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- SASDGV3: DB12 from Zika virus (ZK DB12) -

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Basic information

Entry
Database: SASBDB / ID: SASDGV3
SampleDB12 from Zika virus
  • DB12 from Zika virus (RNA), ZK DB12, 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

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Models

Model #3599
Type: dummy / Software: (DAMFILT 5.0 (r7883)) / Radius of dummy atoms: 3.25 A / Symmetry: P1 / Chi-square value: 0.097 / P-value: 0.053009
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: DB12 from Zika virus / Specimen concentration: 0.75-3.00
BufferName: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2 / pH: 7.5
Entity #1831Name: ZK DB12 / Type: RNA / Description: DB12 from Zika virus / Formula weight: 47.441 / Num. of mol.: 1 / Source: Zika virus
Sequence:
GCGCUUGGAG GCGCAGGAUG GGAAAAGAAG GUGGCGACCU UCCCCACCCU UUAAUCUGGG GCCUGAACUG GAGAUCAGCU GUGGAUCUCC AGAAGAGGGA CUAGUGGUUA GAGGAGACCC CCCGGAAAAC GCAAAACAGC AUAUUG

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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: DB12 from Zika virus / Measurement date: Apr 2, 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 5.0 / Number of points: 120 /
MinMax
Q0.006 0.244
P(R) point1 120
R0 111.6
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
MW50.38 kDa-
Volume-92 nm3

P(R)GuinierGuinier error
Forward scattering, I00.4876 0.48733 0.0073107
Radius of gyration, Rg3.31 nm3.29 nm0.08

MinMax
D-11.16
Guinier point4 19

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