HEADER RNA 02-JUN-25 9OWL TITLE STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS RNASE P RIBOZYME IN TITLE 2 COMPLEX WITH MATURE TRNA IN 5 MM CA2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE P RNA COMPONENT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MATURE TRNA (75-MER); COMPND 7 CHAIN: C; COMPND 8 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; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 8 ORGANISM_TAXID: 1422; SOURCE 9 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 10 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 9OWL 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. 2.99 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) : 2.990 REMARK 3 NUMBER OF PARTICLES : 58945 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 9OWL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1000296526. 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 REMARK 245 COMPLEX WITH MATURE TRNA IN 5 REMARK 245 MM 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 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 C A 11 C2 - N1 - C1' ANGL. DEV. = 6.9 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 CA A 524 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 50 OP1 REMARK 620 2 A A 389 OP1 109.9 REMARK 620 3 A A 390 OP2 74.6 114.8 REMARK 620 4 G C 1 OP1 115.7 126.4 103.5 REMARK 620 N 1 2 3 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 82 OP2 REMARK 620 2 G A 83 OP2 80.7 REMARK 620 3 G A 250 OP2 63.6 141.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 522 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 99 OP2 REMARK 620 2 U A 105 O4 68.5 REMARK 620 N 1 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 G A 139 OP1 REMARK 620 2 G A 140 OP2 79.7 REMARK 620 N 1 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 141 O2 REMARK 620 2 U A 191 O4 88.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 102 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 239 OP1 REMARK 620 2 U C 54 OP1 104.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 507 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 257 OP1 REMARK 620 2 C A 258 OP2 77.7 REMARK 620 3 C C 73 OP1 94.2 170.5 REMARK 620 N 1 2 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 G A 275 OP1 REMARK 620 2 A A 277 OP1 80.2 REMARK 620 3 G A 301 OP1 100.7 120.9 REMARK 620 4 G A 301 OP2 96.4 170.0 50.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 509 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 276 O2' REMARK 620 2 C A 276 O2 73.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 533 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 277 O2' REMARK 620 2 C A 278 OP2 77.2 REMARK 620 3 A A 330 OP1 85.3 100.3 REMARK 620 4 G A 331 OP2 92.6 169.6 80.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 515 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 291 OP2 REMARK 620 2 U A 293 OP2 83.7 REMARK 620 N 1 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 A A 385 OP1 REMARK 620 2 C A 386 OP2 81.