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- SASDGZ3: Subgenomic flavivirus RNAs from Zika virus (Subgenomic flavivirus... -

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Basic information

Entry
Database: SASBDB / ID: SASDGZ3
SampleSubgenomic flavivirus RNAs from Zika virus
  • Subgenomic flavivirus RNA from Zika virus (RNA), ZIKV-sfRNA, Zika virus
Biological speciesZika virus
CitationDate: 2019 Sep 10
Title: Long non‐coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution
Authors: Zhang Y / Zhang Y / Liu Z / Cheng M / Ma J / Wang Y / Qin C
Contact author
  • Zhang Yikan (Tsinghua University)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

Model #3584
Type: dummy / Software: (2.8.3) / Radius of dummy atoms: 6.75 A / Symmetry: P1 / Chi-square value: 0.333 / P-value: 0.129727
Search similar-shape structures of this assembly by Omokage search (details)
Model #3609
Type: atomic / Chi-square value: 0.606
Search similar-shape structures of this assembly by Omokage search (details)
Model #3610
Type: atomic / Chi-square value: 0.606
Search similar-shape structures of this assembly by Omokage search (details)
Model #3611
Type: atomic / Chi-square value: 0.606
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Subgenomic flavivirus RNAs from Zika virus / Specimen concentration: 0.75-3.00
BufferName: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2 / pH: 7.5
Entity #1836Name: ZIKV-sfRNA / Type: RNA / Description: Subgenomic flavivirus RNA from Zika virus / Formula weight: 133.491 / Num. of mol.: 1 / Source: Zika virus
Sequence: UGUCAGGCCU GCUAGUCAGC CACAGCUUGG GGAAAGCUGU GCAGCCUGUG ACCCCCCCAG GAGAAGCUGG GAAACCAAGC CCAUAGUCAG GCCGAGAACG CCAUGGCACG GAAGAAGCCA UGCUGCCUGU GAGCCCCUCA GAGGACACUG AGUCAAAAAA CCCCACGCGC ...Sequence:
UGUCAGGCCU GCUAGUCAGC CACAGCUUGG GGAAAGCUGU GCAGCCUGUG ACCCCCCCAG GAGAAGCUGG GAAACCAAGC CCAUAGUCAG GCCGAGAACG CCAUGGCACG GAAGAAGCCA UGCUGCCUGU GAGCCCCUCA GAGGACACUG AGUCAAAAAA CCCCACGCGC UUGGAGGCGC AGGAUGGGAA AAGAAGGUGG CGACCUUCCC CACCCUUUAA UCUGGGGCCU GAACUGGAGA UCAGCUGUGG AUCUCCAGAA GAGGGACUAG UGGUUAGAGG AGACCCCCCG GAAAACGCAA AACAGCAUAU UGACGCUGGG AAAGACCAGA GACUCCAUGA GUUUCCACCA CGCUGGCCGC CAGGCACAGA UCGCCGAAUA GCGGCGGCCG GUGUGGGGAA AUCCAUGGGU CU

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Experimental information

BeamInstrument name: Advanced Photon Source (APS), Argonne National Laboratory 12ID-B SAXS/WAXS
City: Lemont, IL / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.08857 Å / Dist. spec. to detc.: 2 mm
DetectorName: Pilatus 2M
Scan
Title: Subgenomic flavivirus RNAs from Zika virus / Measurement date: Mar 13, 2017 / Storage temperature: 4 °C / Cell temperature: 25 °C / Exposure time: 1 sec. / Number of frames: 30 / Unit: 1/A /
MinMax
Q0 0.3
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 149 /
MinMax
Q0.004 0.3
P(R) point2 150
R0 296
Result
Type of curve: extrapolated
Comments: The subtracted SAXS data series used to generate the final extrapolated to zero-concentration profile displayed in this entry are provided in the full entry zip archive. The ab initio dummy ...Comments: The subtracted SAXS data series used to generate the final extrapolated to zero-concentration profile displayed in this entry are provided in the full entry zip archive. The ab initio dummy atom model represents the averaged spatial disposition of the RNA in solution (DAMFILT model), derived from several aligned individual models (corresponding fit).
ExperimentalPorod
MW103.67 kDa-
Volume-230 nm3

P(R)GuinierGuinier error
Forward scattering, I00.3759 0.37 -
Radius of gyration, Rg8.21 nm7.5 nm0.13

MinMax
D-29.6
Guinier point1 9

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