DOI: 10.5281/zenodo.4627865
title: Polymerase Structure Alignments - v3 Update (March 2021)

description: v3 update (March 2021) of superposed viral polymerase structures using the methodology described in <br> <em>A Comprehensive Superposition of Viral Polymerase Structures</em> by Olve Peersen, Viruses 2019 11(8) 745. • <strong>_All_PDBs_v3.zip</strong> contains a single directory with coordinate files for 802 structures taken from 534 PDB entries. Uncompressed size is 1.4 GB. • <strong>Polymerases_v3.zip</strong> contains the complete set of files from the superpositions, including the _All_PDBs/ directory. Uncompressed size is 5.0 GB. ----------------------------------------------------------------------------------------------------------<br> POLYMERASE STRUCTURES community page at Zenodo.org v3 Release March 21, 2021 802 structures from 534 PDB entries http://www.zenodo.org/communities/pols/ <br> ========================================================================================= This directory contains a large collection viral polymerase structure coordinates that<br> have been superposed using the methods described in Peersen, Viruses 2019, 11(8), 745. They are released into the public domain under the Creative Commons Attribution (CC BY)<br> license. Please cite the following two references for any derivative work: 1) Reference to the publication describing the methodology:<br> Peersen, OB<br> A Comprehensive Superposition of Viral Polymerase Structures.<br> Viruses 2019, 11(8), 745 <br> https://doi.org/10.3390/v11080745 2) DOI reference that always resolves to the latest release of the dataset:<br> Peersen, OB<br> Polymerase Structure Alignments<br> https://doi.org/10.5281/zenodo.3361874 <br> ---------------------------------------------------------------------------------------------------<br> Olve Peersen Olve.Peersen@ColoState.edu<br> Professor<br> Biochemistry & Molecular Biology<br> 1870 Campus Delivery<br> Colorado State University<br> Ft. Collins, CO 80523-1870<br> -------------------------------------------------------------------------------------------------- ============================================================================= From the included version history file: v3 210322 - Many updates, including five new sets. Newly added PDB entries are <br> listed below. Note several of the negative strand RNA viruses were<br> previously part of the generic nsrn set, but are now in new sets. NEW aren: Arenaviruses - Lassa: 6klc<br> Mapucho: 6kld, 6kle, 6klh NEW buny: Bunyaviruses - LaCrosse: 5amq, 5amr, 6z6b, 6z6g, 6z8k coro: Added extensive list of 21 new CoV nsp12 structures<br> 6m71, 6x2g, 6xez, 6xqb, 6yyt, 7aap, 7b3b, 7b3c, 7b3d,<br> 7btf, 7bv1, 7bv2, 7bw4, 7bzf, 7c2k, 7ctt, 7cxm, 7cxn,<br> 7cyq, 7d4f, 7l1f<br> Added CORO (6nur) to the psrn set (motifs A,B,C,F) cypo: Added 6k32, 6ty8, 6ty9, 6tz0, 6tz1, 6tz2 NEW ev68: Enterovirus D68 with 5xe0, 5zit, 6l4r ev71: Added 6kwq, 6kwr, 6lse, 6lsf, 6lsg, 6lsh flav: DENV: 6izx, 6izy, 6izz, 6j00, 6kr2, 6kr3, 6xd0, 6xd1<br> plus previously missed 4v0r, 4v05, 5dto, 5zqk<br> ZIKA: 6ld1, 6ld2, 6ld3, 6ld4, 6ld5, 6ux2<br> YF: 6qsn<br> TBEV: 7d6n fluv: FluA: 6szu, 6szv, 6t0n, 6t0r, 6t0s, 6t0u, 6t0v, 6t2c, 6tu5, 6tw1<br> FluB: 6t0w<br> FluC: 6xzd, 6xzg, 6xzp, 6xzq, 6xzr, 6y0c<br> FluD: 6kuj, 6kuk, 6kup, 6kur, 6kut, 6kuu, 6kuv, 6kv5 hepc: Added 6w4g hiv1: Added 6waz, 6wb0, 6wb1, 6wb2, 6wpf, 6wph, 6wpj NEW mono: Mononegavirales - VSV: 5a22, 6u1x<br> RSV: 6pzk, 6uen<br> HMPV: 6u5o<br> Rabies: 6ueb<br> <br> nsrn: Restructured as follows to add three NSxx subgroups<br> Added 6l42 (Phlebovirus), 6v85, 6v86 (paramyxovirus)<br> superposed on core motifs only with representative<br> structures from fluv, NSar, NSbu, and NSmo sets pico: Added official releases for 6qwt (sicini) and 6r1i (Aichi/kobu) NEW poxv: Vaccinia virus polymerase complexes - 6rfl, 6ric, 6rid, 6rie psrn: Added a CORO (6nur) structure, but note any downstream alignments<br> are not (yet) updated to reflect subtle changes in the<br> orientations of the non-coronavirus psrn structures.
description: Supported by National Institutes of Health (US) grant R01 AI059130 to O.P.
description: {"references": ["Peersen OB, A Comprehensive Superposition of Viral Polymerase Structures, Viruses 2019 11(8) 745."]}