An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans -cleaving Neurospora Varkud Satellite ribozyme

Dagenais P, Desjardins G, Legault P
Nucleic Acids Research (2021 Oct 28)

doi: 10.1093/nar/gkab963

Submitted to SASBDB: 2020 Nov 13 Published in SASBDB: 2021 Oct 4

SASDKU3 – II-III-VI three-way junction from the Neurospora Varkud Satellite (VS) ribozyme Sample: Neurospora Varkud Satellite ribozyme junction II-III-VI monomer, 20 kDa Neurospora crassa RNA Buffer: 50 mM MES, 50 mM KCl, 5 mM MgCl2,, pH: 6.5 Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2014 Oct 29 RgGuinier 2.2 nm Dmax 7.7 nm VolumePorod 28 nm3

SASDKV3 – III-IV-V three-way junction from the Neurospora Varkud Satellite (VS) ribozyme Sample: Neurospora Varkud Satellite ribozyme junction III-IV-V monomer, 15 kDa Neurospora crassa RNA Buffer: 50 mM MES, 50 mM KCl, 5 mM MgCl2,, pH: 6.5 Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2014 Oct 29 RgGuinier 2.1 nm Dmax 7.5 nm VolumePorod 20 nm3

SASDKW3 – Stem-loop VI from the Neurospora Varkud Satellite (VS) ribozyme Sample: Neurospora Varkud Satellite ribozyme stem-loop VI monomer, 8 kDa Neurospora crassa RNA Buffer: 50 mM MES, 50 mM KCl, 5 mM MgCl2,, pH: 6.5 Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2015 Jul 7 RgGuinier 1.6 nm Dmax 6.1 nm VolumePorod 8 nm3

SASDKX3 – Minimal trans Varkud Satellite (VS) ribozyme without MgCl2 Sample: Neurospora Varkud Satellite minimal trans ribozyme monomer, 33 kDa Neurospora crassa RNA Buffer: 50 mM MES, 50 mM KCl, pH: 6.5 Experiment: SAXS data collected at Xenocs BioXolver L with MetalJet, Département de Biochimie, Université de Montréal on 2019 Sep 19 RgGuinier 3.6 nm Dmax 12.4 nm VolumePorod 55 nm3

SASDKY3 – Minimal trans Varkud Satellite (VS) ribozyme in 5mM MgCl2 Sample: Neurospora Varkud Satellite minimal trans ribozyme monomer, 33 kDa Neurospora crassa RNA Buffer: 50 mM MES, 50 mM KCl, 5 mM MgCl2,, pH: 6.5 Experiment: SAXS data collected at Xenocs BioXolver L with MetalJet, Département de Biochimie, Université de Montréal on 2019 Sep 19 RgGuinier 3.0 nm Dmax 11.0 nm VolumePorod 44 nm3

SASDKZ3 – Minimal trans Varkud Satellite (VS) ribozyme in 20mM MgCl2 Sample: Neurospora Varkud Satellite minimal trans ribozyme monomer, 33 kDa Neurospora crassa RNA Buffer: 50 mM MES, 50 mM KCl, 20 mM MgCl2,, pH: 6.5 Experiment: SAXS data collected at Xenocs BioXolver L with MetalJet, Département de Biochimie, Université de Montréal on 2019 Sep 19 RgGuinier 3.5 nm Dmax 11.4 nm VolumePorod 61 nm3