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- PDB-9o47: RNA dodecamer containing a serinol nucleic acid. -

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Basic information

Entry
Database: PDB / ID: 9o47
TitleRNA dodecamer containing a serinol nucleic acid.
ComponentsChains: A,B
KeywordsRNA / serinol nucleic acid
Function / homology5-BROMO-URIDINE-5'-MONOPHOSPHATE / GUANOSINE-5'-MONOPHOSPHATE / : / CYTIDINE-5'-MONOPHOSPHATE / CYTIDINE-5'-MONOPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.6 Å
AuthorsHarp, J.M. / Egli, M.E.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Acyclic serinol nucleic acid modification of siRNAs overcomes seed region mediated off-target effects while maintaining potency.
Authors: Chickering, T. / Harp, J.M. / Jiang, Y. / Qin, J. / He, G. / Hyde, S. / Ihlefeld, A. / Janas, M. / O'Flaherty, D.K. / Schofield, S. / Szeto, J. / Theile, C.S. / Charisse, K. / Jadhav, V. / ...Authors: Chickering, T. / Harp, J.M. / Jiang, Y. / Qin, J. / He, G. / Hyde, S. / Ihlefeld, A. / Janas, M. / O'Flaherty, D.K. / Schofield, S. / Szeto, J. / Theile, C.S. / Charisse, K. / Jadhav, V. / Maier, M.A. / Manoharan, M. / Egli, M. / Schlegel, M.K.
History
DepositionApr 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chains: A,B
B: Chains: A,B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,96314
Polymers7,7372
Non-polymers4,22612
Water1,71195
1
A: Chains: A,B
hetero molecules

B: Chains: A,B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,96314
Polymers7,7372
Non-polymers4,22612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area4730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.021, 29.185, 29.782
Angle α, β, γ (deg.)110.874, 100.287, 111.585
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain Chains: A,B


Mass: 3868.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 107 molecules

#2: Chemical ChemComp-A1B9T / [2-[2-(2-$l^{3}-oxidanylidene-5-methyl-4-oxidanylidene-4,5-dihydro-2~{H}-pyrimidin-1-yl)ethanoylamino]-3-oxidanyl-propyl] dihydrogen phosphate


Type: RNA linking / Mass: 337.223 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N3O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-5BU / 5-BROMO-URIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 403.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12BrN2O9P
#4: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P
#5: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N3O8P
#6: Chemical ChemComp-C / CYTIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Drops contained 400 nanoliters of 1 mM RNA and 400 nanoliters of buffer containing 10% 2-methyl-2,4- pentanediol (MPD), 12 mM spermine 4 HCl, 80 mM potassium chloride, and 40 mM sodium ...Details: Drops contained 400 nanoliters of 1 mM RNA and 400 nanoliters of buffer containing 10% 2-methyl-2,4- pentanediol (MPD), 12 mM spermine 4 HCl, 80 mM potassium chloride, and 40 mM sodium cacodylate, pH 6.0. Drops were equilibrated against reservoirs containing 70 microliters of 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.342 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Aug 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.342 Å / Relative weight: 1
ReflectionResolution: 1.6→16.24 Å / Num. obs: 8629 / % possible obs: 98.25 % / Redundancy: 2.9 % / Biso Wilson estimate: 16.6 Å2 / CC1/2: 0.997 / Net I/σ(I): 3.4
Reflection shellResolution: 1.6→1.7 Å / Num. unique obs: 2924 / CC1/2: 0.259

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→16.24 Å / SU ML: 0.1939 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 31.0738
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2233 806 4.75 %
Rwork0.1958 16173 -
obs0.1972 16979 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.79 Å2
Refinement stepCycle: LAST / Resolution: 1.6→16.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 254 256 95 605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004562
X-RAY DIFFRACTIONf_angle_d0.9357860
X-RAY DIFFRACTIONf_chiral_restr0.0249108
X-RAY DIFFRACTIONf_plane_restr0.004728
X-RAY DIFFRACTIONf_dihedral_angle_d23.3231336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.70.27821540.26812604X-RAY DIFFRACTION96.84
1.7-1.830.26641270.22762692X-RAY DIFFRACTION97.27
1.83-2.020.27621250.23942738X-RAY DIFFRACTION98.59
2.02-2.310.20221130.21082717X-RAY DIFFRACTION98.95
2.31-2.90.29621300.21522749X-RAY DIFFRACTION99.69
2.9-16.240.17821570.1562673X-RAY DIFFRACTION98.13

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