HEADER RNA 18-DEC-24 9HRO TITLE SOLUTION NMR STRUCTURE OF THE SYNTHETIC TOBRAMYCIN RIBOSWITCH IN TITLE 2 COMPLEX WITH TOBRAMYCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (35-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA-LIGAND COMPLEX, RIBOSWITCH, AMINOGLYCOSIDE, TRANSLATION KEYWDS 2 REGULATION, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR E.DUCHARDT-FERNER,J.WOEHNERT REVDAT 1 01-OCT-25 9HRO 0 JRNL AUTH E.DUCHARDT-FERNER,L.KRAUS,A.LIMOUCHI,B.SUESS,J.WOHNERT JRNL TITL STRUCTURAL BASIS FOR LIGAND RECOGNITION IN THE TOBRAMYCIN JRNL TITL 2 RIBOSWITCH. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 40902004 JRNL DOI 10.1093/NAR/GKAF817 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.KRAUS,E.DUCHARDT-FERNER,E.BRAEUCHLE,S.FUERBACHER,D.KELVIN, REMARK 1 AUTH 2 H.MARX,A.BOUSSEBAYLE,L.M.MAURER,C.BOFILL-BOSCH,J.WOEHNERT, REMARK 1 AUTH 3 B.SUESS REMARK 1 TITL DEVELOPMENT OF A NOVEL TOBRAMYCIN DEPENDENT RIBOSWITCH. REMARK 1 REF NUCLEIC ACIDS RES V. 51 11375 2023 REMARK 1 REFN ESSN 1362-4962 REMARK 1 PMID 37791877 REMARK 1 DOI 10.1093/NAR/GKAD767 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, CYANA REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9HRO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1292143537. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 298 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 85.9; 85.9 REMARK 210 PRESSURE : 1 BAR; 1 BAR REMARK 210 SAMPLE CONTENTS : 1 MM UNLABELED RNA (35-MER), 1.2 REMARK 210 MM UNLABELED TOBRAMYCIN, 95% H2O/ REMARK 210 5% D2O; 0.5 MM [U-100% 15N] RNA REMARK 210 (35-MER), 0.6 MM UNLABELED REMARK 210 TOBRAMYCIN, 95% H2O/5% D2O; 0.75 REMARK 210 MM [U-13C; U-15N]-ADE,CYT RNA REMARK 210 (35-MER), 0.9 MM UNLABELED REMARK 210 TOBRAMYCIN, 95% H2O/5% D2O; 0.75 REMARK 210 MM [U-13C; U-15N]-ADE,CYT RNA REMARK 210 (35-MER), 0.9 MM UNLABELED REMARK 210 TOBRAMYCIN, 100% D2O; 0.5 MM [U- REMARK 210 13C; U-15N]-URA,GUA RNA (35-MER), REMARK 210 0.6 MM UNLABELED TOBRAMYCIN, 95% REMARK 210 H2O/5% D2O; 0.5 MM [U-13C; U- REMARK 210 15N]-URA,GUA RNA (35-MER), 0.6 REMARK 210 MM UNLABELED TOBRAMYCIN, 100% REMARK 210 D2O; 0.84 MM [U-13C; U-15N] RNA REMARK 210 (35-MER), 1.004 MM UNLABELED REMARK 210 TOBRAMYCIN, 95% H2O/5% D2O; 0.84 REMARK 210 MM [U-13C; U-15N] RNA (35-MER), REMARK 210 1.004 MM UNLABELED TOBRAMYCIN, REMARK 210 100% D2O; 1 MM [U-100% 2H] RNA REMARK 210 (35-MER), 1.2 MM UNLABELED REMARK 210 TOBRAMYCIN, 95% H2O/5% D2O; 1 MM REMARK 210 [U-100% 2H] RNA (35-MER), 1.2 MM REMARK 210 UNLABELED TOBRAMYCIN, 100% D2O; REMARK 210 2.8 MM [U-13C; U-15N]-URA RNA REMARK 210 (35-MER), 2.2 MM UNLABELED REMARK 210 TOBRAMYCIN, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-15N HSQC REMARK 210 IMINO; 2D 1H-15N HSQC AMINO; 2D REMARK 210 HNN-COSY; 2D CPMG-NOESY; 3D 1H- REMARK 210 15N NOESY AMINO; 2D LONG-RANGE REMARK 210 