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- SASDG34: Subgenomic flavivirus RNAs from West nile virus (WNV-sfRNA) -

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Basic information

Entry
Database: SASBDB / ID: SASDG34
SampleSubgenomic flavivirus RNAs from West nile virus
  • Subgenomic flavivirus RNAs from West nile virus (RNA), WNV-sfRNA, West Nile virus
Biological speciesWest Nile 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 #3586
Type: dummy / Software: (2.8.3) / Radius of dummy atoms: 7.00 A / Chi-square value: 1.908 / P-value: 0.016729
Search similar-shape structures of this assembly by Omokage search (details)
Model #3603
Type: atomic / Chi-square value: 1.402
Search similar-shape structures of this assembly by Omokage search (details)
Model #3604
Type: atomic / Chi-square value: 1.402
Search similar-shape structures of this assembly by Omokage search (details)
Model #3605
Type: atomic / Chi-square value: 1.402
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Subgenomic flavivirus RNAs from West nile virus / Specimen concentration: 0.75-3.00
BufferName: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2 / pH: 7.5
Entity #1838Name: WNV-sfRNA / Type: RNA
Description: Subgenomic flavivirus RNAs from West nile virus
Formula weight: 170.058 / Num. of mol.: 1 / Source: West Nile virus
Sequence: GGAGUCAGGC CAGAUUAAUG CUGCCACCGG AAGUUGAGUA GACGGUGCUG CCUGCGGCUC AACCCCAGGA GGACUGGGUG ACCAAAGCUG CGAGGUGAUC CACGUAAGCC CUCAGAACCG UCUCGGAAGG AGGACCCCAC GUGCUUUAGC CUCAAGGCCC AGUGUCAGAC ...Sequence:
GGAGUCAGGC CAGAUUAAUG CUGCCACCGG AAGUUGAGUA GACGGUGCUG CCUGCGGCUC AACCCCAGGA GGACUGGGUG ACCAAAGCUG CGAGGUGAUC CACGUAAGCC CUCAGAACCG UCUCGGAAGG AGGACCCCAC GUGCUUUAGC CUCAAGGCCC AGUGUCAGAC CACACUCUAG UGUGCCACUC UGCGGAGAGU GCAGUCUGCG AUAGUGCCCC AGGUGGACUG GGUUAACAAA GGCAAAACAU CGCCCCACGC GGCCAUAACC CUGGCUAUGG UGUUAACCAG GGAGAAGGGA CUAGAGGUUA GAGGAGACCC CGCGUCAAAA AGUGCACGGC CCAACUUGGC UGAAGCUGUA AGCCAAGGGA AGGACUAGAG GUUAGAGGAG ACCCCGUGCC AAAAACACCA AAAGAAACAG CAUAUUGACA CCUGGGAUAG ACUAGGGGAU CUUCUGCUCU GCACAACCAG CCACACGGCA CAGUGCGCCG AUAUAGGUGG CUGGUGGUGC GAGAACACAG GAUCU

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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 synchrotron / Wavelength: 0.08857 Å / Dist. spec. to detc.: 2 mm
DetectorName: Pilatus 2M
Scan
Title: Subgenomic flavivirus RNAs from West nile 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 318
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
MW150.42 kDa163.1 kDa
Volume-261 nm3

P(R)Guinier
Forward scattering, I00.8477 0.83
Radius of gyration, Rg8.61 nm7.9 nm

MinMax
D-31.8
Guinier point2 8

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