HEADER RNA 09-FEB-26 23JZ TITLE PRE-MIR-6074 INTERNAL LOOP IN COMPLEX WITH AMILORIDE (FORM 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (35-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS PRE-MIR-6074, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,M.OKADA,K.TSUZUKI,K.ONIZUKA,R.NAGASAWA,E.MIYASHITA, AUTHOR 2 K.R.KOMATSU,H.SAITO,F.NAGATSUGI REVDAT 2 20-MAY-26 23JZ 1 JRNL REVDAT 1 06-MAY-26 23JZ 0 JRNL AUTH K.TSUZUKI,K.ONIZUKA,M.OKADA,R.NAGASAWA,E.MIYASHITA, JRNL AUTH 2 K.R.KOMATSU,H.SAITO,J.KONDO,F.NAGATSUGI JRNL TITL RNA-BINDING LANDSCAPE OF AMILORIDE: LARGE-SCALE PROFILING JRNL TITL 2 AND STRUCTURAL BASIS OF U-U MISMATCH RECOGNITION. JRNL REF RSC CHEM BIOL 2026 JRNL REFN ESSN 2633-0679 JRNL PMID 42100640 JRNL DOI 10.1039/D6CB00055J REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 3985 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.760 REMARK 3 FREE R VALUE TEST SET COUNT : 389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.6100 - 4.1800 0.99 1252 134 0.1612 0.1814 REMARK 3 2 4.1800 - 3.3200 1.00 1173 129 0.1932 0.2128 REMARK 3 3 3.3200 - 2.9000 0.99 1171 126 0.2353 0.2911 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 851 REMARK 3 ANGLE : 0.997 1323 REMARK 3 CHIRALITY : 0.045 174 REMARK 3 PLANARITY : 0.006 37 REMARK 3 DIHEDRAL : 11.567 417 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 23JZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1300070029. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3993 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 29.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM CHLORIDE, CALCIUM CHLORIDE REMARK 280 DIHYDRATE, SODIUM CACODYLATE TRIHYDRATE, POLYETHYLENE GLYCOL REMARK 280 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.19867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.39733 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 46.39733 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 23.19867 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 104 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 10 O3' REMARK 620 2 A A 10 O2' 56.6 REMARK 620 3 A A 11 OP2 48.1 82.5 REMARK 620 4 G A 12 O6 109.7 74.7 155.4 REMARK 620 5 G A 13 O6 153.7 97.8 130.1 63.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 103 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 16 O4 REMARK 620 2 G A 17 O6 63.4 REMARK 620 3 HOH A 202 O 65.4 71.4 REMARK 620 4 HOH A 204 O 122.5 67.7 72.0 REMARK 620 5 HOH A 209 O 78.6 140.3 83.3 132.7 REMARK 620 6 HOH A 210 O 82.2 75.5 141.3 112.9 111.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 102 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 22 O4 REMARK 620 2 HOH A 201 O 64.0 REMARK 620 3 HOH A 206 O 73.2 109.1 REMARK 620 4 HOH A 207 O 113.8 68.5 82.0 REMARK 620 5 HOH A 211 O 82.9 132.9 90.6 158.5 REMARK 620 6 HOH A 212 O 100.6 73.1 170.9 106.8 81.9 REMARK 620 7 HOH A 217 O 144.8 145.9 76.9 79.6 79.1 106.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 105 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 27 OP2 REMARK 620 2 HOH A 208 O 127.9 REMARK 620 N 1 DBREF 23JZ A 1 35 PDB 23JZ 23JZ 1 35 SEQRES 1 A 35 G C U U G C U C U A A G G SEQRES 2 A 35 C A U G A A A G U G C U A SEQRES 3 A 35 U G A G A U A G C HET AMR A 101 15 HET CA A 102 1 HET CA A 103 1 HET CA A 104 1 HET CA A 105 1 HETNAM AMR 3,5-DIAMINO-N-(AMINOIMINOMETHYL)-6- HETNAM 2 AMR CHLOROPYRAZINECARBOXAMIDE HETNAM CA CALCIUM ION HETSYN AMR AMILORIDE FORMUL 2 AMR C6 H8 CL N7 O FORMUL 3 CA 4(CA 2+) FORMUL 7 HOH *20(H2 O) LINK O3' A A 10 CA CA A 104 1555 1555 3.08 LINK O2' A A 10 CA CA A 104 1555 1555 2.61 LINK OP2 A A 11 CA CA A 104 1555 1555 3.03 LINK O6 G A 12 CA CA A 104 1555 1555 2.87 LINK O6 G A 13 CA CA A 104 1555 1555 3.13 LINK O4 U A 16 CA CA A 103 1555 1555 2.57 LINK O6 G A 17 CA CA A 103 1555 1555 2.56 LINK O4 U A 22 CA CA A 102 1555 1555 2.31 LINK OP2 U A 27 CA CA A 105 1555 1555 2.97 LINK CA CA A 102 O HOH A 201 1555 1555 2.33 LINK CA CA A 102 O HOH A 206 1555 1555 2.34 LINK CA CA A 102 O HOH A 207 1555 1555 2.45 LINK CA CA A 102 O HOH A 211 1555 1555 2.36 LINK CA CA A 102 O HOH A 212 1555 1555 2.32 LINK CA CA A 102 O HOH A 217 1555 1555 2.55 LINK CA CA A 103 O HOH A 202 1555 1555 2.21 LINK CA CA A 103 O HOH A 204 1555 1555 2.30 LINK CA CA A 103 O HOH A 209 1555 1555 2.89 LINK CA CA A 103 O HOH A 210 1555 1555 2.47 LINK CA CA A 105 O HOH A 208 1555 1555 2.97 CRYST1 65.102 65.102 69.596 90.00 90.00 120.00 P 31 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015361 0.008868 0.000000 0.00000 SCALE2 0.000000 0.017737 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014369 0.00000 CONECT 192 766 CONECT 194 766 CONECT 208 766 CONECT 245 766 CONECT 268 766 CONECT 333 765 CONECT 353 765 CONECT 465 764 CONECT 555 767 CONECT 749 750 762 CONECT 750 749 751 757 CONECT 751 750 752 756 CONECT 752 751 753 CONECT 753 752 754 755 CONECT 754 753 CONECT 755 753 CONECT 756 751 CONECT 757 750 758 759 CONECT 758 757 CONECT 759 757 760 CONECT 760 759 761 762 CONECT 761 760 CONECT 762 749 760 763 CONECT 763 762 CONECT 764 465 768 773 774 CONECT 764 778 779 784 CONECT 765 333 353 769 771 CONECT 765 776 777 CONECT 766 192 194 208 245 CONECT 766 268 CONECT 767 555 775 CONECT 768 764 CONECT 769 765 CONECT 771 765 CONECT 773 764 CONECT 774 764 CONECT 775 767 CONECT 776 765 CONECT 777 765 CONECT 778 764 CONECT 779 764 CONECT 784 764 MASTER 247 0 5 0 0 0 0 6 786 1 42 3 END