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

Pierre Dagenais Submitted to SASBDB: 2020 Nov 13
Published in SASBDB:

SASDKU3 – II-III-VI three-way junction from the Neurospora Varkud Satellite (VS) ribozyme

Neurospora Varkud Satellite ribozyme junction II-III-VI experimental SAS data
PDB (PROTEIN DATA BANK) model
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

Neurospora Varkud Satellite ribozyme junction III-IV-V experimental SAS data
PDB (PROTEIN DATA BANK) model
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

Neurospora Varkud Satellite ribozyme stem-loop VI experimental SAS data
PDB (PROTEIN DATA BANK) model
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

Neurospora Varkud Satellite minimal trans ribozyme experimental SAS data
Neurospora Varkud Satellite minimal trans ribozyme Kratky plot
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, 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

Neurospora Varkud Satellite minimal trans ribozyme experimental SAS data
PDB (PROTEIN DATA BANK) model
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, 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

Neurospora Varkud Satellite minimal trans ribozyme experimental SAS data
Neurospora Varkud Satellite minimal trans ribozyme Kratky plot
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, Université de Montréal on 2019 Sep 19
RgGuinier 3.5 nm
Dmax 11.4 nm
VolumePorod 61 nm3