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- PDB-7jnh: Crystal structure of a double-ENE RNA stability element in comple... -

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Basic information

Entry
Database: PDB / ID: 7jnh
TitleCrystal structure of a double-ENE RNA stability element in complex with a 28-mer poly(A) RNA
Components
  • 28-mer poly(A) RNA
  • Core double ENE RNA (Xtal construct) from Oryza sativa transposon,Core double ENE RNA (Xtal construct) from Oryza sativa transposon
KeywordsRNA / RNA stability / element for nuclear expression (ENE) / poly(A) tail / major-groove triple helix / quintuple-base transition motif / WC-H A-minor interaction / poly(A) 3-end binding pocket
Function / homologyCOBALT HEXAMMINE(III) / SPERMIDINE / STRONTIUM ION / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
Oryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.89 Å
AuthorsTorabi, S.F. / Vaidya, A.T. / Tycowski, K.T. / DeGregorio, S.J. / Wang, J. / Shu, M.D. / Steitz, T.A. / Steitz, J.A.
Funding support United States, 4items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA16038 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM022778 United States
Damon Runyon Cancer Research Foundation United States
CitationJournal: Science / Year: 2021
Title: RNA stabilization by a poly(A) tail 3'-end binding pocket and other modes of poly(A)-RNA interaction.
Authors: Torabi, S.F. / Vaidya, A.T. / Tycowski, K.T. / DeGregorio, S.J. / Wang, J. / Shu, M.D. / Steitz, T.A. / Steitz, J.A.
History
DepositionAug 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 28-mer poly(A) RNA
B: Core double ENE RNA (Xtal construct) from Oryza sativa transposon,Core double ENE RNA (Xtal construct) from Oryza sativa transposon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,39124
Polymers36,7142
Non-polymers2,67722
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-179 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.973, 93.973, 202.171
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 28-mer poly(A) RNA


Mass: 9172.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain Core double ENE RNA (Xtal construct) from Oryza sativa transposon,Core double ENE RNA (Xtal construct) from Oryza sativa transposon


Mass: 27541.082 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The terminal C is modified in the structure,The terminal C is modified in the structure
Source: (synth.) Oryza sativa (Asian cultivated rice) / References: GenBank: AL442105.2

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Non-polymers , 5 types, 40 molecules

#3: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Sr
#4: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CoH18N6
#5: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.51 Å3/Da / Density % sol: 64.97 %
Description: Rod shaped crystals appeared within 7 to 20 days
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mM sodium cacodylate, pH 7.0, 9 mM MgCl2, 1.8 mM cobalt (III) hexamine chloride, 0.9 mM spermidine, 2.5 mM spermine and 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9272 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9272 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 11859 / % possible obs: 95.1 % / Redundancy: 16.4 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.037 / Rrim(I) all: 0.151 / Χ2: 0.879 / Net I/σ(I): 17.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.89-310.23.2930.668120.1990.5760.9793.450.744
2.9-2.9519.57.4856460.1411.7097.6820.72499.8
2.95-3.0119.54.956220.3041.135.0790.74799.8
3.01-3.0719.43.7346300.5050.8533.8320.72299.7
3.07-3.14192.2146500.7630.5132.2730.74199.8
3.14-3.2118.51.3586190.920.321.3960.76999.8
3.21-3.2917.31.1126290.8850.2711.1460.76199.4
3.29-3.3818.20.9676450.9490.2280.9940.76599.7
3.38-3.48200.7896350.9650.1780.8090.78499.8
3.48-3.5919.90.6316370.9730.1430.6480.79499.7
3.59-3.7219.50.5046490.9860.1160.5170.8699.8
3.72-3.8719.30.356380.9910.0810.3590.868100
3.87-4.0418.90.2676470.9930.0620.2740.93299.8
4.04-4.2617.70.2276530.9930.0550.2340.948100
4.26-4.5217.80.1676590.9980.0410.1721.043100
4.52-4.8719.50.1396540.9970.0320.1431.074100
4.87-5.36190.116650.9970.0260.1131.155100
5.36-6.1417.90.0866810.9980.0210.0891.152100
6.14-7.7317.50.0616950.9990.0150.0630.96899.4
7.73-5015.90.0477760.9980.0130.0491.00699.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: dENE

Resolution: 2.89→47.03 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.956 / SU B: 16.955 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.707 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 581 4.9 %RANDOM
Rwork0.1842 ---
obs0.1862 11269 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 228.3 Å2 / Biso mean: 108.846 Å2 / Biso min: 75.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å2-0 Å2
2--0.7 Å2-0 Å2
3----2.28 Å2
Refinement stepCycle: final / Resolution: 2.89→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2324 121 0 2445
Biso mean--148.24 --
Num. residues----111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0112700
X-RAY DIFFRACTIONr_bond_other_d0.0030.021301
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.3924284
X-RAY DIFFRACTIONr_angle_other_deg1.6752.9833067
X-RAY DIFFRACTIONr_chiral_restr0.1380.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02564
LS refinement shellResolution: 2.895→2.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 22 -
Rwork0.454 564 -
all-586 -
obs--64.75 %

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