Long non‐coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution

Zhang Y, Zhang Y, Liu Z, Cheng M, Ma J, Wang Y, Qin C, Fang X
EMBO reports (2019 Sep 10)

doi: 10.15252/embr.201847016
Submitted to SASBDB: 2019 Aug 10
Published in SASBDB:

SASDGF3 – Xrn1 resistance RNA1 from Zika virus

Xrn1 resistance RNA2 from Zika virus experimental SAS data
OTHER model
Sample: Xrn1 resistance RNA2 from Zika virus monomer, 22 kDa Zika virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2016 Dec 9
RgGuinier 2.4 nm
Dmax 8.5 nm
VolumePorod 34 nm3

SASDGG3 – Xrn1 resistance RNA1 from Dengue virus 2

Xrn1 resistance RNA1 from Dengue virus 2 experimental SAS data
DAMFILT model
Sample: Xrn1 resistance RNA1 from Dengue virus 2 monomer, 21 kDa Dengue virus 2 RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 14-ID-B (BioCARS), Advanced Photon Source (APS), Argonne National Laboratory on 2016 Dec 9
RgGuinier 2.2 nm
Dmax 8.0 nm
VolumePorod 31 nm3

SASDGH3 – Xrn1 resistance RNA1-2 from Zika virus

Xrn1 resistance RNA1-2 from Dengue virus 2 experimental SAS data
DAMMIN model
Sample: Xrn1 resistance RNA1-2 from Dengue virus 2 monomer, 46 kDa Dengue virus 2 RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Apr 2
RgGuinier 3.9 nm
Dmax 13.4 nm
VolumePorod 67 nm3

SASDGJ3 – Xrn1 resistance RNA1 from West Nile virus

Xrn1 resistance RNA-1 from West Nile virus experimental SAS data
DAMFILT model
Sample: Xrn1 resistance RNA-1 from West Nile virus monomer, 25 kDa West Nile virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2016 Dec 9
RgGuinier 2.4 nm
Dmax 8.4 nm
VolumePorod 34 nm3

SASDGK3 – Xrn1 resistance RNA1 from Murray Valley Encephalitis

Xrn1 resistance RNA-1 from Murray Valley Encephalitis experimental SAS data
DAMFILT model
Sample: Xrn1 resistance RNA-1 from Murray Valley Encephalitis monomer, 26 kDa Murray Valley Encephalitis RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2016 Dec 9
RgGuinier 2.4 nm
Dmax 8.8 nm
VolumePorod 31 nm3

SASDGL3 – 3'SL from Dengue virus 2

3'SL from Dengue virus 2 experimental SAS data
DAMFILT model
Sample: 3'SL from Dengue virus 2 monomer, 31 kDa Dengue virus 2 RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Feb 24
RgGuinier 3.6 nm
Dmax 14.1 nm
VolumePorod 40 nm3

SASDGM3 – Xrn1 resistance RNA1-2 from Dengue virus 2

Xrn1 resistance RNA1-2 from Dengue virus 2 experimental SAS data
DAMFILT model
Sample: Xrn1 resistance RNA1-2 from Dengue virus 2 monomer, 46 kDa Dengue virus 2 RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2016 Dec 9
RgGuinier 3.5 nm
Dmax 12.5 nm
VolumePorod 65 nm3

SASDGN3 – Xrn1 resistance RNA2 from Zika virus

Xrn1 resistance RNA2 from Zika virus experimental SAS data
DAMFILT model
Sample: Xrn1 resistance RNA2 from Zika virus monomer, 22 kDa Zika virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2017 Sep 11
RgGuinier 2.1 nm
Dmax 7.2 nm
VolumePorod 29 nm3

SASDGP3 – Xrn1 resistance RNA1-2 from West Nile virus

Xrn1 resistance RNA1-2 from West Nile virus experimental SAS data
DAMFILT model
Sample: Xrn1 resistance RNA1-2 from West Nile virus monomer, 75 kDa West Nile virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Apr 2
RgGuinier 4.7 nm
Dmax 17.4 nm
VolumePorod 235 nm3

