Citations in PubMed

Primary Citation PubMed: 15306852 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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Biochemical characterization of the fidelity of poliovirus RNA-dependent RNA polymerase.

(2007) Virol J 4

PubMed: 17524144 | PubMedCentral: PMC1904441 | DOI: 10.1186/1743-422X-4-44

The structure of 3D pol has been solved at 2.0 Å resolution and, like other DNA and RNA polymerases, resembles a right hand with fingers, palm, and thumb domains [ 13 , 14 ] {pdb: 1RDR and 1RA... }.

Publication Year: 2007


Nucleic acid polymerases use a general acid for nucleotidyl transfer.

(2009) Nat Struct Mol Biol 16

PubMed: 19151724 | PubMedCentral: PMC2728625 | DOI: 10.1038/nsmb.1540

RdRp: The RdRp from PV (pdb 1RA6) 19 with primer/template and CTP bound to the active site in the presence of two Mn 2+ ions.

Publication Year: 2009


StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.

(2011) BMC Bioinformatics 12

PubMed: 21635786 | PubMedCentral: PMC3121648 | DOI: 10.1186/1471-2105-12-226

C: Structure fragment of poliovirus polymerase ( 1ra6 ) corresponding to the N-terminal region containing position G64; color variations dark blue to bright turquoise indicate N-to-C-terminal directio... of chain.

Analysis of poliovirus RdRp Parameters Based on parameters applied in Zemla et al. 2007 [ 17 ] and the analysis described above, we used StralSV to analyze sequence variability in structure context for poliovirus RdRp (PDB: 1ra6 ; [ 19 ]) using minimum span length of 5, LGA_S cutoff 55%, and window_size/distance_cutoff combinations 50/2.5Å, 70/3.5Å, 80/4.0Å, and 90/4.0Å.

We ran poliovirus RdRp (PDB: 1ra6 ) through the online FireStar server (data not shown), and found considerable overlap between the functional residue list generated by FireStar and the list of 90% dominance residues generated by StralSV (see additional file 2 : StralSV-RdRp_Suppl_Table 1): K158, K167, R174, D233, D238, G289, and K359.

Publication Year: 2011


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

Methods Molecular Dynamics (MD) Simulation The starting apo structure of PV 3D pol was obtained from the crystal structure (PDB code: 1RA6 [2] ) deposited in the protein data bank.

Supporting Information Figure S1 A front view (A) and a top view (B) of the cartoon representation of ligand-free PV 3D pol (PDB code: 1RA6).

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

( B ) In poliovirus (illustrated here with PDB:1RA6), the sequence order of homomorphs is: A (blue), B (gold) and C (red).

( B ) All the structural diagrams in this article are illustrated using poliovirus polymerase (PDB:1RA6).

( B ) The homomorph of Motif D [illustrated using poliovirus (PDB:1RA6)] includes the motif itself (gold) and an adjacent upstream segment (blue).

Figure 2 B and C illustrates the tertiary structure of the homomorph using a poliovirus structure (PDB:1RA6).

( B ) Motif E (gold), [illustrated using poliovirus (PDB:1RA6)] forms part of the NTP entry tunnel.

( B ) In this figure of poliovirus (PDB:1RA6), the N-terminal segment of the homomorph is blue and the C-terminal segment is brown.

The terminal residues of HmA are at the exterior surface of the protein (PDB:1RA6).

( B ) HmB [illustrated using poliovirus (PDB:1RA6)] is the largest homomorph in the RdRps.

Motif C [illustrated using poliovirus (PDB:1RA6)] is tightly folded upon itself in a manner that places the highly conserved residues (yellow) at the tunnel wall, whereas the N-terminal segment of the motif (blue) and C-terminal segment of the motif (brown) are parallel to each other and penetrate the protein.

Viral species and PDB structures used as queries in this study Queries Abbreviations PDB Length of structure Picornaviridae, RdRp, +ssRNA     Poliovirus PV 1RA6 ( 3 ) 461     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.

( B ) HmF1 (light blue), illustrated using the poliovirus structure 1RA6, begins about five amino acids upstream from Motif F1 (dark blue) and ends at hmF3 (dark brown), about 20 amino acids downstream from Motif F3 (orange).

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

From left to right: all five PV ECs compared to one apo form (PDB code 1RA6); one CV EC compared to two apo forms (PDB codes 3DDK and 3DCU); two RV ECs compared to two apo forms (PDB code 1XR7 chains ... & B).

Publication Year: 2013