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- PDB-7y2b: Crystal structure of CUG repeat RNA duplex containing U-U mismatches -

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Basic information

Entry
Database: PDB / ID: 7y2b
TitleCrystal structure of CUG repeat RNA duplex containing U-U mismatches
ComponentsRNA (5'-R(P*UP*UP*CP*UP*GP*CP*UP*GP*CP*UP*GP*AP*A)-3')
KeywordsRNA / CUG repeats / U-U mismatch / Myotonic dystrophy type 1 (DM1) / Water mediated U-U mismatch
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsWang, S.C. / Satange, R.B. / Hou, M.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2628-M-005-001-MY4 Taiwan
Ministry of Science and Technology (MoST, Taiwan)109-2311-B-005-007-MY3 Taiwan
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural basis for water modulating RNA duplex formation in the CUG repeats of myotonic dystrophy type 1.
Authors: Wang, S.C. / Chen, Y.T. / Satange, R. / Chu, J.W. / Hou, M.H.
History
DepositionJun 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
S: RNA (5'-R(P*UP*UP*CP*UP*GP*CP*UP*GP*CP*UP*GP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)4,0951
Polymers4,0951
Non-polymers00
Water1,04558
1
S: RNA (5'-R(P*UP*UP*CP*UP*GP*CP*UP*GP*CP*UP*GP*AP*A)-3')

S: RNA (5'-R(P*UP*UP*CP*UP*GP*CP*UP*GP*CP*UP*GP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)8,1912
Polymers8,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area1240 Å2
ΔGint-11 kcal/mol
Surface area5030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.262, 49.262, 36.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11S-140-

HOH

21S-145-

HOH

31S-151-

HOH

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Components

#1: RNA chain RNA (5'-R(P*UP*UP*CP*UP*GP*CP*UP*GP*CP*UP*GP*AP*A)-3')


Mass: 4095.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.4 mM oligonucleotide, 3.5 mM Spermine tetrahydrochloride, 50 mM HEPES pH 6.5, 10% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→30 Å / Num. obs: 4355 / % possible obs: 99.4 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.02 / Rrim(I) all: 0.063 / Χ2: 1.062 / Net I/σ(I): 11.5 / Num. measured all: 44478
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.87-1.9410.10.3834250.9570.1270.4041.095100
1.94-2.0110.70.2974350.9790.0950.3121.093100
2.01-2.1110.90.2164260.990.0690.2271.068100
2.11-2.2210.80.1794230.9930.0570.1881.089100
2.22-2.3610.10.1414360.9930.0470.1481.03100
2.36-2.5410.60.1084370.9950.0350.1131.071100
2.54-2.7910.40.0794300.9960.0260.0841.042100
2.79-3.210.30.0544420.9990.0190.0571.053100
3.2-4.038.60.0444270.9990.0160.0461.0194.7
4.03-309.60.044740.9990.0140.0431.05899.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zev

1zev


Resolution: 1.88→24.63 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 424 9.8 %
Rwork0.2167 3902 -
obs0.2172 4326 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.49 Å2 / Biso mean: 30.0278 Å2 / Biso min: 20.4 Å2
Refinement stepCycle: final / Resolution: 1.88→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 274 0 58 332
Biso mean---35.5 -
Num. residues----13
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.88-1.940.27811450.25891287100
1.94-2.70.28981380.24281293100
2.71-24.630.19041410.19132297

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