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- PDB-23jz: pre-miR-6074 internal loop in complex with amiloride (Form 1) -

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Basic information

Entry
Database: PDB / ID: 23jz
Titlepre-miR-6074 internal loop in complex with amiloride (Form 1)
ComponentsRNA (35-MER)
KeywordsRNA / pre-miR-6074
Function / homologyChem-AMR / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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: 2026
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
Revision 1.1May 20, 2026Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6766
Polymers11,2861
Non-polymers3905
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area6410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.102, 65.102, 69.596
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: RNA chain RNA (35-MER)


Mass: 11285.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-AMR / 3,5-DIAMINO-N-(AMINOIMINOMETHYL)-6-CHLOROPYRAZINECARBOXAMIDE / AMILORIDE


Mass: 229.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8ClN7O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Potassium chloride, Calcium chloride dihydrate, Sodium cacodylate trihydrate, Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→29.61 Å / Num. obs: 3993 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.57
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.382 / Num. unique obs: 287

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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: 2.9→29.61 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 389 9.76 %
Rwork0.1911 --
obs0.1939 3985 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 747 19 20 786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006851
X-RAY DIFFRACTIONf_angle_d0.9971323
X-RAY DIFFRACTIONf_dihedral_angle_d11.567417
X-RAY DIFFRACTIONf_chiral_restr0.045174
X-RAY DIFFRACTIONf_plane_restr0.00637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.320.29111260.23531171X-RAY DIFFRACTION99
3.32-4.180.21281290.19321173X-RAY DIFFRACTION100
4.18-29.610.18141340.16121252X-RAY DIFFRACTION99

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