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- PDB-6cy4: RNA octamer containing 2'-OMe, 4'- Cbeta-OMe U. -

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Basic information

Entry
Database: PDB / ID: 6cy4
TitleRNA octamer containing 2'-OMe, 4'- Cbeta-OMe U.
ComponentsRNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)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: 1.851 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 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 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

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')
B: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')
C: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')
D: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')
E: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')
F: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')
G: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')
H: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)21,1968
Polymers21,1968
Non-polymers00
Water81145
1
A: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')
B: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,2992
Polymers5,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')
D: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,2992
Polymers5,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')
F: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,2992
Polymers5,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')
H: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,2992
Polymers5,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.438, 90.438, 64.123
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-104-

HOH

21C-101-

HOH

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Components

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


Mass: 2649.510 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 1 mM RNA; 40 mM sodium cacodylate, 80 mM sodium chloride, 12 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: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.43
ReflectionResolution: 1.851→18.727 Å / Num. obs: 16493 / % possible obs: 98.4 % / Redundancy: 51.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.19 / Net I/σ(I): 17.9
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 2 / Num. unique obs: 1637 / CC1/2: 0.478 / Rpim(I) all: 0.579

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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: 1.851→18.727 Å / Cross valid method: THROUGHOUT / σ(F): 0.13 / Phase error: 46.69
RfactorNum. reflection% reflection
Rfree0.2312 1656 5.03 %
Rwork0.227 --
obs0.2498 16409 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.5 Å2 / Biso mean: 48.2227 Å2 / Biso min: 18.26 Å2
Refinement stepCycle: final / Resolution: 1.851→18.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1368 0 45 1413
Biso mean---40.11 -
Num. residues----64
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8529-1.90730.38211100.40782634274494
1.9073-1.96860.4387920.4262644273695
1.9686-2.03870.47361060.4362629273595
2.0387-2.11990.44731180.39082576269494
2.1199-2.21590.40411640.3652568273293
2.2159-2.3320.32491140.36032667278195
2.332-2.47710.38351240.32762554267894
2.4771-2.66670.3011380.2892626276495
2.6667-2.93190.25991640.26792573273793
2.9319-3.34910.32691920.26272580277293
3.3491-4.19310.21321830.19612548273193
4.1931-12.54180.13671490.14992570271993

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