HEADER RNA 07-JUN-24 9C6I TITLE CRYO-EM STRUCTURE OF A GROUP IIC INTRON RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROUP IIC INTRON; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OCEANOBACILLUS IHEYENSIS; SOURCE 3 ORGANISM_TAXID: 182710; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SPLICING, RIBOZYME, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR N.TOOR REVDAT 3 05-FEB-25 9C6I 1 JRNL REVDAT 2 29-JAN-25 9C6I 1 JRNL REVDAT 1 04-DEC-24 9C6I 0 JRNL AUTH D.B.HAACK,B.RUDOLFS,S.JIN,A.KHITUN,K.M.WEEKS,N.TOOR JRNL TITL SCAFFOLD-ENABLED HIGH-RESOLUTION CRYO-EM STRUCTURE JRNL TITL 2 DETERMINATION OF RNA. JRNL REF NAT COMMUN V. 16 880 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 39837824 JRNL DOI 10.1038/S41467-024-55699-5 REMARK 2 REMARK 2 RESOLUTION. 2.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 2.560 REMARK 3 NUMBER OF PARTICLES : 382753 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 9C6I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1000284879. 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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) : 5000.00 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: 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 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 U A 389 REMARK 465 G A 390 REMARK 465 A A 391 REMARK 465 G A 392 REMARK 465 A A 393 REMARK 465 G A 394 REMARK 465 G A 395 REMARK 465 A A 396 REMARK 465 G A 397 REMARK 465 U A 398 REMARK 465 U A 399 REMARK 465 C A 400 REMARK 465 G A 401 REMARK 465 C A 402 REMARK 465 U A 403 REMARK 465 C A 404 REMARK 465 U A 405 REMARK 465 A A 406 REMARK 465 C A 407 REMARK 465 U A 408 REMARK 465 C A 409 REMARK 465 U A 410 REMARK 465 A A 411 REMARK 465 U A 412 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 N7 A A 333 O2 U A 347 2.09 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 267 O4' - C1' - N9 ANGL. DEV. = 5.5 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 507 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 66 OP2 REMARK 620 2 A A 67 OP1 98.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 511 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 119 OP1 REMARK 620 2 G A 239 OP1 160.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 518 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 287 OP2 REMARK 620 2 G A 321 OP1 85.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 519 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 289 O2 REMARK 620 2 A A 355 OP2 152.2 REMARK 620 3 A A 356 OP2 76.4 76.3 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-45247 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF A GROUP IIC INTRON RNA REMARK 900 RELATED ID: 9C6I RELATED DB: PDB REMARK 900 CRYO-EM STRUCTURE OF A GROUP IIC INTRON RNA REMARK 900 RELATED ID: EMD-45248 RELATED DB: EMDB REMARK 900 GROUP IIC INTRON EMBEDDED WITH THE TPP RIBOSWITCH REMARK 900 RELATED ID: 9C6J RELATED DB: PDB REMARK 900 GROUP IIC INTRON EMBEDDED WITH THE TPP RIBOSWITCH REMARK 900 RELATED ID: EMD-45249 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE TPP RIBOSWITCH EMBEDDED IN AN