HEADER RNA 18-FEB-25 9NDV TITLE SCAFFOLD ATTACHED TO QUININE-I APTAMER (TONIC) LOCAL REFINEMENT OF TITLE 2 APTAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (67-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 SYNTHETIC, APTAMER, ENGINEERING, RIBOSWITCH, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR C.P.JONES,A.R.FERRE-D'AMARE REVDAT 1 04-MAR-26 9NDV 0 JRNL AUTH C.P.JONES,A.R.FERRE-D'AMARE JRNL TITL SYMMETRIC SCAFFOLDS ENABLE DE NOVO MODELLING OF RNA BY JRNL TITL 2 CRYOEM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.920 REMARK 3 NUMBER OF PARTICLES : 882884 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9NDV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000293138. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : SCAFFOLD ATTACHED TO QUININE-I REMARK 245 APTAMER (TONIC) LOCAL REMARK 245 REFINEMENT OF APTAMER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4509.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 G A 1 REMARK 465 G A 2 REMARK 465 G A 3 REMARK 465 C A 4 REMARK 465 C A 5 REMARK 465 A A 6 REMARK 465 C A 7 REMARK 465 U A 8 REMARK 465 G A 9 REMARK 465 U A 10 REMARK 465 U A 11 REMARK 465 U A 12 REMARK 465 C A 13 REMARK 465 A A 14 REMARK 465 C A 15 REMARK 465 U A 16 REMARK 465 G A 17 REMARK 465 U A 18 REMARK 465 U A 19 REMARK 465 G A 20 REMARK 465 C A 21 REMARK 465 G A 22 REMARK 465 C A 23 REMARK 465 U A 24 REMARK 465 A A 25 REMARK 465 C A 26 REMARK 465 A A 27 REMARK 465 U A 28 REMARK 465 C A 29 REMARK 465 U A 30 REMARK 465 C A 31 REMARK 465 C A 32 REMARK 465 G A 33 REMARK 465 G A 34 REMARK 465 A A 35 REMARK 465 U A 103 REMARK 465 C A 104 REMARK 465 C A 105 REMARK 465 G A 106 REMARK 465 G A 107 REMARK 465 A A 108 REMARK 465 G A 109 REMARK 465 G A 110 REMARK 465 C A 111 REMARK 465 C A 112 REMARK 465 A A 113 REMARK 465 C A 114 REMARK 465 A A 115 REMARK 465 C A 116 REMARK 465 G A 117 REMARK 465 A A 118 REMARK 465 A A 119 REMARK 465 A A 120 REMARK 465 G A 121 REMARK 465 U A 122 REMARK 465 G A 123 REMARK 465 U A 124 REMARK 465 G A 125 REMARK 465 G A 126 REMARK 465 A A 127 REMARK 465 G A 128 REMARK 465 U A 129 REMARK 465 G A 130 REMARK 465 A A 131 REMARK 465 C A 132 REMARK 465 C A 133 REMARK 465 A A 134 REMARK 465 G A 135 REMARK 465 U A 136 REMARK 465 G A 137 REMARK 465 G A 138 REMARK 465 C A 139 REMARK 465 C A 140 REMARK 465 C A 141 REMARK 465 C A 142 REMARK 465 A A 143 REMARK 465 C A 144 REMARK 465 C A 145 REMARK 465 C A 146 REMARK 465 U A 147 REMARK 465 G A 148 REMARK 465 A A 149 REMARK 465 A A 150 REMARK 465 G A 151 REMARK 465 G A 152 REMARK 465 U A 153 REMARK 465 A A 154 REMARK 465 A A 155 REMARK 465 A A 156 REMARK 465 C A 157 REMARK 465 U A 158 REMARK 465 U A 159 REMARK 465 G A 160 REMARK 465 U A 161 REMARK 465 A A 162 REMARK 465 G A 163 REMARK 465 C A 164 REMARK 465 G A 165 REMARK 465 C A 166 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 C A 64 C6 - N1 - C2 ANGL. DEV. = -3.1 DEGREES REMARK 500 C A 64 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 A A 65 O5' - P - OP2 ANGL. DEV. = -5.6 DEGREES REMARK 500 G A 83 C5 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 C A 101 OP1 - P - OP2 ANGL. DEV. = 10.2 DEGREES REMARK 500 C A 101 O5' - P - OP2 ANGL. DEV. = -6.8 DEGREES REMARK 500 C A 101 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 C A 101 C2 - N1 - C1' ANGL. DEV. = 7.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 68 OP2 REMARK 620 2 A A 71 OP2 138.2 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49278 RELATED DB: EMDB REMARK 900 SCAFFOLD ATTACHED TO QUININE-I APTAMER (TONIC) LOCAL REFINEMENT OF REMARK 900 APTAMER DBREF 9NDV A 1 166 PDB 9NDV 9NDV 1 166 SEQRES 1 A 166 G G G C C A C U G U U U C SEQRES 2 A 166 A C U G U U G C G C U A C SEQRES 3 A 166 A U C U C C G G A C G A C SEQRES 4 A 166 U C U A U A C C G C G U G SEQRES 5 A 166 G A U A U G G C A C G C A SEQRES 6 A 166 A C U U C A A G A C G G G SEQRES 7 A 166 C A C C G U A A A U G U C SEQRES 8 A 166 C U C G G G C G U C G U C SEQRES 9 A 166 C G G A G G C C A C A C G SEQRES 10 A 166 A A A G U G U G G A G U G SEQRES 11 A 166 A C C A G U G G C C C C A SEQRES 12 A 166 C C C U G A A G G U A A A SEQRES 13 A 166 C U U G U A G C G C HET QI9 A 201 24 HET MG A 202 1 HET K A 203 1 HET K A 204 1 HETNAM QI9 QUININE HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETSYN QI9 (3ALPHA,8ALPHA,9R)-6'-METHOXYCINCHONAN-9-OL FORMUL 2 QI9 C20 H24 N2 O2 FORMUL 3 MG MG 2+ FORMUL 4 K 2(K 1+) FORMUL 6 HOH *17(H2 O) LINK OP2 U A 68 MG MG A 202 1555 1555 2.04 LINK OP2 A A 71 MG MG A 202 1555 1555 2.31 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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 CONECT 683 1453 CONECT 743 1453 CONECT 1429 1430 CONECT 1430 1429 1431 1441 CONECT 1431 1430 1432 1440 CONECT 1432 1431 1433 1435 CONECT 1433 1432 1434 CONECT 1434 1433 1439 CONECT 1435 1432 1436 CONECT 1436 1435 1437 1439 CONECT 1437 1436 1438 CONECT 1438 1437 CONECT 1439 1434 1436 1440 CONECT 1440 1431 1439 CONECT 1441 1430 1442 1446 CONECT 1442 1441 1443 CONECT 1443 1442 1444 CONECT 1444 1443 1445 CONECT 1445 1444 1446 1448 CONECT 1446 1441 1445 1447 CONECT 1447 1446 1450 CONECT 1448 1445 1449 CONECT 1449 1448 1450 CONECT 1450 1447 1449 1451 CONECT 1451 1450 1452 CONECT 1452 1451 CONECT 1453 683 743 MASTER 244 0 4 0 0 0 0 6 1471 1 27 13 END