HEADER RNA 10-APR-25 9QU6 TITLE CRYO-EM STRUCTURE OF OCEANOBACILLUS IHEYENSIS GROUP II INTRON DOMAINS TITLE 2 D1-D5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROUP IIC INTRON; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GROUP IIC INTRON 5'-EXON; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: OCEANOBACILLUS IHEYENSIS; SOURCE 4 ORGANISM_TAXID: 182710; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: OCEANOBACILLUS IHEYENSIS; SOURCE 8 ORGANISM_TAXID: 182710 KEYWDS RIBOZYME, METALLOENZYMES, SPLICING, PROTEIN-FREE RNA CRYO-EM, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR S.S.JADHAV,M.MAIORCA,T.MULVANEY,M.TOPF,M.MARCIA REVDAT 1 25-FEB-26 9QU6 0 JRNL AUTH S.JADHAV,M.MARCIA JRNL TITL CRYO-SPECIMEN PREPARATION AND IMAGING OF HIGHLY-STRUCTURED JRNL TITL 2 AND DYNAMIC LARGE NON-CODING RNAS JRNL REF BMC METHODS V. 2 26 2025 JRNL REFN ESSN 3004-8729 JRNL DOI 10.1186/S44330-025-00045-4 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC 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 : 55181 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 9QU6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-APR-25. REMARK 100 THE DEPOSITION ID IS D_1292147022. 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 : GROUP IIC INTRON 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 : 6.50 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 3740.00 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 -4 REMARK 465 U A -3 REMARK 465 U A -2 REMARK 465 A A -1 REMARK 465 U A 0 REMARK 465 G A 1 REMARK 465 U A 2 REMARK 465 U A 84 REMARK 465 C A 91 REMARK 465 U A 152 REMARK 465 U A 162 REMARK 465 A A 163 REMARK 465 U A 164 REMARK 465 C A 165 REMARK 465 A A 166 REMARK 465 A A 167 REMARK 465 U A 168 REMARK 465 G A 169 REMARK 465 U A 202 REMARK 465 G A 203 REMARK 465 C A 204 REMARK 465 C A 205 REMARK 465 A A 206 REMARK 465 A A 207 REMARK 465 A A 208 REMARK 465 G A 209 REMARK 465 U A 210 REMARK 465 U A 211 REMARK 465 G A 212 REMARK 465 A A 215 REMARK 465 C A 216 REMARK 465 G A 275 REMARK 465 A A 276 REMARK 465 A A 277 REMARK 465 A A 278 REMARK 465 G A 288 REMARK 465 C A 289 REMARK 465 A A 290 REMARK 465 G A 291 REMARK 465 A A 292 REMARK 465 A A 293 REMARK 465 C A 305 REMARK 465 U A 306 REMARK 465 G A 307 REMARK 465 U A 308 REMARK 465 U A 309 REMARK 465 C A 310 REMARK 465 G A 311 REMARK 465 C A 312 REMARK 465 G A 325 REMARK 465 A A 326 REMARK 465 A A 327 REMARK 465 C A 328 REMARK 465 A A 329 REMARK 465 A A 330 REMARK 465 G A 331 REMARK 465 U A 332 REMARK 465 A A 333 REMARK 465 U A 334 REMARK 465 G A 335 REMARK 465 G A 336 REMARK 465 C A 337 REMARK 465 G A 338 REMARK 465 U A 339 REMARK 465 U A 340 REMARK 465 C A 341 REMARK 465 G A 342 REMARK 465 C A 343 REMARK 465 G A 344 REMARK 465 C A 345 REMARK 465 C A 346 REMARK 465 U A 347 REMARK 465 A A 348 REMARK 465 A A 349 REMARK 465 G A 350 REMARK 465 C A 351 REMARK 465 U A 352 REMARK 465 U A 353 REMARK 465 G A 354 REMARK 465 A A 355 REMARK 465 A A 356 REMARK 465 U A 389 REMARK 465 G A 390 REMARK 465 G A 391 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 G A 269 O5' 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 O6 G A 83 N6 A A 99 2.11 REMARK 500 O6 G A 160 N6 A A 217 2.11 REMARK 500 O6 G A 48 O2' G A 58 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 G A 98 N3 - C4 - N9 ANGL. DEV. = -4.0 DEGREES REMARK 500 G A 107 C4 - N9 - C1' ANGL. DEV. = 8.4 DEGREES 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 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 67 OP2 REMARK 620 2 G A 68 N7 97.