binding site for residue IPA A 901
2AC2SOFTWAREPRO A:580 , GLN A:581 , ARG A:583 , PRO A:584 , GLN A:588binding site for residue IPA A 902
3AC3SOFTWARELEU A:650 , TYR A:654 , GLU A:695 , TYR A:698binding site for residue IPH A 903
4AC4SOFTWAREPHE A:587 , GLN A:589 , VAL A:591 , ALA A:620 , PHE A:653binding site for residue IPH A 904
5AC5SOFTWAREASP A:537 , GLY A:541 , MET A:542 , ALA A:543 , LYS A:570 , THR A:852 , THR A:855 , TYR A:857binding site for residue IPH A 905
6AC6SOFTWAREASP A:597 , VAL A:598 , HOH A:1022 , HOH A:1023 , HOH A:1024 , HOH A:1025binding site for residue MG A 906
7AC7SOFTWAREU D:6 , HOH D:201 , HOH D:202 , HOH D:204binding site for residue MG D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W5R)

(-) 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 4W5R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W5R)

(-) Exons   (0, 0)

(no "Exon" information available for 4W5R)

(-) 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..eeeeeeeeeeeee....eeeeeeeeeeeee...hhhhhhhhhh...hhhhh....hhhhhhhhhhhhh..eee...eeeeeeeeeee....ee....eehhhhhhhh..........eeeee.......eee.hhhee..........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhh..ee....eeeeeee.....ee.......ee......................eeeee.......hhhhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhh....eeeeehhhhhh.hhhhhhhhhhhhhhhh.....ee.hhhhhhhhhh.eeeeeeeee..........eeeeeeee.......eeeeeeee........hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee......eee.hhhhh..........eee..........eeeee...........eeeeeeee....hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w5r A  22 AFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEIKRKYRVCNVTRRPASHQTFPLVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEGRDHQALAKAVQVHQDTLRTMYFA 859
                                    31        41        51        61        71        81     || 93       103       113      |129       139       149       159       169       179       189       199       209       219       229       239       249       259       269|      285       295||     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   
                                                                                            87|                           120|                                                                                                                                           269|                 296|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  821|                       
                                                                                             90                            127                                                                                                                                            276                  304                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   836                       


Chain B from PDB  Type:RNA  Length:11
                                           
                 4w5r B   1 UUCACAUUGUU  21
                                    20 
                                    9| 
                                    20 


Chain D from PDB  Type:DNA/RNA  Length:9
                                         
                 4w5r D   4 AAUGUGAAA  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 4W5R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W5R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W5R)

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

4w5n 4w5o 4w5q 4w5t