RNA SCAFFOLD REMARK 900 BOUND TO THIAMINE PYROPHOSPHATE REMARK 900 RELATED ID: 9C6K RELATED DB: PDB REMARK 900 CRYO-EM STRUCTURE OF THE TPP RIBOSWITCH EMBEDDED IN AN RNA SCAFFOLD REMARK 900 BOUND TO THIAMINE PYROPHOSPHATE REMARK 900 RELATED ID: EMD-45250 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE APO TPP RIBOSWITCH EMBEDDED IN AN RNA REMARK 900 SCAFFOLD REMARK 900 RELATED ID: EMD-45251 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF A GROUP IIC INTRON EMBEDDED IN AN RNP SCAFFOLD DBREF 9C6I A -5 412 PDB 9C6I 9C6I -5 412 SEQRES 1 A 417 G U U A U G U G U G C C C SEQRES 2 A 417 G G C A U G G G U G C A G SEQRES 3 A 417 U C U A U A G G G U G A G SEQRES 4 A 417 A G U C C C G A A C U G U SEQRES 5 A 417 G A A G G C A G A A G U A SEQRES 6 A 417 A C A G U U A G C C U A A SEQRES 7 A 417 C G C A A G G G U G U C C SEQRES 8 A 417 G U G G C G A C A U G G A SEQRES 9 A 417 A U C U G A A G G A A G C SEQRES 10 A 417 G G A C G G C A A A C C U SEQRES 11 A 417 U C G G U C U G A G G A A SEQRES 12 A 417 C A C G A A C U U C A U A SEQRES 13 A 417 U G A G G C U A G G U A U SEQRES 14 A 417 C A A U G G A U G A G U U SEQRES 15 A 417 U G C A U A A C A A A A C SEQRES 16 A 417 A A A G U C C U U U C U G SEQRES 17 A 417 C C A A A G U U G G U A C SEQRES 18 A 417 A G A G U A A A U G A A G SEQRES 19 A 417 C A G A U U G A U G A A G SEQRES 20 A 417 G G A A A G A C U G C A U SEQRES 21 A 417 U C U U A C C C G G G G A SEQRES 22 A 417 G G U C U G G A A A C A G SEQRES 23 A 417 A A G U C A G C A G A A G SEQRES 24 A 417 U C A U A G U A C C C U G SEQRES 25 A 417 U U C G C A G G G G A A G SEQRES 26 A 417 G A C G G A A C A A G U A SEQRES 27 A 417 U G G C G U U C G C G C C SEQRES 28 A 417 U A A G C U U G A A C C A SEQRES 29 A 417 C C G U A U A C C G A A C SEQRES 30 A 417 G G U A C G U A C G G U G SEQRES 31 A 417 G U G U G A G A G G A G U SEQRES 32 A 417 U C G C U C U A C U C U A SEQRES 33 A 417 U HET MG A 501 1 HET MG A 502 1 HET MG A 503 1 HET MG A 504 1 HET MG A 505 1 HET MG A 506 1 HET MG A 507 1 HET MG A 508 1 HET MG A 509 1 HET MG A 510 1 HET MG A 511 1 HET MG A 512 1 HET MG A 513 1 HET MG A 514 1 HET MG A 515 1 HET MG A 516 1 HET MG A 517 1 HET MG A 518 1 HET MG A 519 1 HET MG A 520 1 HET MG A 521 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 21(MG 2+) LINK OP2 U A 4 MG MG A 503 1555 1555 2.39 LINK OP2 U A 66 MG MG A 507 1555 1555 1.93 LINK OP1 A A 67 MG MG A 507 1555 1555 1.94 LINK OP1 G A 111 MG MG A 505 1555 1555 2.02 LINK OP1 C A 119 MG MG A 511 1555 1555 1.92 LINK OP1 A A 120 MG MG A 510 1555 1555 2.11 LINK OP2 G A 136 MG MG A 516 1555 1555 2.00 LINK OP2 C A 145 MG MG A 515 1555 1555 2.88 LINK OP2 A A 186 MG MG A 502 1555 1555 2.08 LINK OP1 G A 239 MG MG A 511 1555 1555 1.89 LINK OP2 G A 269 MG MG A 517 1555 1555 2.38 LINK OP2 A A 287 MG MG A 518 1555 1555 2.04 LINK O2 C A 289 MG MG A 519 1555 1555 2.09 LINK OP2 G A 320 MG MG A 520 1555 1555 2.41 LINK OP1 G A 321 MG MG A 518 1555 1555 2.01 LINK OP2 A A 355 MG MG A 519 1555 1555 1.97 LINK OP2 A A 356 MG MG A 519 1555 1555 2.72 LINK OP2 C A 372 MG MG A 521 1555 1555 2.14 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