HEADER RNA 29-MAY-25 9OV6 TITLE STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS RNASE P RIBOZYME SUB- TITLE 2 CONFORMATION 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE P RNA COMPONENT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS RIBOZYME, RNA, RNASE P EXPDTA ELECTRON MICROSCOPY AUTHOR Y.-T.LEE,J.R.STAGNO,Y.-X.WANG REVDAT 1 20-MAY-26 9OV6 0 JRNL AUTH Y.T.LEE,M.F.S.DEGENHARDT,I.SKEPARNIAS,S.Y.CHEN,B.A.BHOGE, JRNL AUTH 2 S.G.TARASOV,M.A.DYBA,J.ZHANG,J.R.STAGNO,Y.X.WANG JRNL TITL STRUCTURAL BASIS FOR PROTEIN-FREE CATALYSIS BY RIBONUCLEASE JRNL TITL 2 P RIBOZYME. JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 41986363 JRNL DOI 10.1038/S41467-026-71597-4 REMARK 2 REMARK 2 RESOLUTION. 3.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2A64 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT 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) : 3.460 REMARK 3 NUMBER OF PARTICLES : 86624 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 9OV6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1000296409. 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 : RNASE P RNA COMPONENT IN 5 MM REMARK 245 CA2+ REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 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 TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : 4D-STEM REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5700.00 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) : 200 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 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 CA A 506 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 25 O6 REMARK 620 2 G A 41 O6 110.0 REMARK 620 3 U A 42 O4 83.6 85.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 512 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 50 OP1 REMARK 620 2 A A 389 OP1 105.9 REMARK 620 3 A A 390 OP2 68.3 117.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 508 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 82 OP2 REMARK 620 2 G A 83 OP2 73.4 REMARK 620 3 G A 250 OP2 76.9 150.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 514 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 99 OP2 REMARK 620 2 U A 105 O4 76.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 527 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 139 OP1 REMARK 620 2 G A 140 OP2 102.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 516 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 275 OP1 REMARK 620 2 A A 277 OP1 90.1 REMARK 620 3 G A 301 OP2 99.9 150.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 513 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 276 O2' REMARK 620 2 C A 276 O2 77.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 517 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 277 O2' REMARK 620 2 C A 278 OP2 75.1 REMARK 620 3 G A 331 OP2 74.9 125.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 519 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 291 OP2 REMARK 620 2 U A 293 OP2 85.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 510 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 385 OP1 REMARK 620 2 C A 386 OP2 101.2 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70891 RELATED DB: EMDB REMARK 900 STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS RNASE P RIBOZYME SUB- REMARK 900 CONFORMATION 1 DBREF 9OV6 A 1 417 GB 143442 M19021.1 1 417 SEQADV 9OV6 C A 417 GB 143442 G 417 ENGINEERED MUTATION SEQRES 1 A 417 G U U A A U C A U G C U C SEQRES 2 A 417 G G G U A A U C G C U G C SEQRES 3 A 417 G G C C G G U U U C G G C SEQRES 4 A 417 C G U A G A G G A A A G U SEQRES 5 A 417 C C A U G C U C G C A C G SEQRES 6 A 417 G U G C U G A G A U G