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D H5(C5C4N4)H4; 2D REMARK 210 H1/H8-C5 HMBC; 2D H(CC)H-TOCSY; REMARK 210 2D H(N)CO; 2D H(C)N AROMATIC; 2D REMARK 210 H(C)N ALIPHATIC; 3D 1H-13C NOESY- REMARK 210 HSQC ARO; 3D 1H-13C NOESY-HSQC REMARK 210 ALI; 3D HCCH-COSY; 3D HCCH-TOCSY; REMARK 210 2D F1-FILTERED 1H-1H TOCSY; 2D REMARK 210 FI1-FILTERED 1H-1H TOCSY; 2D 1H- REMARK 210 1H TOCSY; 2D F1,F2-FILTERED 1H- REMARK 210 1H NOESY; 3D HCP REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ; 900 REMARK 210 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO; AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CARA REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34972 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF THE SYNTHETIC TOBRAMYCIN RIBOSWITCH IN REMARK 900 COMPLEX WITH TOBRAMYCIN DBREF 9HRO A 1 35 PDB 9HRO 9HRO 1 35 SEQRES 1 A 35 G G U G U U U C G G A A A SEQRES 2 A 35 G C U U C G G C U U C U A SEQRES 3 A 35 C C G A G C A C C HET TOY A 101 74 HETNAM TOY TOBRAMYCIN HETSYN TOY 4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5- HETSYN 2 TOY HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY- HETSYN 3 TOY CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5- HETSYN 4 TOY DIOL FORMUL 2 TOY C18 H37 N5 O9 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL CONECT 1121 1122 1123 1129 1153 CONECT 1122 1121 1137 CONECT 1123 1121 1124 1125 1154 CONECT 1124 1123 1155 1156 CONECT 1125 1123 1126 1157 1158 CONECT 1126 1125 1127 1128 1159 CONECT 1127 1126 1160 CONECT 1128 1126 1129 1130 1161 CONECT 1129 1121 1128 CONECT 1130 1128 1131 1162 1163 CONECT 1131 1130 1164 1165 CONECT 1132 1133 1134 1140 1166 CONECT 1133 1132 1167 1168 CONECT 1134 1132 1135 1169 1170 CONECT 1135 1134 1136 1137 1171 CONECT 1136 1135 1172 1173 CONECT 1137 1122 1135 1138 1174 CONECT 1138 1137 1139 1140 1175 CONECT 1139 1138 1176 CONECT 1140 1132 1138 1141 1177 CONECT 1141 1140 1142 CONECT 1142 1141 1143 1150 1178 CONECT 1143 1142 1144 1145 1179 CONECT 1144 1143 1180 CONECT 1145 1143 1146 1147 1181 CONECT 1146 1145 1182 1183 CONECT 1147 1145 1148 1149 1184 CONECT 1148 1147 1185 CONECT 1149 1147 1150 1151 1186 CONECT 1150 1142 1149 CONECT 1151 1149 1152 1187 1188 CONECT 1152 1151 1189 CONECT 1153 1121 CONECT 1154 1123 CONECT 1155 1124 CONECT 1156 1124 CONECT 1157 1125 CONECT 1158 1125 CONECT 1159 1126 CONECT 1160 1127 CONECT 1161 1128 CONECT 1162 1130 CONECT 1163 1130 CONECT 1164 1131 CONECT 1165 1131 CONECT 1166 1132 CONECT 1167 1133 CONECT 1168 1133 CONECT 1169 1134 CONECT 1170 1134 CONECT 1171 1135 CONECT 1172 1136 CONECT 1173 1136 CONECT 1174 1137 CONECT 1175 1138 CONECT 1176 1139 CONECT 1177 1140 CONECT 1178 1142 CONECT 1179 1143 CONECT 1180 1144 CONECT 1181 1145 CONECT 1182 1146 CONECT 1183 1146 CONECT 1184 1147 CONECT 1185 1148 CONECT 1186 1149 CONECT 1187 1151 CONECT 1188 1151 CONECT 1189 1152 MASTER 125 0 1 0 0 0 0 6 774 1 69 3 END