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 103 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G C 58 OP1 REMARK 620 2 U C 59 O4 79.9 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70935 RELATED DB: EMDB REMARK 900 STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS RNASE P RIBOZYME IN REMARK 900 COMPLEX WITH MATURE TRNA IN 5 MM CA2+ DBREF 9OWL A 1 417 GB 143442 M19021.1 1 417 DBREF1 9OWL C 1 75 GB CP063162.1 DBREF2 9OWL C 1919315002 90589 90663 SEQADV 9OWL 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 SEQRES 1 C 75 G C G G A A G U A G U U C SEQRES 2 C 75 A G U G G U A G A A C A C SEQRES 3 C 75 C A C C U U G C C A A G G SEQRES 4 C 75 U G G G G G U C G C G G G SEQRES 5 C 75 U U C G A G U C C C G U C SEQRES 6 C 75 U U C C G C U C C A 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 HET CA A 528 1 HET CA A 529 1 HET CA A 530 1 HET CA A 531 1 HET CA A 532 1 HET CA A 533 1 HET CA A 534 1 HET CA A 535 1 HET CA C 101 1 HET CA C 102 1 HET CA C 103 1 HETNAM CA CALCIUM ION FORMUL 3 CA 38(CA 2+) LINK OP2 G A 47 CA CA A 514 1555 1555 2.30 LINK OP1 A A 50 CA CA A 524 1555 1555 2.28 LINK O6 G A 71 CA CA A 527 1555 1555 2.36 LINK OP2 A A 82 CA CA A 510 1555 1555 2.32 LINK OP2 G A 83 CA CA A 510 1555 1555 2.96 LINK O6 G A 98 CA CA A 504 1555 1555 2.38 LINK OP2 A A 99 CA CA A 522 1555 1555 2.32 LINK O4 U A 105 CA CA A 522 1555 1555 2.84 LINK OP1 G A 139 CA CA A 512 1555 1555 2.33 LINK OP2 G A 140 CA CA A 512 1555 1555 2.35 LINK O2 C A 141 CA CA A 513 1555 1555 2.37 LINK O4 U A 191 CA CA A 513 1555 1555 2.38 LINK OP1 A A 239 CA CA C 102 1555 1555 2.45 LINK OP2 G A 250 CA CA A 510 1555 1555 2.84 LINK OP1 A A 257 CA CA A 507 1555 1555 2.35 LINK OP2 C A 258 CA CA A 507 1555 1555 2.23 LINK OP1 G A 275 CA CA A 517 1555 1555 2.35 LINK O2' C A 276 CA CA A 509 1555 1555 2.46 LINK O2 C A 276 CA CA A 509 1555 1555 2.56 LINK OP1 A A 277 CA CA A 517 1555 1555 2.34 LINK O2' A A 277 CA CA A 533 1555 1555 2.38 LINK OP2 C A 278 CA CA A 533 1555 1555 2.24 LINK O6 G A 289 CA CA A 503 1555 1555 2.37 LINK OP2 A A 291 CA CA A 515 1555 1555 2.56 LINK OP2 U A 293 CA CA A 515 1555 1555 2.76 LINK O6 G A 299 CA CA A 534 1555 1555 2.38 LINK OP1 G A 301 CA CA A 517 1555 1555 3.16 LINK OP2 G A 301 CA CA A 517 1555 1555 2.83 LINK OP1 A A 330 CA CA A 533 1555 1555 2.50 LINK OP2 G A 331 CA CA A 533 1555 1555 2.22 LINK OP1 A A 385 CA CA A 506 1555 1555 2.40 LINK OP2 C A 386 CA CA A 506 1555 1555 2.32 LINK OP1 A A 389 CA CA A 524 1555 1555 2.31 LINK OP2 A A 390 CA CA A 524 1555 1555 2.30 LINK CA CA A 507 OP1 C C 73 1555 1555 2.25 LINK CA CA A 524 OP1 G C 1 1555 1555 2.27 LINK OP2 U C 54 CA CA C 101 1555 1555 2.70 LINK OP1 U C 54 CA CA C 102 1555 1555 3.01 LINK OP1 G C 58 CA CA C 103 1555 1555 2.38 LINK O4 U C 59 CA CA C 103 1555 1555 2.37 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 98210576 CONECT 104810586 CONECT 150810589 CONECT 172910572 CONECT 175110572 CONECT 208310566 CONECT 209110584 CONECT 223210584 CONECT 294510574 CONECT 296910574 CONECT 300410575 CONECT 408110575 CONECT 510210599 CONECT 533610572 CONECT 549010569 CONECT 551310569 CONECT 588010579 CONECT 591210571 CONECT 591610571 CONECT 592310579 CONECT 593210595 CONECT 594610595 CONECT 619110565 CONECT 622110577 CONECT 626510577 CONECT 641010596 CONECT 643910579 CONECT 644010579 CONECT 707010595 CONECT 709310595 CONECT 825610568 CONECT 827910568 CONECT 834310586 CONECT 836610586 CONECT 896210586 CONECT1010710599 CONECT1010810598 CONECT1019210600 CONECT1023110600 CONECT1050110569 CONECT10565 6191 CONECT10566 2083 CONECT10568 8256 8279 CONECT10569 5490 551310501 CONECT10571 5912 5916 CONECT10572 1729 1751 5336 CONECT10574 2945 2969 CONECT10575 3004 4081 CONECT10576 982 CONECT10577 6221 6265 CONECT10579 5880 5923 6439 6440 CONECT10584 2091 2232 CONECT10586 1048 8343 8366 8962 CONECT10589 1508 CONECT10595 5932 5946 7070 7093 CONECT10596 6410 CONECT1059810108 CONECT10599 510210107 CONECT106001019210231 MASTER 224 0 38 0 0 0 0 610598 2 59 39 END