NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin.

Tants JN, Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A
Nucleic Acids Res (2022 Mar 31)

PMID: 35357505 doi: 10.1093/nar/gkac212

Submitted to SASBDB: 2022 Feb 23 Published in SASBDB: 2022 Mar 14

SASDNW5 – apo Roquin-1 (coreROQ) at 50 µM, including concentration series data at 100, 200, 300 µM Sample: Roquin-1 monomer, 18 kDa Mus musculus protein Buffer: 150 mM NaCl, 20 mM Tris, 2 mM TCEP, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 1.9 nm Dmax 7.0 nm VolumePorod 35 nm3

SASDNX5 – apo Roquin-1 (extROQ) at 50 µM, including concentration series data at 100, 200, 300 µM Sample: Roquin-1 extROQ monomer, 35 kDa Mus musculus protein Buffer: 150 mM NaCl, 20 mM Tris, 2 mM TCEP, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 2.8 nm Dmax 14.0 nm VolumePorod 53 nm3

SASDNY5 – apo Roquin-1 (Nterm ROQ) at 50 µM, including concentration series data at 100, 300 µM Sample: Roquin-1 Nterm monomer, 51 kDa Mus musculus protein Buffer: 150 mM NaCl, 20 mM Tris, 2 mM TCEP, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 3.4 nm Dmax 15.0 nm VolumePorod 88 nm3

SASDNZ5 – apo Roquin-1 (Nterm A-site mut ROQ) at 50 µM, including concentration series data at 100, 300 µM Sample: Roquin-1 Nterm Amut (K220A, K239A, R260A) monomer, 51 kDa Mus musculus protein Buffer: 150 mM NaCl, 20 mM Tris, 2 mM TCEP, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 3.3 nm Dmax 14.0 nm VolumePorod 80 nm3

SASDN26 – apo Roquin-1 (Nterm B-site mut ROQ) at 50 µM, including concentration series data at 100, 300 µM Sample: Roquin-1 Nterm Bmut (R135E, K136E, D322A, K323A) monomer, 51 kDa Mus musculus protein Buffer: 150 mM NaCl, 20 mM Tris, 2 mM TCEP, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 3.5 nm Dmax 15.0 nm VolumePorod 92 nm3

SASDN36 – Ox40 RNA (untranslated region, UTR) full-length Sample: Ox40 3'UTR full-length monomer, 50 kDa Mus musculus RNA Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 3.7 nm Dmax 12.0 nm VolumePorod 115 nm3

SASDN46 – Ox40 RNA (untranslated region, UTR) alternative decay element (ADE) Sample: Ox40 3 UTR ADE monomer, 16 kDa Mus musculus RNA Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 2.1 nm Dmax 7.2 nm VolumePorod 21 nm3

SASDN56 – Ox40 RNA (untranslated region, UTR) constitutive decay element (CDE) Sample: Ox40 3 UTR CDE monomer, 9 kDa Mus musculus RNA Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 2.0 nm Dmax 9.5 nm VolumePorod 16 nm3

SASDN66 – Ox40 RNA (untranslated region, UTR) alternative and constitutive decay element (ADE-CDE) Sample: Ox40 3 UTR ADE-CDE monomer, 24 kDa Mus musculus RNA Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 2.6 nm Dmax 10.0 nm VolumePorod 26 nm3

SASDN76 – Ox40 RNA (untranslated region, UTR) Bulge Sample: Ox40 3 UTR Bulge monomer, 11 kDa Mus musculus RNA Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 1.8 nm Dmax 6.5 nm VolumePorod 17 nm3

SASDN86 – Ox40 RNA (untranslated region, UTR) Bulge with alternative decay element (Bulge-ADE) Sample: Ox40 3 UTR Bulge-ADE monomer, 27 kDa Mus musculus RNA Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 3.3 nm Dmax 12.5 nm VolumePorod 37 nm3

SASDN96 – Ox40 RNA (untranslated region, UTR) Bulge with alternative and constitutive decay elements (Bulge-ADE-CDE) Sample: Ox40 3 UTR Bulge-ADE-CDE monomer, 35 kDa Mus musculus RNA Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 3.4 nm Dmax 11.0 nm VolumePorod 46 nm3

SASDNA6 – Ox40 RNA (untranslated region, UTR) constitutive decay element (CDEshort) Sample: Ox40 3 UTR CDEshort monomer, 5 kDa Mus musculus RNA Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Jun 1 RgGuinier 1.5 nm

SASDNB6 – Ox40 RNA (untranslated region, UTR) terminal stem (Terminusuucg) Sample: Ox40 3 UTR Terminusuucg monomer, 10 kDa Mus musculus RNA Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 7 RgGuinier 1.6 nm Dmax 5.5 nm VolumePorod 16 nm3

SASDNC6 – Ox40 RNA (untranslated region, UTR), alternative decay element (ADEshort) Sample: Ox40 3 UTR ADEshort monomer, 7 kDa Mus musculus RNA Buffer: 50 mM KCl, 25 mM sodium phosphate, pH: 7 Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 7 RgGuinier 1.7 nm Dmax 9.0 nm VolumePorod 12 nm3