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- PDB-7y2p: Crystal structure of CUG repeat RNA duplex containing A-U base pa... -

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Basic information

Entry
Database: PDB / ID: 7y2p
TitleCrystal structure of CUG repeat RNA duplex containing A-U base pair and U-U mismatches
Components
  • RNA (5'-R(P*UP*UP*CP*UP*GP*CP*AP*GP*CP*UP*GP*AP*A)-3')
  • RNA (5'-R(P*UP*UP*CP*UP*GP*CP*UP*GP*CP*UP*GP*AP*A)-3')
KeywordsRNA / CUG repeats / Myotonic dystrophy type 1 (DM1) / U-U mismatches / A-U base pair
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,2142
Polymers8,2142
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-9 kcal/mol
Surface area5010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.228, 49.228, 35.802
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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


Mass: 4118.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.4 mM Oligonucleotide, 50 mM HEPES pH 6.5, 0.5 mM Spermine tetrahydrochloride, 10% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→30 Å / Num. obs: 12483 / % possible obs: 94 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.017 / Rrim(I) all: 0.051 / Χ2: 1.052 / Net I/σ(I): 23.4 / Num. measured all: 126315
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.6410.80.39813420.9830.1270.4181.091100
1.64-1.710.90.24613100.9940.0790.2581.088100
1.7-1.78110.19413230.9920.0620.2041.071100
1.78-1.87110.16413330.9930.0520.1721.02399.9
1.87-1.998.60.11710090.990.0450.1261.08977.1
1.99-2.1410.70.08513370.9980.0270.0891.059100
2.14-2.369.10.06810910.9940.0260.0731.03681.6
2.36-2.710.50.0513220.9990.0160.0521.038100
2.7-3.49.70.04113290.9990.0140.0431.00599.8
3.4-307.90.03410870.9990.0120.0361.00281.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Y2B

7y2b


Resolution: 1.58→24.61 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 34.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2549 1246 10.08 %
Rwork0.2363 11119 -
obs0.2382 12365 93.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.34 Å2 / Biso mean: 28.2375 Å2 / Biso min: 17.24 Å2
Refinement stepCycle: final / Resolution: 1.58→24.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 550 0 113 663
Biso mean---35.33 -
Num. residues----26
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.640.34381480.2671309145797
1.64-1.720.28761440.24781279142399
1.72-1.810.28521370.248913571494100
1.81-1.920.36931220.37261093121583
1.93-2.070.28031390.28711247138695
2.07-2.280.32271150.30361089120482
2.28-2.610.25831580.254913241482100
2.61-3.280.2561580.215413261484100
3.29-24.610.20111250.18581095122084

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