HEADER RNA 18-FEB-25 9NDW TITLE SCAFFOLD ATTACHED TO QUININE-I APTAMER (TONIC) LOCAL REFINEMENT OF TITLE 2 CORE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (91-MER); COMPND 3 CHAIN: A, B; 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 9NDW 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. 2.71 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) : 2.710 REMARK 3 NUMBER OF PARTICLES : 132018 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 9NDW 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_1000293155. 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 CORE 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 34 REMARK 465 A A 35 REMARK 465 C A 36 REMARK 465 G A 37 REMARK 465 A A 38 REMARK 465 C A 39 REMARK 465 U A 40 REMARK 465 C A 41 REMARK 465 U A 42 REMARK 465 A A 43 REMARK 465 U A 44 REMARK 465 A A 45 REMARK 465 C A 46 REMARK 465 C A 47 REMARK 465 G A 48 REMARK 465 C A 49 REMARK 465 G A 50 REMARK 465 U A 51 REMARK 465 G A 52 REMARK 465 G A 53 REMARK 465 A A 54 REMARK 465 U A 55 REMARK 465 A A 56 REMARK 465 U A 57 REMARK 465 G A 58 REMARK 465 G A 59 REMARK 465 C A 60 REMARK 465 A A 61 REMARK 465 C A 62 REMARK 465 G A 63 REMARK 465 C A 64 REMARK 465 A A 65 REMARK 465 A A 66 REMARK 465 C A 67 REMARK 465 U A 68 REMARK 465 U A 69 REMARK 465 C A 70 REMARK 465 A A 71 REMARK 465 A A 72 REMARK 465 G A 73 REMARK 465 A A 74 REMARK 465 C A 75 REMARK 465 G A 76 REMARK 465 G A 77 REMARK 465 G A 78 REMARK 465 C A 79 REMARK 465 A A 80 REMARK 465 C A 81 REMARK 465 C A 82 REMARK 465 G A 83 REMARK 465 U A 84 REMARK 465 A A 85 REMARK 465 A A 86 REMARK 465 A A 87 REMARK 465 U A 88 REMARK 465 G A 89 REMARK 465 U A 90 REMARK 465 C A 91 REMARK 465 C A 92 REMARK 465 U A 93 REMARK 465 C A 94 REMARK 465 G A 95 REMARK 465 G A 96 REMARK 465 G A 97 REMARK 465 C A 98 REMARK 465 G A 99 REMARK 465 U A 100 REMARK 465 C A 101 REMARK 465 G A 102 REMARK 465 U A 103 REMARK 465 C A 104 REMARK 465 C A 146 REMARK 465 U A 147 REMARK 465 G A 148 REMARK 465 A A 149 REMARK 465 G B 34 REMARK 465 A B 35 REMARK 465 C B 36 REMARK 465 G B 37 REMARK 465 A B 38 REMARK 465 C B 39 REMARK 465 U B 40 REMARK 465 C B 41 REMARK 465 U B 42 REMARK 465 A B 43 REMARK 465 U B 44 REMARK 465 A B 45 REMARK 465 C B 46 REMARK 465 C B 47 REMARK 465 G B 48 REMARK 465 C B 49 REMARK 465 G B 50 REMARK 465 U B 51 REMARK 465 G B 52 REMARK 465 G B 53 REMARK 465 A B 54 REMARK 465 U B 55 REMARK 465 A B 56 REMARK 465 U B 57 REMARK 465 G B 58 REMARK 465 G B 59 REMARK 465 C B 60 REMARK 465 A B 61 REMARK 465 C B 62 REMARK 465 G B 63 REMARK 465 C B 64 REMARK 465 A B 65 REMARK 465 A B 66 REMARK 465 C B 67 REMARK 465 U B 68 REMARK 465 U B 69 REMARK 465 C B 70 REMARK 465 A B 71 REMARK 465 A B 72 REMARK 465 G B 73 REMARK 465 A B 74 REMARK 465 C B 75 REMARK 465 G B 76 REMARK 465 G B 77 REMARK 465 G B 78 REMARK 465 C B 79 REMARK 465 A B 80 REMARK 465 C B 81 REMARK 465 C B 82 REMARK 465 G B 83 REMARK 465 U B 84 REMARK 465 A B 85 REMARK 465 A B 86 REMARK 465 A B 87 REMARK 465 U B 88 REMARK 465 G B 89 REMARK 465 U B 90 REMARK 465 C B 91 REMARK 465 C B 92 REMARK 465 U B 93 REMARK 465 C B 94 REMARK 465 G B 95 REMARK 465 G B 96 REMARK 465 G B 97 REMARK 465 C B 98 REMARK 465 G B 99 REMARK 465 U B 100 REMARK 465 C B 101 REMARK 465 G B 102 REMARK 465 U B 103 REMARK 465 C B 104 REMARK 465 C B 146 REMARK 465 U B 147 REMARK 465 G B 148 REMARK 465 A B 149 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 K A 201 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 109 O3' REMARK 620 2 G A 109 O2' 47.1 REMARK 620 3 HOH A 364 O 80.1 126.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 201 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 109 O3' REMARK 620 2 G B 109 O2' 47.1 REMARK 620 3 HOH B 364 O 79.8 126.1 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49279 RELATED DB: EMDB REMARK 900 SCAFFOLD ATTACHED TO QUININE-I APTAMER (TONIC) LOCAL REFINEMENT OF REMARK 900 CORE DBREF 9NDW A 1 166 PDB 9NDW 9NDW 1 166 DBREF 9NDW B 1 166 PDB 9NDW 9NDW 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 SEQRES 1 B 166 G G G C C A C U G U U U C SEQRES 2 B 166 A C U G U U G C G C U A C SEQRES 3 B 166 A U C U C C G G A C G A C SEQRES 4 B 166 U C U A U A C C G C G U G SEQRES 5 B 166 G A U A U G G C A C G C A SEQRES 6 B 166 A C U U C A A G A C G G G SEQRES 7 B 166 C A C C G U A A A U G U C SEQRES 8 B 166 C U C G G G C G U C G U C SEQRES 9 B 166 C G G A G G C C A C A C G SEQRES 10 B 166 A A A G U G U G G A G U G SEQRES 11 B 166 A C C A G U G G C C C C A SEQRES 12 B 166 C C C U G A A G G U A A A SEQRES 13 B 166 C U U G U A G C G C HET K A 201 1 HET K B 201 1 HETNAM K POTASSIUM ION FORMUL 3 K 2(K 1+) FORMUL 5 HOH *390(H2 O) LINK O3' G A 109 K K A 201 1555 1555 3.44 LINK O2' G A 109 K K A 201 1555 1555 3.48 LINK K K A 201 O HOH A 364 1555 1555 2.85 LINK O3' G B 109 K K B 201 1555 1555 3.46 LINK O2' G B 109 K K B 201 1555 1555 3.47 LINK K K B 201 O HOH B 364 1555 1555 2.80 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 786 3875 CONECT 788 3875 CONECT 2723 3876 CONECT 2725 3876 CONECT 3875 786 788 3940 CONECT 3876 2723 2725 4137 CONECT 3940 3875 CONECT 4137 3876 MASTER 278 0 2 0 0 0 0 6 4264 2 8 26 END