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- PDB-7u4a: Crystal Structure of Zika virus xrRNA1 mutant -

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Basic information

Entry
Database: PDB / ID: 7u4a
TitleCrystal Structure of Zika virus xrRNA1 mutant
ComponentsRNA (70-MER)
KeywordsRNA / xrRNA / Viral RNA / Flavivirus
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsThompson, R.D. / Carbaugh, D.L. / Nielsen, J.R. / Witt, C. / Meganck, R.M. / Rangadurai, A. / Zhao, B. / Bonin, J.P. / Nathan, N.T. / Marzluff, W.F. ...Thompson, R.D. / Carbaugh, D.L. / Nielsen, J.R. / Witt, C. / Meganck, R.M. / Rangadurai, A. / Zhao, B. / Bonin, J.P. / Nathan, N.T. / Marzluff, W.F. / Frank, A.T. / Lazear, H.M. / Zhang, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
University of North Carolina at Chapel Hill United States
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Lifetime of ground conformational state determines the activity of structured RNA.
Authors: Thompson, R.D. / Carbaugh, D.L. / Nielsen, J.R. / Witt, C.M. / Faison, E.M. / Meganck, R.M. / Rangadurai, A. / Zhao, B. / Bonin, J.P. / Nicely, N.I. / Marzluff, W.F. / Frank, A.T. / Lazear, H.M. / Zhang, Q.
History
DepositionFeb 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (70-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3502
Polymers23,3261
Non-polymers241
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.421, 39.137, 66.583
Angle α, β, γ (deg.)90.000, 94.339, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: RNA chain RNA (70-MER)


Mass: 23325.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zika virus
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: RNA was exchanged and concentrated into 10 mM HEPES-KOH, pH 7.5, 2.5 mM magnesium chloride. After concentration to 7.5 mg/mL (~330 uM), RNA was diluted to 4 mg/mL, 100 mM spermidine was ...Details: RNA was exchanged and concentrated into 10 mM HEPES-KOH, pH 7.5, 2.5 mM magnesium chloride. After concentration to 7.5 mg/mL (~330 uM), RNA was diluted to 4 mg/mL, 100 mM spermidine was added to a final concentration of 0.5 mM. 0.5 uL RNA was added to 2 uL crystallization solution (50 mM sodium cacodylate, pH 6.0, 150 mM sodium chloride, 4 mM calcium chloride, 0.6 mM spermine, 36% 1,6-hexanediol) and crystallized via hanging drop vapor diffusion over 1 mL crystallization solution. Crystals formed within 24 hours at 20 degrees C and were harvested after 36 hours.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→33.2 Å / Num. obs: 4391 / % possible obs: 95.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 58.32 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.074 / Rrim(I) all: 0.136 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
7.46-33.23440.9911
5.92-7.463500.9861
5.17-5.923370.9841
4.7-5.173380.9861
4.36-4.73380.9811
4.11-4.363440.9811
3.9-4.113190.9861
3.73-3.93340.9871
3.59-3.733470.9851
3.46-3.593240.9791
3.36-3.463460.991
3.26-3.363280.9821
3.17-3.263420.9841

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5TPY

5tpy


Resolution: 3.15→33.2 Å / SU ML: 0.3436 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 19.4835
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2704 218 5.1 %
Rwork0.214 4058 -
obs0.2168 4276 95.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.85 Å2
Refinement stepCycle: LAST / Resolution: 3.15→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1501 1 1 1503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021679
X-RAY DIFFRACTIONf_angle_d0.52562617
X-RAY DIFFRACTIONf_chiral_restr0.0259350
X-RAY DIFFRACTIONf_plane_restr0.003870
X-RAY DIFFRACTIONf_dihedral_angle_d12.905837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.970.321030.24051952X-RAY DIFFRACTION93.2
3.97-33.20.24441150.19942106X-RAY DIFFRACTION98.27

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