C C SEQRES 7 A 417 C G U A G U G U U C G U G SEQRES 8 A 417 C C U A G C G A A U C C A SEQRES 9 A 417 U A A G C U A G G G C A G SEQRES 10 A 417 C C U G G C U U C G G C U SEQRES 11 A 417 G G G C U G A C G G C G G SEQRES 12 A 417 G G A A A G A A C C U A C SEQRES 13 A 417 G U C C G G C U G G G A U SEQRES 14 A 417 A U G G U U C G A U U A C SEQRES 15 A 417 C C U G A A A G U G C C A SEQRES 16 A 417 C A G U G A C G G A G C U SEQRES 17 A 417 C U A A G G G A A A C C U SEQRES 18 A 417 U A G A G G U G G A A C G SEQRES 19 A 417 C G G U A A A C C C C A C SEQRES 20 A 417 G A G C G A G A A A C C C SEQRES 21 A 417 A A A U G A U G G U A G G SEQRES 22 A 417 G G C A C C U U C C C G A SEQRES 23 A 417 A G G A A A U G A A C G G SEQRES 24 A 417 A G G G A A G G A C A G G SEQRES 25 A 417 C G G C G C A U G C A G C SEQRES 26 A 417 C U G U A G A U A G A U G SEQRES 27 A 417 A U U A C C G C C G G A G SEQRES 28 A 417 U A C G A G G C G C A A A SEQRES 29 A 417 G C C G C U U G C A G U A SEQRES 30 A 417 C G A A G G U A C A G A A SEQRES 31 A 417 C A U G G C U U A U A G A SEQRES 32 A 417 G C A U G A U U A A C G U SEQRES 33 A 417 C HET CA A 501 1 HET CA A 502 1 HET CA A 503 1 HET CA A 504 1 HET CA A 505 1 HET CA A 506 1 HET CA A 507 1 HET CA A 508 1 HET CA A 509 1 HET CA A 510 1 HET CA A 511 1 HET CA A 512 1 HET CA A 513 1 HET CA A 514 1 HET CA A 515 1 HET CA A 516 1 HET CA A 517 1 HET CA A 518 1 HET CA A 519 1 HET CA A 520 1 HET CA A 521 1 HET CA A 522 1 HET CA A 523 1 HET CA A 524 1 HET CA A 525 1 HET CA A 526 1 HET CA A 527 1 HETNAM CA CALCIUM ION FORMUL 2 CA 27(CA 2+) LINK O6 G A 25 CA CA A 506 1555 1555 2.56 LINK O6 G A 41 CA CA A 506 1555 1555 2.68 LINK O4 U A 42 CA CA A 506 1555 1555 2.38 LINK OP2 G A 47 CA CA A 511 1555 1555 2.35 LINK OP1 A A 50 CA CA A 512 1555 1555 2.56 LINK OP2 A A 82 CA CA A 508 1555 1555 2.37 LINK OP2 G A 83 CA CA A 508 1555 1555 2.99 LINK OP2 A A 99 CA CA A 514 1555 1555 2.33 LINK O4 U A 105 CA CA A 514 1555 1555 2.35 LINK OP1 G A 139 CA CA A 527 1555 1555 2.46 LINK OP2 G A 140 CA CA A 527 1555 1555 2.41 LINK OP2 G A 250 CA CA A 508 1555 1555 2.34 LINK OP1 G A 275 CA CA A 516 1555 1555 2.35 LINK O2' C A 276 CA CA A 513 1555 1555 2.41 LINK O2 C A 276 CA CA A 513 1555 1555 2.32 LINK OP1 A A 277 CA CA A 516 1555 1555 2.98 LINK O2' A A 277 CA CA A 517 1555 1555 2.46 LINK OP2 C A 278 CA CA A 517 1555 1555 2.27 LINK O6 G A 289 CA CA A 505 1555 1555 2.37 LINK OP2 A A 291 CA CA A 519 1555 1555 2.71 LINK OP2 U A 293 CA CA A 519 1555 1555 3.00 LINK O6 G A 299 CA CA A 504 1555 1555 2.40 LINK OP2 A A 300 CA CA A 525 1555 1555 3.17 LINK OP2 G A 301 CA CA A 516 1555 1555 3.12 LINK OP2 G A 331 CA CA A 517 1555 1555 2.18 LINK OP1 A A 385 CA CA A 510 1555 1555 2.86 LINK OP2 C A 386 CA CA A 510 1555 1555 2.40 LINK OP1 A A 389 CA CA A 512 1555 1555 2.37 LINK OP2 A A 390 CA CA A 512 1555 1555 2.31 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 526 8969 CONECT 867 8969 CONECT 890 8969 CONECT 985 8974 CONECT 1051 8975 CONECT 1732 8971 CONECT 1754 8971 CONECT 2094 8977 CONECT 2235 8977 CONECT 2948 8990 CONECT 2972 8990 CONECT 5339 8971 CONECT 5883 8979 CONECT 5915 8976 CONECT 5919 8976 CONECT 5926 8979 CONECT 5935 8980 CONECT 5949 8980 CONECT 6194 8968 CONECT 6224 8982 CONECT 6268 8982 CONECT 6413 8967 CONECT 6421 8988 CONECT 6443 8979 CONECT 7096 8980 CONECT 8259 8973 CONECT 8282 8973 CONECT 8346 8975 CONECT 8369 8975 CONECT 8967 6413 CONECT 8968 6194 CONECT 8969 526 867 890 CONECT 8971 1732 1754 5339 CONECT 8973 8259 8282 CONECT 8974 985 CONECT 8975 1051 8346 8369 CONECT 8976 5915 5919 CONECT 8977 2094 2235 CONECT 8979 5883 5926 6443 CONECT 8980 5935 5949 7096 CONECT 8982 6224 6268 CONECT 8988 6421 CONECT 8990 2948 2972 MASTER 180 0 27 0 0 0 0 6 8989 1 43 33 END