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- PDB-9yre: RNA oligonucleotides containing 4'-(R)-methyl-alpha-(L)-threofura... -

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Basic information

Entry
Database: PDB / ID: 9yre
TitleRNA oligonucleotides containing 4'-(R)-methyl-alpha-(L)-threofuranosyl nucleic acid.
ComponentsChains: A,B,C,D,E,F,G,H
KeywordsRNA / Me-TNA / modified 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 / SYNCHROTRON / SAD / Resolution: 1.54 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

Downloads & links

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Assembly

Deposited unit
A: Chains: A,B,C,D,E,F,G,H
B: Chains: A,B,C,D,E,F,G,H
C: Chains: A,B,C,D,E,F,G,H
D: Chains: A,B,C,D,E,F,G,H
E: Chains: A,B,C,D,E,F,G,H
F: Chains: A,B,C,D,E,F,G,H
G: Chains: A,B,C,D,E,F,G,H
H: Chains: A,B,C,D,E,F,G,H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,68456
Polymers30,8998
Non-polymers16,78548
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.787, 90.821, 48.947
Angle α, β, γ (deg.)90.000, 98.723, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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RNA chain , 1 types, 8 molecules ABCDEFGH

#1: RNA chain
Chains: A,B,C,D,E,F,G,H


Mass: 3862.394 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 6 types, 291 molecules

#2: Chemical
ChemComp-A1CY1 / 1-(5-deoxy-3-O-phosphono-beta-D-xylofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione


Type: RNA linking / Mass: 322.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-5BU / 5-BROMO-URIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 403.077 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H12BrN2O9P
#4: Chemical
ChemComp-C / CYTIDINE-5'-MONOPHOSPHATE


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


Mass: 363.221 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H14N5O8P
#6: Chemical
ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C9H14N3O8P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 43.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Drops contained 400 nl of 1 mM RNA and 400 nl of buffer containing 10% 2-methyl-2,4-pentanediol (MPD), 12 mM spermine 4 HCl, 80 mM potassium chloride, 12 mM NaCl and 40 mM sodium cacodylate, pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9187 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9187 Å / Relative weight: 1
ReflectionResolution: 1.54→30.43 Å / Num. obs: 36267 / % possible obs: 91.8 % / Redundancy: 13.2 % / Biso Wilson estimate: 22.78 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.99
Reflection shellResolution: 1.54→1.56 Å / Num. unique obs: 883 / CC1/2: 0.571

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
DIALSdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.54→30.43 Å / SU ML: 0.2168 / Cross valid method: FREE R-VALUE / σ(F): 0.25 / Phase error: 35.794
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2835 3532 4.96 %
Rwork0.2434 67714 -
obs0.2455 36163 91.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.42 Å2
Refinement stepCycle: LAST / Resolution: 1.54→30.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1019 1016 243 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01732251
X-RAY DIFFRACTIONf_angle_d1.81843468
X-RAY DIFFRACTIONf_chiral_restr0.0825465
X-RAY DIFFRACTIONf_plane_restr0.018896
X-RAY DIFFRACTIONf_dihedral_angle_d25.50591491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.3912880.34791650X-RAY DIFFRACTION57.38
1.56-1.580.3144930.30881885X-RAY DIFFRACTION62.52
1.58-1.610.3188660.30251967X-RAY DIFFRACTION67.5
1.61-1.630.3341360.30382157X-RAY DIFFRACTION71.06
1.63-1.660.27321270.29032310X-RAY DIFFRACTION80.59
1.66-1.690.33081250.2732619X-RAY DIFFRACTION87
1.69-1.720.36551830.27142739X-RAY DIFFRACTION93.53
1.72-1.750.32461360.26352811X-RAY DIFFRACTION96.81
1.75-1.790.29571570.272944X-RAY DIFFRACTION99.26
1.79-1.830.33271450.27622980X-RAY DIFFRACTION99.55
1.83-1.870.33151450.27872894X-RAY DIFFRACTION99.38
1.87-1.910.31631770.27912970X-RAY DIFFRACTION99.49
1.91-1.970.3061430.26222921X-RAY DIFFRACTION99.58
1.97-2.020.32461220.26012951X-RAY DIFFRACTION99.07
2.02-2.090.29831280.26382933X-RAY DIFFRACTION99.38
2.09-2.160.33581460.25822938X-RAY DIFFRACTION99.1
2.16-2.250.34061520.27562930X-RAY DIFFRACTION99.45
2.25-2.350.26731510.27142862X-RAY DIFFRACTION96.39
2.35-2.480.33421450.27192874X-RAY DIFFRACTION97.51
2.48-2.630.2951750.26922923X-RAY DIFFRACTION99.55
2.63-2.830.31951270.26732982X-RAY DIFFRACTION99.42
2.84-3.120.29121740.25112884X-RAY DIFFRACTION98.61
3.12-3.570.27551430.2132906X-RAY DIFFRACTION98.58
3.57-4.50.21431780.21052833X-RAY DIFFRACTION96.35
4.5-30.430.25771700.2042851X-RAY DIFFRACTION97.67

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