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- PDB-8utg: An RNA G-Quadruplex from the NS5 gene in the West Nile Virus Genome -

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Basic information

Entry
Database: PDB / ID: 8utg
TitleAn RNA G-Quadruplex from the NS5 gene in the West Nile Virus Genome
ComponentsRNA (5'-R(*UP*AP*UP*GP*GP*AP*AP*GP*AP*GP*GP*CP*GP*GP*UP*UP*GP*GP*UP*AP*U)-3')
KeywordsRNA / RNA Quadruplex / G-Quadruplex / G-tetrad / West Nile Virus / Orthoflavivirus
Function / homology: / AMMONIUM ION / RNA / RNA (> 10)
Function and homology information
Biological speciesWest Nile virus strain NY-99
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsTerrell, J.R. / Le, T.T. / Wilson, W.D. / Siemer, J.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U19AI171403-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111749 United States
National Science Foundation (NSF, United States)MCB2028902 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL155178 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structure of an RNA G-quadruplex from the West Nile virus genome.
Authors: Terrell, J.R. / Le, T.T. / Paul, A. / Brinton, M.A. / Wilson, W.D. / Poon, G.M.K. / Germann, M.W. / Siemer, J.L.
History
DepositionOct 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 10, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 17, 2024Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*UP*AP*UP*GP*GP*AP*AP*GP*AP*GP*GP*CP*GP*GP*UP*UP*GP*GP*UP*AP*U)-3')
B: RNA (5'-R(*UP*AP*UP*GP*GP*AP*AP*GP*AP*GP*GP*CP*GP*GP*UP*UP*GP*GP*UP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8337
Polymers13,7002
Non-polymers1325
Water39622
1
A: RNA (5'-R(*UP*AP*UP*GP*GP*AP*AP*GP*AP*GP*GP*CP*GP*GP*UP*UP*GP*GP*UP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9254
Polymers6,8501
Non-polymers753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (5'-R(*UP*AP*UP*GP*GP*AP*AP*GP*AP*GP*GP*CP*GP*GP*UP*UP*GP*GP*UP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9073
Polymers6,8501
Non-polymers572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.805, 33.805, 163.376
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: U / Beg label comp-ID: U / End auth comp-ID: U / End label comp-ID: U / Auth seq-ID: 1 / Label seq-ID: 1

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.971509729087, -0.0247860338485, 0.2357000187), (-0.0253816548387, -0.999677705292, -0.000507088737204), (0.23563662255, -0.00548981487841, -0.971825727199)Vector: 2. ...NCS oper: (Code: given
Matrix: (0.971509729087, -0.0247860338485, 0.2357000187), (-0.0253816548387, -0.999677705292, -0.000507088737204), (0.23563662255, -0.00548981487841, -0.971825727199)
Vector: 2.58901536556, -5.83114676972, -23.0204857678)

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Components

#1: RNA chain RNA (5'-R(*UP*AP*UP*GP*GP*AP*AP*GP*AP*GP*GP*CP*GP*GP*UP*UP*GP*GP*UP*AP*U)-3')


Mass: 6850.101 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) West Nile virus strain NY-99
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.97 Å3/Da / Density % sol: 37.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sitting-drop tray prepared 1:1 using an Art Robbins Crystal Gryphon. Molecular Dimensions Helix HT condition F4 (50mM KCl, 50mM Bis-Tris pH=7.0, 1.1M ammonium sulfate) yielded loopable ...Details: Sitting-drop tray prepared 1:1 using an Art Robbins Crystal Gryphon. Molecular Dimensions Helix HT condition F4 (50mM KCl, 50mM Bis-Tris pH=7.0, 1.1M ammonium sulfate) yielded loopable crystals after 6 weeks. Crystals were directly flash frozen without cryoprotection

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 25, 2023
RadiationMonochromator: Horizontal double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.97→29.28 Å / Num. obs: 8368 / % possible obs: 99.9 % / Redundancy: 14.1 % / Biso Wilson estimate: 41.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.039 / Rrim(I) all: 0.148 / Net I/σ(I): 11.7
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 14.8 % / Rmerge(I) obs: 3.286 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 567 / CC1/2: 0.831 / Rpim(I) all: 0.85 / Rrim(I) all: 3.397 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→29.28 Å / SU ML: 0.2867 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7178
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2426 835 10.08 %
Rwork0.1937 7450 -
obs0.1987 8285 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.08 Å2
Refinement stepCycle: LAST / Resolution: 1.97→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 908 5 22 935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01491018
X-RAY DIFFRACTIONf_angle_d1.87741588
X-RAY DIFFRACTIONf_chiral_restr0.0889208
X-RAY DIFFRACTIONf_plane_restr0.022342
X-RAY DIFFRACTIONf_dihedral_angle_d20.0557496
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.12272322381 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.090.31971350.2721208X-RAY DIFFRACTION99.33
2.09-2.250.3061360.20911205X-RAY DIFFRACTION99.33
2.26-2.480.28561380.28691201X-RAY DIFFRACTION99.85
2.48-2.840.33781320.24741230X-RAY DIFFRACTION99.85
2.84-3.580.22411430.19711244X-RAY DIFFRACTION99
3.58-29.280.20571510.15111362X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -14.0899780457 Å / Origin y: -2.73395615904 Å / Origin z: -13.195263151 Å
111213212223313233
T0.231130571944 Å20.0511127752448 Å2-0.00114318782027 Å2-0.212141126461 Å2-0.0233739124629 Å2--0.330229233167 Å2
L3.02636150006 °20.34372271488 °2-1.27786046885 °2-3.44926737682 °20.480283526773 °2--6.49243527035 °2
S-0.0235758115069 Å °0.210337475713 Å °-0.0703362067196 Å °-0.260594213232 Å °0.0214087386391 Å °0.0313088932687 Å °-0.0392337612711 Å °-0.200641100158 Å °-0.00258182373177 Å °
Refinement TLS groupSelection details: all

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