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- PDB-7lyf: Dengue virus RNA promoter stem-loop A fused with tRNA-scaffold -

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Basic information

Entry
Database: PDB / ID: 7lyf
TitleDengue virus RNA promoter stem-loop A fused with tRNA-scaffold
ComponentsRNA promoter stem-loop A fused with tRNA
KeywordsRNA
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesDengue virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsLee, E.H. / Choi, K.H.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
CitationJournal: Nat Commun / Year: 2021
Title: Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase.
Authors: Lee, E. / Bujalowski, P.J. / Teramoto, T. / Gottipati, K. / Scott, S.D. / Padmanabhan, R. / Choi, K.H.
History
DepositionMar 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 promoter stem-loop A fused with tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8942
Polymers44,8701
Non-polymers241
Water1267
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.924, 137.558, 336.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: RNA chain RNA promoter stem-loop A fused with tRNA


Mass: 44869.621 Da / Num. of mol.: 1
Fragment: Residues 1-32 and 81-139 form the tRNA scaffold, whereas residues 33-80 match to residues 69-116 of the Dengue virus 2 complete genome GB:KP188569.1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Production host: Escherichia coli (E. coli) / References: GenBank: KP188569.1
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.83 Å3/Da / Density % sol: 67.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM sodium cacodylate pH 6.9, 9% (w/v) polyethylene glycol 8000, 200 mM KCl, and 100 mM magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.366→50 Å / Num. obs: 10308 / % possible obs: 97.2 % / Redundancy: 7.1 % / CC1/2: 0.991 / Net I/σ(I): 37
Reflection shellResolution: 3.37→3.46 Å / Num. unique obs: 10308 / CC1/2: 0.636

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TN1,5EW4

1tn1

5ew4


Resolution: 3.4→33.688 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 1029 9.98 %
Rwork0.2255 9279 -
obs0.2299 10308 94.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 252.2 Å2 / Biso mean: 155.1158 Å2 / Biso min: 74.06 Å2
Refinement stepCycle: final / Resolution: 3.4→33.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2972 1 7 2980
Biso mean--129.26 125.94 -
Num. residues----139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073323
X-RAY DIFFRACTIONf_angle_d1.2815181
X-RAY DIFFRACTIONf_chiral_restr0.057695
X-RAY DIFFRACTIONf_plane_restr0.007139
X-RAY DIFFRACTIONf_dihedral_angle_d18.9011665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4-3.54310.435960.382588365
3.5431-3.76480.37181500.3223134298
3.7648-4.05510.31841500.28231353100
4.0551-4.46230.31031560.25941395100
4.4623-5.10610.29211540.23561396100
5.1061-6.42580.29041570.23521409100
6.4258-33.6880.22161660.186150199

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