HEADER RNA 25-JUL-23 8TKK TITLE CRYO-EM STRUCTURE OF RNA DEVICE 43 TRUNCATION MUTANT 3 (U100C), APO TITLE 2 STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA DEVICE 43 TRUNCATION MUTANT 3 (U100C); 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 RNA DEVICE, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR J.R.STAGNO,J.C.DEME,Y.-T.LEE,Y.-X.WANG,S.M.LEA REVDAT 1 19-FEB-25 8TKK 0 JRNL AUTH J.R.STAGNO,J.C.DEME,Y.-T.LEE,Y.-X.WANG,S.M.LEA JRNL TITL CRYO-EM STRUCTURE OF RNA DEVICE 43 TRUNCATION MUTANT JRNL TITL 2 (U100C), APO STATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.37 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) : 3.370 REMARK 3 NUMBER OF PARTICLES : 404781 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 8TKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1000275427. 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 : SYNTHETIC RNA DEVICE CONTAINING REMARK 245 HAMMERHEAD RIBOZYME AND REMARK 245 TETRACYCLINE-BINDING APTAMER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.20 REMARK 245 SAMPLE SUPPORT DETAILS : 30S AT 30MA ON EACH SIDE REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.80 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 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) : 5450.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM 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 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 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 210 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 53 OP1 REMARK 620 2 G A 54 OP2 76.2 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8SYK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE, WITH LIGAND REMARK 900 RELATED ID: 8T50 RELATED DB: PDB REMARK 900 CRYO-EM STRUCTURE OF THE FULL-LENGTH, WITH LIGAND REMARK 900 RELATED ID: EMD-41354 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF RNA DEVICE 43 TRUNCATION MUTANT 3, APO STATE DBREF 8TKK A 9 115 PDB 8TKK 8TKK 9 115 SEQRES 1 A 107 C A G G U A C A U C C A G SEQRES 2 A 107 C U G A U G A G U C C C A SEQRES 3 A 107 A A U A G G A C A A A A A SEQRES 4 A 107 G G G A G A G G U G A A G SEQRES 5 A 107 A A U A C G A C C A C C U SEQRES 6 A 107 A G G C U C G A A A G A G SEQRES 7 A 107 C C U A A A A C A U A C C SEQRES 8 A 107 C U U C C U G G A U U C C SEQRES 9 A 107 U G C HET GTP A 201 32 HET MG A 202 1 HET MG A 203 1 HET MG A 204 1 HET MG A 205 1 HET MG A 206 1 HET MG A 207 1 HET MG A 208 1 HET MG A 209 1 HET MG A 210 1 HET MG A 211 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 MG 10(MG 2+) LINK P C A 9 O3' GTP A 201 1555 1555 1.61 LINK OP1 A A 53 MG MG A 210 1555 1555 2.00 LINK OP2 G A 54 MG MG A 210 1555 1555 2.68 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 1 2308 CONECT 952 2331 CONECT 975 2331 CONECT 2291 2292 2293 2294 2295 CONECT 2292 2291 CONECT 2293 2291 CONECT 2294 2291 CONECT 2295 2291 2296 CONECT 2296 2295 2297 2298 2299 CONECT 2297 2296 CONECT 2298 2296 CONECT 2299 2296 2300 CONECT 2300 2299 2301 2302 2303 CONECT 2301 2300 CONECT 2302 2300 CONECT 2303 2300 2304 CONECT 2304 2303 2305 CONECT 2305 2304 2306 2307 CONECT 2306 2305 2311 CONECT 2307 2305 2308 2309 CONECT 2308 1 2307 CONECT 2309 2307 2310 2311 CONECT 2310 2309 CONECT 2311 2306 2309 2312 CONECT 2312 2311 2313 2322 CONECT 2313 2312 2314 CONECT 2314 2313 2315 CONECT 2315 2314 2316 2322 CONECT 2316 2315 2317 2318 CONECT 2317 2316 CONECT 2318 2316 2319 CONECT 2319 2318 2320 2321 CONECT 2320 2319 CONECT 2321 2319 2322 CONECT 2322 2312 2315 2321 CONECT 2331 952 975 MASTER 116 0 11 0 0 0 0 6 2331 1 36 9 END