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- PDB-6cy2: RNA octamer containing 2'-OMe, 4'Calpha-OMe U. -

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Basic information

Entry
Database: PDB / ID: 6cy2
TitleRNA octamer containing 2'-OMe, 4'Calpha-OMe U.
ComponentsRNA (5'-R(*(CBV)P*GP*AP*AP*(UOA)P*UP*CP*G)-3')
KeywordsRNA / oligonucleotide / modified base
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsHarp, J.M. / Egli, M.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis for the synergy of 4'- and 2'-modifications on siRNA nuclease resistance, thermal stability and RNAi activity.
Authors: Harp, J.M. / Guenther, D.C. / Bisbe, A. / Perkins, L. / Matsuda, S. / Bommineni, G.R. / Zlatev, I. / Foster, D.J. / Taneja, N. / Charisse, K. / Maier, M.A. / Rajeev, K.G. / Manoharan, M. / Egli, M.
History
DepositionApr 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 2.0Oct 3, 2018Group: Atomic model / Data collection / Database references / Category: atom_site / atom_site_anisotrop / citation
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,2992
Polymers5,2992
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint3 kcal/mol
Surface area3060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.500, 31.500, 85.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 2649.510 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1 mM RNA; 40 mM sodium cacodylate, 80 mM potassium chloride, 20 mM magnesium chloride, 12 mM spermine. Reservoir 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9183 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 1.4→21.4 Å / Num. obs: 16014 / % possible obs: 98.7 % / Redundancy: 13.5 % / CC1/2: 0.997 / Rpim(I) all: 0.03 / Net I/σ(I): 11
Reflection shellResolution: 1.4→1.45 Å / CC1/2: 0.529 / Rpim(I) all: 0.684

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Processing

Software
NameVersionClassification
PHENIX1.13_2992refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→21.4 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.94 / Phase error: 25.48
RfactorNum. reflection% reflection
Rfree0.2051 726 4.53 %
Rwork0.184 --
obs0.185 16009 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.32 Å2 / Biso mean: 27.5932 Å2 / Biso min: 17.7 Å2
Refinement stepCycle: final / Resolution: 1.4→21.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 342 0 61 403
Biso mean---37.53 -
Num. residues----16
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.50810.30351500.24963022317298
1.5081-1.65980.2391120.18213089320198
1.6598-1.89990.18911690.1493022319199
1.8999-2.39310.23041430.199130903233100
2.3931-21.40250.19051520.18043060321299

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