Citations in PubMed

Primary Citation PubMed: 21148772 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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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 [25] , model building was done using Coot [26] , and simulated annealing composite omit maps were generated using CNS [27] .

Publication Year: 2013


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).

Publication Year: 2013


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

PubMedCentral: PMC4490480

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