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- PDB-9yrd: RNA oligonucleotides containing 4prime-(S)-methyl-alpha-(L)-threo... -

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Basic information

Entry
Database: PDB / ID: 9yrd
TitleRNA oligonucleotides containing 4prime-(S)-methyl-alpha-(L)-threofuranosyl nucleic acid.
ComponentsRNA oligonucleotide
KeywordsRNA / TNA / RNA duplex / threofuranosyl nuclei acid
Function / homologyGUANOSINE-5'-MONOPHOSPHATE / : / CYTIDINE-5'-MONOPHOSPHATE / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsHarp, J.M. / Egli, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Chiral-4'-Methyl-alpha-(l)-Threofuranosyl Nucleic Acids: Synthesis, Structure, Binding Affinity, Nuclease Resistance, and Polymerase Recognition.
Authors: Mikami, A. / Datta, D. / Kundu, J. / Kumar, V. / Erande, N. / Medina, E. / Maola, V.A. / Lee, E.M. / Matsuda, S. / Harp, J.M. / Egli, M. / Chaput, J.C. / Manoharan, M.
History
DepositionOct 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2026Provider: repository / Type: Initial release
Revision 1.1Nov 4, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA oligonucleotide
B: RNA oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1768
Polymers5,1592
Non-polymers2,0176
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.791, 44.791, 67.761
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: RNA chain RNA oligonucleotide


Mass: 2579.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Chemical ChemComp-A1CY0 / 1-(5-deoxy-3-O-phosphono-alpha-L-arabinofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione


Type: RNA linking / Mass: 322.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-C / CYTIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Drops contained 400 nL of 1 mM RNA and 400 nL of buffer containing 10% MPD, 12 mM spermine 4 HCl, 80 mM potassium chloride, and 40 mM sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→22.4 Å / Num. obs: 1740 / % possible obs: 93.41 % / Redundancy: 9.8 % / Biso Wilson estimate: 69.36 Å2 / CC1/2: 0.979 / Net I/σ(I): 5.46
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 178 / CC1/2: 0.735

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
DIALSdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→22.4 Å / SU ML: 0.2557 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 38.6892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3032 171 5.86 %
Rwork0.2582 2749 -
obs0.2609 1498 93.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.67 Å2
Refinement stepCycle: LAST / Resolution: 2.6→22.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 210 126 1 337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0019368
X-RAY DIFFRACTIONf_angle_d1.2675562
X-RAY DIFFRACTIONf_chiral_restr0.034176
X-RAY DIFFRACTIONf_plane_restr0.001416
X-RAY DIFFRACTIONf_dihedral_angle_d23.8852226
LS refinement shellResolution: 2.6→2.69 Å
RfactorNum. reflection% reflection
Rfree0.3032 171 -
Rwork0.2582 2749 -
obs--93.41 %

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