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- PDB-4pqv: Crystal structure of an Xrn1-resistant RNA from the 3' untranslat... -

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Basic information

Entry
Database: PDB / ID: 4pqv
TitleCrystal structure of an Xrn1-resistant RNA from the 3' untranslated region of a flavivirus (Murray Valley Encephalitis virus)
ComponentsXRN1-resistant flaviviral RNA
KeywordsRNA / flavivirus / 3' untranslated region / sfRNA / pseudoknot / Type C RNA three-way junction / Xrn1 resistant RNA / xrRNA) / resists degradation / exonuclease Xrn1 / small flaviviral RNA
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesMurray Valley encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.463 Å
AuthorsChapman, E.G. / Costantino, D.A. / Rabe, J.L. / Moon, S.L. / Wilusz, J. / Nix, J.C. / Kieft, J.S.
CitationJournal: Science / Year: 2014
Title: The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production.
Authors: Chapman, E.G. / Costantino, D.A. / Rabe, J.L. / Moon, S.L. / Wilusz, J. / Nix, J.C. / Kieft, J.S.
History
DepositionMar 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XRN1-resistant flaviviral RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,31410
Polymers22,0951
Non-polymers2199
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.698, 76.698, 76.448
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: RNA chain XRN1-resistant flaviviral RNA


Mass: 22095.186 Da / Num. of mol.: 1 / Mutation: U2G, G-U pair insertion / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 polymerase
Source: (synth.) Murray Valley encephalitis virus / References: GenBank: KC852196.1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / 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

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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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: drop: 1 uL 5 mg/mL RNA in 2.5 mM magnesium chloride, 10 mM HEPES-KOH pH 7.5 (heated to 65 C for 3 minutes, cooled at room temperature, 0.5 mM spermidine added, centrifuged for 10 minutes at ...Details: drop: 1 uL 5 mg/mL RNA in 2.5 mM magnesium chloride, 10 mM HEPES-KOH pH 7.5 (heated to 65 C for 3 minutes, cooled at room temperature, 0.5 mM spermidine added, centrifuged for 10 minutes at 13000 x g) + 2 uL 10% MPD, 40 mM sodium cacodylate, pH 6.0, 12 mM spermine, 80 mM sodium chloride, 20 mM magnesium chloride (Nucleic Acid Mini-Screen kit, Hampton Research), well: 20-35% MPD, crystals appeared within 2-3 days and grew to full size over 1-2 weeks. To obtain derivatized crystals for phasing, 5 uL 4 mM iridium (III) hexammine in RNase-free water was added directly to crystallization drops and well solutions <35% MPD were replaced with 35% MPD. Wells were then re-sealed and allowed to re-equilibrate for at least 2 days, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0972 Å
DetectorType: TAURUS-1 / Detector: CMOS / Date: Sep 27, 2013
RadiationMonochromator: Rosenbaum-Rock sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0972 Å / Relative weight: 1
ReflectionResolution: 2.45→50.14 Å / Num. obs: 9499
Reflection shellHighest resolution: 2.45 Å

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.463→50.14 Å / SU ML: 0.35 / σ(F): 1.39 / Phase error: 38.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2835 824 9.91 %RANDOM
Rwork0.2303 ---
obs0.2357 8418 85.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.463→50.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1466 9 7 1482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061641
X-RAY DIFFRACTIONf_angle_d1.2472560
X-RAY DIFFRACTIONf_dihedral_angle_d14.545813
X-RAY DIFFRACTIONf_chiral_restr0.05340
X-RAY DIFFRACTIONf_plane_restr0.00768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.463-2.54220.6652240.478180X-RAY DIFFRACTION13
2.5422-2.63310.4572630.438611X-RAY DIFFRACTION40
2.6331-2.73850.38441420.36321344X-RAY DIFFRACTION91
2.7385-2.86310.38261650.33571450X-RAY DIFFRACTION100
2.8631-3.01410.3751650.31151495X-RAY DIFFRACTION100
3.0141-3.20290.27771660.26231478X-RAY DIFFRACTION100
3.2029-3.45010.28811660.23031483X-RAY DIFFRACTION100
3.4501-3.79720.25161590.21661507X-RAY DIFFRACTION100
3.7972-4.34640.2711640.2011481X-RAY DIFFRACTION100
4.3464-5.47490.25771650.20511510X-RAY DIFFRACTION100
5.4749-50.15050.27141630.20511477X-RAY DIFFRACTION99

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