HEADER RNA 05-DEC-24 9ELY TITLE RAIA RNA MOTIF (CLOSTRIDIUM ACETOBUTYLICUM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAIA RNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: CLOSTRIDIUM ACETOBUTYLICUM ATCC 824; SOURCE 4 ORGANISM_TAXID: 272562 KEYWDS RAIA, NCRNA, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR R.C.KRETSCH,Y.WU,G.NYE,R.DAS,W.CHIU REVDAT 3 30-JUL-25 9ELY 1 JRNL REVDAT 2 21-MAY-25 9ELY 1 JRNL REVDAT 1 23-APR-25 9ELY 0 JRNL AUTH R.C.KRETSCH,Y.WU,S.A.SHABALINA,H.LEE,G.NYE,E.V.KOONIN,A.GAO, JRNL AUTH 2 W.CHIU,R.DAS JRNL TITL NATURALLY ORNATE RNA-ONLY COMPLEXES REVEALED BY CRYO-EM. JRNL REF NATURE V. 643 1135 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 40328315 JRNL DOI 10.1038/S41586-025-09073-0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.C.KRETSCH,Y.WU,S.A.SHABALINA,H.LEE,G.NYE,E.V.KOONIN,A.GAO, REMARK 1 AUTH 2 W.CHIU,R.DAS REMARK 1 TITL NATURALLY ORNATE RNA-ONLY COMPLEXES REVEALED BY CRYO-EM REMARK 1 REF BIORXIV 2024 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2024.12.08.627333 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC, EPU, REMARK 3 CRYOSPARC, RELION, ROSETTA, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, PHENIX, ROSETTA, REMARK 3 ISOLDE, COOT REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 2.900 REMARK 3 NUMBER OF PARTICLES : 318464 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 9ELY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1000290749. 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 : RAIA RNA - CLOSTRIDIUM REMARK 245 ACETOBUTYLICUM REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.30 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 10825 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) : 600.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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 0 REMARK 465 U A 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 U A 2 P OP1 OP2 O5' REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-48162 RELATED DB: EMDB REMARK 900 RAIA RNA MOTIF (CLOSTRIDIUM ACETOBUTYLICUM) DBREF1 9ELY A -1 203 GB AE001437.1 DBREF2 9ELY A 25168256 2985435 2985231 SEQADV 9ELY G A -1 GB 25168256 U 85435 CONFLICT SEQADV 9ELY G A 0 GB 25168256 A 85434 CONFLICT SEQRES 1 A 205 G G U U A A G U U A G G U SEQRES 2 A 205 U U G U G G U U G A A A G SEQRES 3 A 205 U C G A U G C C A G U C G SEQRES 4 A 205 C A G G C A A A A C G A U SEQRES 5 A 205 C C A C G U A A G U U A A SEQRES 6 A 205 A C A A A G U U U U A A U SEQRES 7 A 205 G A G C A U G G U G C G G SEQRES 8 A 205 C U U A G A A G U A A G U SEQRES 9 A 205 C C U G C C G C U U U A G SEQRES 10 A 205 G C G A G A G U A U U A G SEQRES 11 A 205 U A G U G A G A G G G U A SEQRES 12 A 205 A U U C C G G G U A G C G SEQRES 13 A 205 A A A C U U C C A G C A G SEQRES 14 A 205 G C G A G U G U G G G G U SEQRES 15 A 205 C A A A G A C C A G G U C SEQRES 16 A 205 A A C U A A C U U A CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 4335 A A 203 MASTER 127 0 0 0 0 0 0 6 4334 1 0 16 END