Primary Citation PubMed: 21148772
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What is the role of motif D in the nucleotide incorporation catalyzed by the RNA-dependent RNA polymerase from poliovirus?
(2012) PLoS Comput Biol 8
PubMed: 23300428 | PubMedCentral: PMC3531290 | DOI: 10.1371/journal.pcbi.1002851
In fact, the large global conformational change was not observed for the NTP binding to PV 3D pol because the RMSD value between the two 3D pol -RNA complexes with NTP binding (PDB code: 3OLB) and wit... out NTP binding (PDB code: 3OL6) was measured of less 1.5 Å.
Publication Year: 2012
Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases.
(2013) Nucleic Acids Res 41
PubMed: 23275546 | PubMedCentral: PMC3561941 | DOI: 10.1093/nar/gks1251
Viral species and PDB structures used as queries in this study Queries Abbreviations PDB Length of structure Picornaviridae, RdRp, +ssRNA Poliovirus PV 1RA6 ( 3 ) 4... 1 Poliovirus (open) PV 3OL6 ( 9 ) 471 Poliovirus (closed) PV 3OL7 ( 9 ) 471 Coxsackie virus COXV 3DDK ( 11 ) 462 Human rhinovirus HRV 1XR6 ( 12 ) 460 Human rhinovirus HRV 1XR7 ( 12 ) 460 Foot and mouth disease virus FMDV 1U09 ( 2 ) 476 Caliciviridae, RdRp, +ssRNA Norwalk virus NV 1SH0 ( 13 ) 510 Rabbit hemorrhagic disease virus RHDV 1KHV ( 14 ) 516 Rabbit hemorrhagic disease virus RHDV 1KHW ( 14 ) 516 Sapporo virus SAPV 2CKW ( 15 ) 515 Flaviviridae, RdRp, +ssRNA Hepatitis C virus HCV 1NB4 ( 16 ) 570 Hepatitis C virus HCV 1NB7 ( 16 ) 570 Bovine viral diarrhea virus BVDV 1S48 ( 17 ) 609 West Nile (Kunjin) virus WNV 2HCS ( 18 ) 595 Dengue virus DENV 2J7U ( 19 ) 635 Cystoviridae, RdRp, dsRNA Bacteriophage Phi6 PHI6 1HHS ( 20 ) 664 Bacteriophage Phi6 PHI6 1HI0 ( 20 ) 664 Reoviridae, RdRp, dsRNA Reovirus lambda 3 REOV 1MUK ( 21 ) 1267 Reovirus lambda 3 REOV 1N35 ( 21 ) 1267 Rotavirus ROTAV 2R7X ( 22 ) 1095 Birnaviridae, RdRp, dsRNA Infectious bursal disease, birnavirus IBDV 2PGG ( 5 ) 774 Infectious pancreatic necrosis IPNV 2YI8 ( 23 ) 799 Infectious pancreatic necrosis IPNV 2YI9 ( 23 ) 799 Infectious pancreatic necrosis IPNV 2YIA ( 23 ) 799 RdDp HIV1 HIV1 1RT1 ( 24 ) 560 HIV1 (closed) HIV1 1RTD ( 25 ) 554 HIV1 (open) HIV1 2HMI ( 26 ) 558 Tribolium castaneum TERT 3DU6 ( 27 ) 596 DdRp Bacteriophage T7 (closed) T7 RNAP 1S77 ( 28 ) 883 Bacteriophage T7 (closed) T7 RNAP 2AJQ ( 29 ) 704 Bacteriophage T7 (open) T7 RNAP 1MSW ( 30 ) 883 Bacteriophage N4 N4 3C2P ( 31 ) 1117 DdDp Thermus aquaticus (open) TAQ 2KTQ ( 32 ) 538 Thermus aquaticus (closed) TAQ 3KTQ ( 32 ) 540 Thermus aquaticus (open) TAQ 4KTQ ( 32 ) 539 Bacteriophage T7 T7 DNAP 1T7P ( 33 ) 698 Queries of both open and closed structures were used to assess the impact of this feature on R2R correspondence.
Publication Year: 2013
Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts.
(2013) PLoS One 8
PubMed: 23667424 | PubMedCentral: PMC3648537 | DOI: 10.1371/journal.pone.0060272
Right: Space group P1 unit cells showing the EC packing arrangements of the new structures compared to the original PV_r1 poliovirus EC structure (PDB code 3OL6).
Molecular replacement was done with the original PV EC structure (PDB code 3OL6) as a search model, structure refinement was done using Phenix  , model building was done using Coot  , and simulated annealing composite omit maps were generated using CNS  .
Crystal Structure of the full-length Japanese encephalitis virus NS5 reveals a conserved methyltransferase-polymerase interface.
(2013) PLoS Pathog 9
PubMed: 23950717 | PubMedCentral: PMC3738499 | DOI: 10.1371/journal.ppat.1003549
The pdb entries used in the above superimpositions with JEV NS5 are: 2PX2 (MVEV MTase), 1L9K (DENV MTase), 2OY0 (WNV MTase), 3EVA (YFV MTase), 3ELD (WESSV MTase), 3GCZ (YOKV MTase), 2WA1 (MODV MTase),... 2OXT (MEAV MTase), 2HFZ (WNV RdRP), 2J7U (DENV RdRP), 1S4F (BVDV NS5B), 1NB7 (HCV NS5B in complex with DNA), 3OL6 (PV 3D elongation complex), 3VWS (DENV RdRP with inhibitor).
Viruses and viral proteins.
(2014) IUCrJ 1
PubMed: 25485129 | PubMedCentral: PMC4224467 | DOI: 10.1107/S205225251402003X
The different structures correspond to the 3D-RNA (PDB entry 3ol6 , Gong & Peersen, 2010 ▶ ), 3D-RNA-CTP open complex (PDB entry 3olb , Gong & Peersen, 2010 ▶ ) and 3D-... NA-CTP closed complex (PDB entry 3ol7 , Gong & Peersen, 2010 ▶ ) structures of poliovirus elongation complexes, respectively.
Publication Year: 2014
PubMed ID is not available.
Published in 2015
The color-coding is as in Figure 1 b; ( b ) A structure-based sequence alignment depicting the conservation of RdRP motifs (pdb entries: 4K6M, 1S4F, 1NB4, 3OL6, 3BSO, 3AVT [ 36 ], 1HI0, 2PGG [ 37 ], 4... RT [ 38 ], 1RTD [ 39 ], and 3DU6 [ 40 ]).
Publication Year: 2015
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