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- PDB-9if1: Unliganded structure of RNA duplex containing UGGAA/UGGAA motif -

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Basic information

Entry
Database: PDB / ID: 9if1
TitleUnliganded structure of RNA duplex containing UGGAA/UGGAA motif
ComponentsRNA (5'-R(*GP*GP*CP*AP*CP*UP*GP*GP*AP*AP*GP*UP*GP*CP*C)-3')
KeywordsRNA / UGGAA motif / SCA31
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsMateja-Pluta, M. / Kiliszek, A.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2022/45/B/NZ7/03543 Poland
Polish National Science Centre2017/26/E/NZ1/00950 Poland
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Naphthyridine carbamate dimer ligand induces formation of Z-RNA-like fold of disease-related RNA and exhibits a molecular glue characteristics in crystal lattice formation.
Authors: Mateja-Pluta, M. / Blaszczyk, L. / Bejger, M. / Nakatani, K. / Kiliszek, A.
History
DepositionFeb 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: 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
AAA: RNA (5'-R(*GP*GP*CP*AP*CP*UP*GP*GP*AP*AP*GP*UP*GP*CP*C)-3')
BBB: RNA (5'-R(*GP*GP*CP*AP*CP*UP*GP*GP*AP*AP*GP*UP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8553
Polymers9,6942
Non-polymers1611
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-8 kcal/mol
Surface area5570 Å2
Unit cell
Length a, b, c (Å)33.818, 33.818, 170.094
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: RNA chain RNA (5'-R(*GP*GP*CP*AP*CP*UP*GP*GP*AP*AP*GP*UP*GP*CP*C)-3')


Mass: 4846.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 0.012M Sodium chloride, 0.08M Potassium chloride, 0.04M Sodium cacodylate trihydrate pH 5.5 45% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.002M Hexammine cobalt(III) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.79→42.52 Å / Num. obs: 2764 / % possible obs: 97.3 % / Redundancy: 6.26 % / CC1/2: 0.999 / Net I/σ(I): 16.72
Reflection shellResolution: 2.79→2.96 Å / Num. unique obs: 348 / CC1/2: 0.982

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→42.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 20.997 / SU ML: 0.409 / Cross valid method: FREE R-VALUE / ESU R Free: 0.462
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3085 277 10.029 %
Rwork0.2573 2485 -
all0.262 --
obs-2762 97.254 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 28.256 Å2
Baniso -1Baniso -2Baniso -3
1-3.992 Å2-0 Å2-0 Å2
2--3.992 Å2-0 Å2
3----7.984 Å2
Refinement stepCycle: LAST / Resolution: 2.79→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 642 7 6 655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.011726
X-RAY DIFFRACTIONr_bond_other_d0.0030.02316
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.2861139
X-RAY DIFFRACTIONr_angle_other_deg1.5873755
X-RAY DIFFRACTIONr_chiral_restr0.1040.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02168
X-RAY DIFFRACTIONr_nbd_refined0.1630.2114
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2490.2395
X-RAY DIFFRACTIONr_nbtor_refined0.2520.2272
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.2155
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.28
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1520.222
X-RAY DIFFRACTIONr_nbd_other0.2230.219
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3760.21
X-RAY DIFFRACTIONr_scbond_it03726
X-RAY DIFFRACTIONr_scbond_other03727
X-RAY DIFFRACTIONr_scangle_it04.51138
X-RAY DIFFRACTIONr_scangle_other04.51139
X-RAY DIFFRACTIONr_lrange_it029.4811023
X-RAY DIFFRACTIONr_lrange_other029.4921024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.8620.496120.499104X-RAY DIFFRACTION60.4167
2.862-2.940.322190.367166X-RAY DIFFRACTION100
2.94-3.0240.249200.321184X-RAY DIFFRACTION100
3.024-3.1170.49180.266161X-RAY DIFFRACTION100
3.117-3.2190.431170.253157X-RAY DIFFRACTION100
3.219-3.3310.375180.275161X-RAY DIFFRACTION99.4444
3.331-3.4560.353180.278159X-RAY DIFFRACTION100
3.456-3.5960.267150.3140X-RAY DIFFRACTION100
3.596-3.7550.417170.264146X-RAY DIFFRACTION100
3.755-3.9360.456150.274137X-RAY DIFFRACTION100
3.936-4.1470.352140.239128X-RAY DIFFRACTION100
4.147-4.3960.306140.231124X-RAY DIFFRACTION100
4.396-4.6960.263140.273123X-RAY DIFFRACTION100
4.696-5.0670.37120.272115X-RAY DIFFRACTION100
5.067-5.5430.228120.301103X-RAY DIFFRACTION100
5.543-6.1840.171110.25397X-RAY DIFFRACTION100
6.184-7.1160.283100.22990X-RAY DIFFRACTION100
7.116-8.6550.36690.25582X-RAY DIFFRACTION100
8.655-11.9940.22270.21866X-RAY DIFFRACTION100
11.994-42.520.24450.18842X-RAY DIFFRACTION97.9167

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