SASDGQ3 – SL3 from West Nile virus

SL3 from West Nile virus experimental SAS data
DAMFILT model
Sample: SL3 from West Nile virus monomer, 23 kDa West Nile virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2017 Jun 27
RgGuinier 2.8 nm
Dmax 9.5 nm
VolumePorod 29 nm3

SASDGR3 – Xrn1 resistance RNA2 from Dengue virus 2

Xrn1 resistance RNA2 from Dengue virus 2 experimental SAS data
DAMFILT model
Sample: Xrn1 resistance RNA2 from Dengue virus 2 monomer, 21 kDa Dengue virus 2 RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Mar 16
RgGuinier 2.2 nm
Dmax 7.6 nm
VolumePorod 29 nm3

SASDGS3 – DB12 from Dengue virus 2

DB12 from Dengue virus 2 experimental SAS data
DAMFILT model
Sample: DB12 from Dengue virus 2 monomer, 56 kDa Dengue virus 2 RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Feb 24
RgGuinier 4.7 nm
Dmax 16.2 nm
VolumePorod 96 nm3

SASDGT3 – Xrn1 resistance RNA2 from West Nile virus

Xrn1 resistance RNA2 from West Nile virus experimental SAS data
DAMFILT model
Sample: Xrn1 resistance RNA2 from West Nile virus monomer, 23 kDa West Nile virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2017 Apr 7
RgGuinier 2.2 nm
Dmax 7.7 nm
VolumePorod 30 nm3

SASDGU3 – Xrn1 resistance RNA2 from Murray Valley Encephalitis

Xrn1 resistance RNA2 from Murray Valley Encephalitis experimental SAS data
DAMMIF model
Sample: Xrn1 resistance RNA2 from Murray Valley Encephalitis monomer, 22 kDa Murray Valley Encephalitis RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2016 Dec 14
RgGuinier 2.2 nm
Dmax 8.2 nm
VolumePorod 28 nm3

SASDGV3 – DB12 from Zika virus

DB12 from Zika virus experimental SAS data
DAMFILT model
Sample: DB12 from Zika virus monomer, 47 kDa Zika virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Apr 2
RgGuinier 3.3 nm
Dmax 11.2 nm
VolumePorod 92 nm3

SASDGW3 – DB12 from West Nile virus

DB12 from West Nile virus experimental SAS data
DAMFILT model
Sample: DB12 from West Nile virus monomer, 59 kDa West Nile virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Jan 19
RgGuinier 3.9 nm
Dmax 13.4 nm
VolumePorod 160 nm3

SASDGX3 – 3'SL from Zika virus

3'SL from Zika virus experimental SAS data
DAMFILT model
Sample: 3'SL from Zika virus monomer, 32 kDa Zika virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2016 Dec 9
RgGuinier 3.9 nm
Dmax 14.1 nm
VolumePorod 52 nm3

SASDGY3 – 3'SL from West Nile virus

3'SL from West Nile virus experimental SAS data
DAMMIF model
Sample: 3'SL from West Nile virus monomer, 31 kDa West Nile virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2017 Apr 7
RgGuinier 3.5 nm
Dmax 13.2 nm
VolumePorod 39 nm3

SASDGZ3 – Subgenomic flavivirus RNAs from Zika virus

Subgenomic flavivirus RNA from Zika virus experimental SAS data
Sample: Subgenomic flavivirus RNA from Zika virus monomer, 133 kDa Zika virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Mar 13
RgGuinier 7.5 nm
Dmax 29.6 nm
VolumePorod 230 nm3

SASDG24 – Subgenomic flavivirus RNAs from Dengue virus 2

Subgenomic flavivirus RNAs from Dengue virus 2 experimental SAS data
Sample: Subgenomic flavivirus RNAs from Dengue virus 2 monomer, 137 kDa Dengue virus 2 RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2016 Dec 16
RgGuinier 7.9 nm
Dmax 30.5 nm
VolumePorod 236 nm3

SASDG34 – Subgenomic flavivirus RNAs from West nile virus

Subgenomic flavivirus RNAs from West nile virus experimental SAS data
Sample: Subgenomic flavivirus RNAs from West nile virus monomer, 170 kDa West Nile virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Mar 13
RgGuinier 7.9 nm
Dmax 31.8 nm
VolumePorod 261 nm3