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- PDB-23ka: pre-miR-6074 internal loop in complex with amiloride (Form 2) -

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Basic information

Entry
Database: PDB / ID: 23ka
Titlepre-miR-6074 internal loop in complex with amiloride (Form 2)
ComponentsRNA (35-MER)
KeywordsRNA / pre-miR-6074
Function / homologyChem-AMR / CACODYLIC ACID / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,75310
Polymers33,8573
Non-polymers8967
Water70339
1
A: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5383
Polymers11,2861
Non-polymers2532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6764
Polymers11,2861
Non-polymers3913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5383
Polymers11,2861
Non-polymers2532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.511, 61.511, 106.158
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: RNA chain RNA (35-MER)


Mass: 11285.740 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: C6H8ClN7O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE


Mass: 137.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Sodium citrate tribasic dihydrate, Sodium cacodylate trihydrate, 2-Propanol

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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: Oct 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.59→37.6 Å / Num. obs: 13907 / % possible obs: 99.9 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 23.51
Reflection shellResolution: 2.59→2.69 Å / Rmerge(I) obs: 0.343 / Num. unique obs: 1026

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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: 2.59→37.6 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 2.04 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2192 1413 10.16 %
Rwork0.182 --
obs0.1858 13903 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2241 53 39 2333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092557
X-RAY DIFFRACTIONf_angle_d1.5913975
X-RAY DIFFRACTIONf_dihedral_angle_d14.4021251
X-RAY DIFFRACTIONf_chiral_restr0.089522
X-RAY DIFFRACTIONf_plane_restr0.011111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.690.3131280.33241228X-RAY DIFFRACTION99
2.69-2.790.43981500.3731282X-RAY DIFFRACTION100
2.79-2.920.39481400.32341244X-RAY DIFFRACTION100
2.92-3.070.35171460.25881266X-RAY DIFFRACTION100
3.07-3.270.25621420.20291215X-RAY DIFFRACTION100
3.27-3.520.24541360.20231254X-RAY DIFFRACTION100
3.52-3.870.21531440.16231263X-RAY DIFFRACTION100
3.87-4.430.17161360.15221256X-RAY DIFFRACTION100
4.43-5.580.13931390.12461265X-RAY DIFFRACTION100
5.58-37.60.16491520.13351217X-RAY DIFFRACTION100

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