HEADER RNA 25-JUL-23 8TKJ TITLE CRYO-EM STRUCTURE OF RNA DEVICE 43, APO STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA DEVICE 43; 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 8TKJ 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, APO JRNL TITL 2 STATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.20 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 731795 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 8TKJ 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_1000275757. 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) : 2.50 REMARK 245 SAMPLE SUPPORT DETAILS : NULL 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) : 5220.00 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 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 U A 2 REMARK 465 G A 3 REMARK 465 A A 4 REMARK 465 A A 113 REMARK 465 C A 114 REMARK 465 U A 118 REMARK 465 A A 119 REMARK 465 U A 120 REMARK 465 C A 121 REMARK 465 C A 122 REMARK 465 A A 123 REMARK 465 C A 124 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 N6 A A 28 O2' A A 43 2.17 REMARK 500 N4 C A 9 O6 G A 116 2.19 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 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 53 OP1 REMARK 620 2 A A 53 OP2 75.5 REMARK 620 3 A A 53 O5' 58.1 59.6 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8T5O RELATED DB: PDB REMARK 900 8T5O IS THE SAME RNA COMPLEXED WITH TETRACYCLINE REMARK 900 RELATED ID: 8SYK RELATED DB: PDB REMARK 900 8SYK IS A TRUNCATION MUTANT OF THE SAME RNA COMPLEXED WITH REMARK 900 TETRACYCLINE REMARK 900 RELATED ID: EMD-41353 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF RNA DEVICE 43, APO STATE DBREF 8TKJ A 1 124 PDB 8TKJ 8TKJ 1 124 SEQRES 1 A 124 G U G A G G U G C A G G U SEQRES 2 A 124 A C A U C C A G C U G A U SEQRES 3 A 124 G A G U C C C A A A U A G SEQRES 4 A 124 G A C A A A A A G G G A G SEQRES 5 A 124 A G G U G A A G A A U A C SEQRES 6 A 124 G A C C A C C U A G G C U SEQRES 7 A 124 C G A A A G A G C C U A A SEQRES 8 A 124 A A C A U A C C U U U C C SEQRES 9 A 124 U G G A U U C C A C U G C SEQRES 10 A 124 U A U C C A C HET MG A 201 1 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 HETNAM MG MAGNESIUM ION FORMUL 2 MG 8(MG 2+) LINK OP1 A A 53 MG MG A 201 1555 1555 2.20 LINK OP2 A A 53 MG MG A 201 1555 1555 1.97 LINK O5' A A 53 MG MG A 201 1555 1555 2.81 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 TER 3579 C A 117 HETATM 3580 MG MG A 201 153.375 144.502 176.539 1.00141.99 MG HETATM 3581 MG MG A 202 159.215 163.635 116.795 1.00 99.56 MG HETATM 3582 MG MG A 203 156.929 166.382 121.990 1.00 80.93 MG HETATM 3583 MG MG A 204 155.163 144.105 129.528 1.00101.41 MG HETATM 3584 MG MG A 205 145.024 139.843 128.806 1.00 76.90 MG HETATM 3585 MG MG A 206 147.982 151.535 179.699 1.00 56.28 MG HETATM 3586 MG MG A 207 157.810 151.521 194.176 1.00107.37 MG HETATM 3587 MG MG A 208 169.637 151.831 200.259 1.00 70.83 MG CONECT 1562 3580 CONECT 1563 3580 CONECT 1564 3580 CONECT 3580 1562 1563 1564 MASTER 147 0 8 0 0 0 0 6 2386 1 4 10 END