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- PDB-7kga: Crystal structure of a mosquito-borne flavivirus dumbbell RNA -

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Basic information

Entry
Database: PDB / ID: 7kga
TitleCrystal structure of a mosquito-borne flavivirus dumbbell RNA
ComponentsRNA (90-MER)
KeywordsRNA / viral RNA / noncoding RNA / flavivirus / viral replication
Function / homologyIRIDIUM HEXAMMINE ION / : / RNA / RNA (> 10)
Function and homology information
Biological speciesDonggang virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsAkiyama, B.M. / Graham, M.E. / O'Donoghue, Z. / Beckham, J.D. / Kieft, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication.
Authors: Akiyama, B.M. / Graham, M.E. / O Donoghue, Z. / Beckham, J.D. / Kieft, J.S.
History
DepositionOct 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (90-MER)
B: RNA (90-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,92246
Polymers57,9692
Non-polymers12,95444
Water2,288127
1
A: RNA (90-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,28319
Polymers28,9841
Non-polymers5,29918
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (90-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,63927
Polymers28,9841
Non-polymers7,65426
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.93, 49.67, 73.46
Angle α, β, γ (deg.)90, 99.741, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (90-MER)


Mass: 28984.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Donggang virus / References: GenBank: 380877198
#2: Chemical...
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: H18IrN6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM Bis-Tris pH 7.0, 25 mM NaCl, 25 mM LiCl, 4.5 mM CaCl2, 50 mM Guanidine HCl, 23.75% polyethylene glycol 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.10208 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10208 Å / Relative weight: 1
ReflectionResolution: 2.1→44.74 Å / Num. obs: 27633 / % possible obs: 99.81 % / Redundancy: 10.9 % / Biso Wilson estimate: 34.69 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1303 / Rpim(I) all: 0.04105 / Rrim(I) all: 0.1367 / Net I/av σ(I): 17.95 / Net I/σ(I): 17.95
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 10 % / Rmerge(I) obs: 0.8781 / Mean I/σ(I) obs: 3.17 / Num. unique obs: 2741 / CC1/2: 0.834 / CC star: 0.954 / Rpim(I) all: 0.2917 / Rrim(I) all: 0.9265 / % possible all: 99.89

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXPhenixdev-3758refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→44.74 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2585 3809 7.25 %
Rwork0.2276 --
obs0.2298 27604 98.01 %
Displacement parametersBiso max: 148.73 Å2 / Biso mean: 38.6332 Å2 / Biso min: 14.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3822 308 127 4257
LS refinement shellResolution: 2.1→2.175 Å
RfactorNum. reflection
Rfree0.3254 -
Rwork0.31116 -
obs-2741

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