HEADER RNA 18-FEB-25 9NDX TITLE SCAFFOLD ATTACHED TO QUININE-I APTAMER (TONIC) REFINEMENT OF APTAMER TITLE 2 AND CORE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (162-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 9NDX 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. 2.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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) : 2.940 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 9NDX 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_1000293157. 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: 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 C A 146 REMARK 465 U A 147 REMARK 465 G A 148 REMARK 465 A A 149 REMARK 465 C B 146 REMARK 465 U B 147 REMARK 465 G B 148 REMARK 465 A B 149 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2 C A 144 N2 G B 152 2.03 REMARK 500 O2' A B 56 O6 G B 58 2.14 REMARK 500 O2' A A 56 O6 G A 58 2.15 REMARK 500 N2 G A 152 O2 C B 144 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49280 RELATED DB: EMDB REMARK 900 SCAFFOLD ATTACHED TO QUININE-I APTAMER (TONIC) REFINEMENT OF REMARK 900 APTAMER AND CORE DBREF 9NDX A 1 166 PDB 9NDX 9NDX 1 166 DBREF 9NDX B 1 166 PDB 9NDX 9NDX 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 QI9 A 201 24 HET QI9 B 201 24 HETNAM QI9 QUININE HETSYN QI9 (3ALPHA,8ALPHA,9R)-6'-METHOXYCINCHONAN-9-OL FORMUL 3 QI9 2(C20 H24 N2 O2) 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 6899 6900 CONECT 6900 6899 6901 6911 CONECT 6901 6900 6902 6910 CONECT 6902 6901 6903 6905 CONECT 6903 6902 6904 CONECT 6904 6903 6909 CONECT 6905 6902 6906 CONECT 6906 6905 6907 6909 CONECT 6907 6906 6908 CONECT 6908 6907 CONECT 6909 6904 6906 6910 CONECT 6910 6901 6909 CONECT 6911 6900 6912 6916 CONECT 6912 6911 6913 CONECT 6913 6912 6914 CONECT 6914 6913 6915 CONECT 6915 6914 6916 6918 CONECT 6916 6911 6915 6917 CONECT 6917 6916 6920 CONECT 6918 6915 6919 CONECT 6919 6918 6920 CONECT 6920 6917 6919 6921 CONECT 6921 6920 6922 CONECT 6922 6921 CONECT 6923 6924 CONECT 6924 6923 6925 6935 CONECT 6925 6924 6926 6934 CONECT 6926 6925 6927 6929 CONECT 6927 6926 6928 CONECT 6928 6927 6933 CONECT 6929 6926 6930 CONECT 6930 6929 6931 6933 CONECT 6931 6930 6932 CONECT 6932 6931 CONECT 6933 6928 6930 6934 CONECT 6934 6925 6933 CONECT 6935 6924 6936 6940 CONECT 6936 6935 6937 CONECT 6937 6936 6938 CONECT 6938 6937 6939 CONECT 6939 6938 6940 6942 CONECT 6940 6935 6939 6941 CONECT 6941 6940 6944 CONECT 6942 6939 6943 CONECT 6943 6942 6944 CONECT 6944 6941 6943 6945 CONECT 6945 6944 6946 CONECT 6946 6945 MASTER 129 0 2 0 0 0 0 6 6944 2 48 26 END