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 154 OP2 REMARK 620 2 G A 155 N7 89.8 REMARK 620 3 G A 155 O6 138.4 75.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 406 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 269 OP1 REMARK 620 2 G A 269 OP2 48.7 REMARK 620 3 G A 270 O6 153.1 125.9 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-53372 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF OCEANOBACILLUS IHEYENSIS GROUP II INTRON REMARK 900 DOMAINS D1-D5 DBREF 9QU6 A -4 391 PDB 9QU6 9QU6 -4 391 DBREF 9QU6 B -4 0 PDB 9QU6 9QU6 -4 0 SEQRES 1 A 396 G U U A U G U G U G C C C SEQRES 2 A 396 G G C A U G G G U G C A G SEQRES 3 A 396 U C U A U A G G G U G A G SEQRES 4 A 396 A G U C C C G A A C U G U SEQRES 5 A 396 G A A G G C A G A A G U A SEQRES 6 A 396 A C A G U U A G C C U A A SEQRES 7 A 396 C G C A A G G G U G U C C SEQRES 8 A 396 G U G G C G A C A U G G A SEQRES 9 A 396 A U C U G A A G G A A G C SEQRES 10 A 396 G G A C G G C A A A C C U SEQRES 11 A 396 U C G G U C U G A G G A A SEQRES 12 A 396 C A C G A A C U U C A U A SEQRES 13 A 396 U G A G G C U A G G U A U SEQRES 14 A 396 C A A U G G A U G A G U U SEQRES 15 A 396 U G C A U A A C A A A A C SEQRES 16 A 396 A A A G U C C U U U C U G SEQRES 17 A 396 C C A A A G U U G G U A C SEQRES 18 A 396 A G A G U A A A U G A A G SEQRES 19 A 396 C A G A U U G A U G A A G SEQRES 20 A 396 G G A A A G A C U G C A U SEQRES 21 A 396 U C U U A C C C G G G G A SEQRES 22 A 396 G G U C U G G A A A C A G SEQRES 23 A 396 A A G U C A G C A G A A G SEQRES 24 A 396 U C A U A G U A C C C U G SEQRES 25 A 396 U U C G C A G G G G A A G SEQRES 26 A 396 G A C G G A A C A A G U A SEQRES 27 A 396 U G G C G U U C G C G C C SEQRES 28 A 396 U A A G C U U G A A C C G SEQRES 29 A 396 C C G U A U A C C G A A C SEQRES 30 A 396 G G U A C G U A C G G U G SEQRES 31 A 396 G U G U G G SEQRES 1 B 5 G U U A U HET MG A 401 1 HET MG A 402 1 HET MG A 403 1 HET MG A 404 1 HET MG A 405 1 HET K A 406 1 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION FORMUL 3 MG 5(MG 2+) FORMUL 8 K K 1+ LINK OP2 A A 67 MG MG A 403 1555 1555 1.88 LINK N7 G A 68 MG MG A 403 1555 1555 1.93 LINK OP2 G A 136 MG MG A 402 1555 1555 1.90 LINK OP2 A A 154 MG MG A 404 1555 1555 2.04 LINK N7 G A 155 MG MG A 404 1555 1555 2.01 LINK O6 G A 155 MG MG A 404 1555 1555 2.91 LINK OP1 G A 269 K K A 406 1555 1555 3.39 LINK OP2 G A 269 K K A 406 1555 1555 2.56 LINK O6 G A 270 K K A 406 1555 1555 3.50 LINK OP2 C A 372 MG MG A 401 1555 1555 2.20 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 1384 6834 CONECT 1418 6834 CONECT 2832 6833 CONECT 3195 6835 CONECT 3229 6835 CONECT 3232 6835 CONECT 5218 6837 CONECT 5219 6837 CONECT 5256 6837 CONECT 6359 6832 CONECT 6832 6359 CONECT 6833 2832 CONECT 6834 1384 1418 CONECT 6835 3195 3229 3232 CONECT 6837 5218 5219 5256 MASTER 257 0 6 0 0 0 0 6 6835 2 15 32 END