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- PDB-6mj0: Crystal structure of the complete turnip yellow mosaic virus 3'UTR -

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Basic information

Entry
Database: PDB / ID: 6mj0
TitleCrystal structure of the complete turnip yellow mosaic virus 3'UTR
ComponentsRNA (101-MER)
KeywordsRNA / tRNA like-structure / tRNA mimicry / translation enhancer / programmed conformational changes
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesTurnip yellow mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHartwick, E.W. / Costantino, D.A. / MacFadden, A. / Nix, J.C. / Tian, S. / Das, R. / Kieft, J.S.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35GM118070 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM097333 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P30CA046934 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10OD012033 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: Nat Commun / Year: 2018
Title: Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels.
Authors: Hartwick, E.W. / Costantino, D.A. / MacFadden, A. / Nix, J.C. / Tian, S. / Das, R. / Kieft, J.S.
History
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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 (101-MER)
B: RNA (101-MER)


Theoretical massNumber of molelcules
Total (without water)66,6412
Polymers66,6412
Non-polymers00
Water00
1
A: RNA (101-MER)


Theoretical massNumber of molelcules
Total (without water)33,3211
Polymers33,3211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA (101-MER)


Theoretical massNumber of molelcules
Total (without water)33,3211
Polymers33,3211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.032, 129.126, 172.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: RNA chain RNA (101-MER)


Mass: 33320.738 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Turnip yellow mosaic virus

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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: 4.29 Å3/Da / Density % sol: 71.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5 mg/mL RNA was resuspended in 2.5 mM magnesium chloride and 10 mM HEPES KOH pH 7.4 and DPEC treated water. The RNA was heated at 65 degrees Celsius and slow cooled to room temperature ...Details: 5 mg/mL RNA was resuspended in 2.5 mM magnesium chloride and 10 mM HEPES KOH pH 7.4 and DPEC treated water. The RNA was heated at 65 degrees Celsius and slow cooled to room temperature followed by the addition of spermidine (0.5 mM final). Crystals were grown in 50 mM cacodylate, 2.5 M ammonium sulfate, 20 mM magnesium chloride, 1.0 mM spermine, and 2 mM hexamine cobalt chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.072 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 3.1→35.79 Å / Num. obs: 21141 / % possible obs: 89.41 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.036 / Rrim(I) all: 0.095 / Net I/σ(I): 16.69
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.69 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 1352 / Rpim(I) all: 0.69 / Rrim(I) all: 1.83 / % possible all: 64.37

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4p5j

4p5j


Resolution: 3.1→35.79 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 1629 8.59 %
Rwork0.2269 --
obs0.2303 18974 89.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→35.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4286 0 0 4286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084786
X-RAY DIFFRACTIONf_angle_d1.5177450
X-RAY DIFFRACTIONf_dihedral_angle_d15.7162418
X-RAY DIFFRACTIONf_chiral_restr0.0591010
X-RAY DIFFRACTIONf_plane_restr0.01202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.19120.3627970.3761018X-RAY DIFFRACTION64
3.1912-3.29410.37651040.32451103X-RAY DIFFRACTION69
3.2941-3.41170.35451120.3091216X-RAY DIFFRACTION76
3.4117-3.54820.33321230.27641299X-RAY DIFFRACTION82
3.5482-3.70960.31761340.30171422X-RAY DIFFRACTION88
3.7096-3.90490.31931450.27641536X-RAY DIFFRACTION97
3.9049-4.14920.29251490.23791592X-RAY DIFFRACTION99
4.1492-4.4690.28511510.24321604X-RAY DIFFRACTION99
4.469-4.91770.28791500.21981609X-RAY DIFFRACTION100
4.9177-5.6270.25831520.20381624X-RAY DIFFRACTION100
5.627-7.08040.28931550.2131643X-RAY DIFFRACTION100
7.0804-35.7920.18891570.18031679X-RAY DIFFRACTION98

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