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- PDB-23jy: pre-miR-6074 internal loop -

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Basic information

Entry
Database: PDB / ID: 23jy
Titlepre-miR-6074 internal loop
ComponentsRNA (5'-R(*UP*UP*GP*CP*GP*GP*AP*UP*AP*CP*CP*CP*GP*GP*GP*UP*UP*GP*CP*CP*GP*C)-3')
KeywordsRNA / pre-miR-6074
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKondo, J. / Okada, M. / Tsuzuki, K. / Onizuka, K. / Nagasawa, R. / Miyashita, E. / Komatsu, K.R. / Saito, H. / Nagatsugi, F.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP25ama121014 Japan
CitationJournal: Rsc Chem Biol / Year: 2025
Title: RNA-binding Landscape of Amiloride: Large-scale Profiling and Structural Basis of U-U Mismatch Recognition
Authors: Tsuzuki, K. / Onizuka, K. / Okada, M. / Nagasawa, R. / Miyashita, E. / Komatsu, K.R. / Saito, H. / Kondo, J. / Nagatsugi, F.
History
DepositionFeb 9, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*UP*UP*GP*CP*GP*GP*AP*UP*AP*CP*CP*CP*GP*GP*GP*UP*UP*GP*CP*CP*GP*C)-3')
B: RNA (5'-R(*UP*UP*GP*CP*GP*GP*AP*UP*AP*CP*CP*CP*GP*GP*GP*UP*UP*GP*CP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)14,0842
Polymers14,0842
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-11 kcal/mol
Surface area7650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.662, 66.662, 53.348
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 7042.202 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.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Sodium chloride, Spermine, MPD, MOPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→28.87 Å / Num. obs: 3137 / % possible obs: 92.6 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 13.31
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.89 / Num. unique obs: 190

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→28.87 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 304 9.92 %
Rwork0.1906 --
obs0.1962 3066 90.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 856 0 7 863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008954
X-RAY DIFFRACTIONf_angle_d1.4691484
X-RAY DIFFRACTIONf_dihedral_angle_d11.65474
X-RAY DIFFRACTIONf_chiral_restr0.087200
X-RAY DIFFRACTIONf_plane_restr0.00740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.530.43641430.36031258X-RAY DIFFRACTION83
3.53-28.870.19421610.1421504X-RAY DIFFRACTION98

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