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(-) Description

Title :  COMPLEX STRUCTURE OF VIRAL RNA POLYMERASE FORM III
 
Authors :  D. Takeshita, K. Tomita
Date :  02 Jul 12  (Deposition) - 08 Aug 12  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,G,T
Keywords :  Rna Polymerase, Translation, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Takeshita, S. Yamashita, K. Tomita
Mechanism For Template-Independent Terminal Adenylation Activity Of Q Beta Replicase
Structure V. 20 1661 2012
PubMed-ID: 22884418  |  Reference-DOI: 10.1016/J.STR.2012.07.004

(-) Compounds

Molecule 1 - ELONGATION FACTOR TS, ELONGATION FACTOR TU, LINKER, Q BETA REPLICASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Organism Taxid: 83334, 39803
 
Molecule 2 - RNA (5'-R(*C*CP*CP*UP*AP*CP*CP*C)-3')
    Chains: G
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED.
    Synthetic: YES
 
Molecule 3 - RNA (5'-R(*GP*GP*GP*UP*AP*GP*GP*G)-3')
    Chains: T
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AGT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:908 , ARG A:914 , ILE A:916 , ASP A:968 , LEU A:969 , SER A:970 , ALA A:972 , SER A:973 , MET A:1017 , GLY A:1018 , PHE A:1023 , GLU A:1026 , ASP A:1053 , ASN A:1077 , CA A:2502 , C G:2008 , G T:2101BINDING SITE FOR RESIDUE GTP A 2501
2AC2SOFTWAREASP A:968 , LEU A:969 , ASP A:1053 , GTP A:2501BINDING SITE FOR RESIDUE CA A 2502
3AC3SOFTWAREASP A:968 , ASP A:1053 , ASP A:1054 , C G:2008BINDING SITE FOR RESIDUE CA A 2503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FWT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FWT)

(-) 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:1203
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh.....hhhhhh........hhhhhhhhhhhhhhhhh.............eeee..eeeeeeee..hhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh......eeeeeeeee..eeeeeee...eeeeeee......hhhhhhhhhhhhh............hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.....eeeee...........hhhhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhhhhhhhhh.......eeee....eeeeee..hhhhhhhhhh.......eeeeeee.......hhhhhhhhhh......eeeeee......hhhhhhhhhhhhhhhhhh...hhhhh.eee..hhhhhhhhhhhhhhhhhhhhhhh.......hhhhh.......eeeee...eeeeeee.....ee...eeee......eeeeeeeee.......ee....eeeeee...hhhhh.............eeeeeeeeeee............................eeee...........eeeeeeeeeeeeee.....eeeeee..eeeeeeeeeee......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.......hhhhh.......hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh...hhhhhhh............hhhhhhhhhhhh..eee...hhhhhhhhhhhh.....eeee..eeee.............ee...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee..........hhhhhhhhhhhhhhhhhhhh...hhhhheee..eeeee..hhhhhhhhhhhhh.............eeee..eeee..ee...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhh.ee........ee.........eee..eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhh...............eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4fwt A    2 AEITASLVKELRERTGAGMMDCKKALTEANGDIELAIENMRKSGAIKAAKKAGNVAADGVIKTKIDGNYGIILEVNCQTDFVAKDAGFQAFADKVLDAAVAGKITDVEVLKAQFEEERVALVAKIGENINIRRVAALEGDVLGSYQHGARIGVLVAAKGADEELVKHIAMHVAASKPEFIKPEDVSAEVVEKEYQVQLDIAMQSGKPKEIAEKMVEGRMKKFTGEVSLTGQPFVMEPSKTVGQLLKEHNAEVTGFIRFEVGEGIEKVETDFAAEVAAMSKQSHMSFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGNTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLSGASSRNSLSAQLRRAANTRIEVEGNLALSIANDLLLAYGQSPFNSEAECISFSPRFDGTPDDFRINYLKAEIMSKYDDFSLGIDTEAVAWEKFLAAEAECALTNARLYRPDYSEDFNFSLGESCIHMARRKIAKLIGDVPSVEGMLRHCRFSGGATTTNNRSYGHPSFKFALPQACTPRALKYVLALRASTHFDIRISDISPFNKAVTVPKNSKTDRCIAIEPGWNMFFQLGIGGILRDRLRCWGIDLNDQTINQRRAHEGSVTNNLATVDLSAASDSISLALCELLLPPGWFEVLMDLRSPKGRLPDGSVVTYEKISSMGNGYTFELESLIFASLARSVCEILDLDSSEVTVYGDDIILPSCAVPALREVFKYVGFTTNTKKTFSEGPFRESCGKHYYSGVDVTPFYIRHRIVSPADLILVLNNLYRWATIDGVWDPRAHSVYLKYRKLLPKQLQRNTIPDGYGDGALVGSVLINPFAKNRGWIRYVPVITDHTRDRERAELGSYLYDLFSRCLSESNAIDQLICRSNPTKISRSTGKFDIQYIACSSR 1264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281    || 294       304       314       324 ||    355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675    || 704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214 ||   1241      1251      1261   
                                                                                                                                                                                                                                                                                                                      286|                                 326|                                                                                                                                                                                                                                                                                                                                         680|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                1216|                              
                                                                                                                                                                                                                                                                                                                       290                                  348                                                                                                                                                                                                                                                                                                                                          700                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 1234                              


Chain G from PDB  Type:DNA/RNA  Length:7
                                        
                4fwt G 2002 CCUACCC 2008


Chain T from PDB  Type:RNA  Length:6
                                       
                4fwt T 2101 GGGUAG 2106
   Legend:   → Mismatch (orange background)
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  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 4FWT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 48)

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
        EFTS_ECO57 | P0A6P3: 3agp 3agq 3avt 3avu 3avv 3avw 3avx 3avy 3vnu 3vnv
        EFTS_ECOLI | P0A6P1: 1efu 3agp 3agq 3avt 3avu 3avv 3avw 3avx 3avy 3mmp 3vnu 3vnv 4pc3 4pc7 4q7j 4r71
        EFTU2_ECOLI | P0CE48: 1d8t 1dg1 1efc 1efm 1efu 1etu 1ls2 1ob2 1qzd 2bvn 2hcj 2hdn 3agp 3agq 3avt 3avu 3avv 3avw 3avx 3avy 3ep2 3eq3 3eq4 3mmp 3vnu 3vnv 4r71 4v69 4v6k 4v6l 5afi
        EFTU_ECO57 | P0A6N3: 1efm 3agp 3agq 3avt 3avu 3avv 3avw 3avx 3avy 3vnu 3vnv
        RDRP_BPQBE | P14647: 3agp 3agq 3avt 3avu 3avv 3avw 3avx 3avy 3mmp 3vnu 3vnv 4q7j 4r71

(-) Related Entries Specified in the PDB File

3agp 3agq 3vnu 3vnv