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- PDB-7nrp: The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG -

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Basic information

Entry
Database: PDB / ID: 7nrp
TitleThe crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG
Components
  • DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3')
  • RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
KeywordsDNA-RNA HYBRID / Amide-LNA / duplex / DNA:RNA / unmodified
Function / homologyCACODYLATE ION / DNA / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsThorpe, C. / Hardwick, J. / McDonough, M.A. / Hall, J.P. / Baker, Y.R. / El-Sagheer, A.H. / Brown, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S018794/1 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides.
Authors: Baker, Y.R. / Thorpe, C. / Chen, J. / Poller, L.M. / Cox, L. / Kumar, P. / Lim, W.F. / Lie, L. / McClorey, G. / Epple, S. / Singleton, D. / McDonough, M.A. / Hardwick, J.S. / Christensen, K. ...Authors: Baker, Y.R. / Thorpe, C. / Chen, J. / Poller, L.M. / Cox, L. / Kumar, P. / Lim, W.F. / Lie, L. / McClorey, G. / Epple, S. / Singleton, D. / McDonough, M.A. / Hardwick, J.S. / Christensen, K.E. / Wood, M.J.A. / Hall, J.P. / El-Sagheer, A.H. / Brown, T.
History
DepositionMar 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
B: DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3843
Polymers6,2472
Non-polymers1371
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-4 kcal/mol
Surface area3780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.338, 54.338, 45.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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


Mass: 3255.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3')


Mass: 2991.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.5 mM duplex, 12 mM Mg(OAc)2, 0.6 mM Spermidine.HCl, 0.075% b-Octylglucoside, 12 mM Sodium cacodylate, 12 % (v/v) 2-Methyl-2,4-pentanediol (MPD); equilibrated against 50% MPD in H2O

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97862 Å / Relative weight: 1
ReflectionResolution: 2.67→27.17 Å / Num. obs: 2243 / % possible obs: 98.8 % / Redundancy: 19.3 % / Biso Wilson estimate: 84.71 Å2 / CC1/2: 0.996 / Net I/σ(I): 25.2
Reflection shellResolution: 2.67→2.8 Å / Num. unique obs: 275 / CC1/2: 0.646

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PJO

1pjo


Resolution: 2.67→27.17 Å / SU ML: 0.1955 / Cross valid method: FREE R-VALUE / σ(F): 0.82 / Phase error: 23.6638
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1905 270 6.33 %
Rwork0.1697 3996 -
obs0.171 2226 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.06 Å2
Refinement stepCycle: LAST / Resolution: 2.67→27.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 414 5 3 422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086466
X-RAY DIFFRACTIONf_angle_d1.2044720
X-RAY DIFFRACTIONf_chiral_restr0.044989
X-RAY DIFFRACTIONf_plane_restr0.005320
X-RAY DIFFRACTIONf_dihedral_angle_d10.0941212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-3.370.31631380.27191995X-RAY DIFFRACTION99.12
3.37-27.170.15711320.14322001X-RAY DIFFRACTION99.86

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