HEADER RNA 03-DEC-25 9ZGM TITLE CRYO-EM STRUCTURE OF RNASE P RNA FROM GEOBACILLUS STEAROTHERMOPHILUS, TITLE 2 CONFORMER 4 CAVEAT 9ZGM RESIDUES C A 233 AND G A 234 THAT ARE NEXT TO EACH OTHER IN CAVEAT 2 9ZGM THE SAMPLE SEQUENCE ARE NOT PROPERLY LINKED: DISTANCE CAVEAT 3 9ZGM BETWEEN O3' AND P IS 3.15 A. RESIDUES C A 367 AND G A 368 CAVEAT 4 9ZGM THAT ARE NEXT TO EACH OTHER IN THE SAMPLE SEQUENCE ARE NOT CAVEAT 5 9ZGM PROPERLY LINKED: DISTANCE BETWEEN O3' AND P IS 3.25 A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE P RNA; 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 RNASE P RNA, GEOBACILLUS STEAROTHERMOPHILUS, CATALYTIC RNA, CRYO-EM KEYWDS 2 STRUCTURE, CONFORMATIONAL HETEROGENEITY, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR M.F.S.DEGENHARDT,J.STAGNO,Y.X.WANG REVDAT 1 13-MAY-26 9ZGM 0 JRNL AUTH M.F.S.DEGENHARDT,J.STAGNO,Y.X.WANG JRNL TITL CRYO-EM STRUCTURE OF RNASE P RNA FROM GEOBACILLUS JRNL TITL 2 STEAROTHERMOPHILUS, CONFORMER 2 AT 3 ANGSTROMS RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 9OV3 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : MAXIMIZATION OF MAP-TO-MODEL REMARK 3 CORRELATION 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) : 3.010 REMARK 3 NUMBER OF PARTICLES : 76942 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 9ZGM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1000302485. 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 : RIBONUCLEASE P RNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.80 REMARK 245 SAMPLE SUPPORT DETAILS : GLOW-DISCHARGED QUANTIFOIL REMARK 245 R1.2/1.3 AU 300 MESH GRIDS REMARK 245 PREPARED ON A VITROBOT. GRIDS REMARK 245 WERE GLOW-DISCHARGED ON BOTH REMARK 245 SIDES FOR 60 S AT 25 MA PRIOR REMARK 245 TO SAMPLE APPLICATION. SAMPLE REMARK 245 CONCENTRATION WAS 2.7 MG/ML. A REMARK 245 10 S WAIT TIME AND 3 S BLOT REMARK 245 WITH FORCE 3 TO 10 AT 277K WERE REMARK 245 USED DURING VITRIFICATION. REMARK 245 SAMPLE VITRIFICATION DETAILS : GRIDS WERE GLOW-DISCHARGED ON REMARK 245 BOTH SIDES PRIOR TO REMARK 245 VITRIFICATION. VITRIFICATION REMARK 245 WAS PERFORMED USING A VITROBOT REMARK 245 MARK IV WITH A 10S WAIT TIME, REMARK 245 FOLLOWED BY A 3S BLOT AND BLOT REMARK 245 FORCE 3 TO 10 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 : 78777 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 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) : 5300.00 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: 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 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 355 C6 G A 375 2.15 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 505 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 50 OP1 REMARK 620 2 A A 390 OP2 84.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 510 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 103 OP1 REMARK 620 2 C A 103 OP2 66.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 532 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 113 N7 REMARK 620 2 G A 113 O6 87.6 REMARK 620 3 G A 114 N7 109.4 98.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 528 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 139 OP1 REMARK 620 2 G A 140 OP2 109.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 515 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 140 N1 REMARK 620 2 G A 140 N2 64.9 REMARK 620 3 C A 243 O2 112.6 77.4 REMARK 620 4 C A 243 N3 85.1 114.3 62.0 REMARK 620 5 C A 244 N1 136.6 92.0 95.8 138.2 REMARK 620 6 C A 244 N3 94.6 110.1 152.0 130.4 57.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 509 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 257 OP1 REMARK 620 2 C A 258 OP2 93.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 535 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 272 N7 REMARK 620 2 G A 272 O6 84.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 513 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 275 OP1 REMARK 620 2 A A 277 OP1 83.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 512 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 277 O2' REMARK 620 2 C A 278 OP2 86.6 REMARK 620 3 A A 330 OP1 82.3 80.9 REMARK 620 4 G A 331 OP2 88.1 158.7 78.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 293 OP2 REMARK 620 2 G A 294 N7 82.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 517 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 300 OP2 REMARK 620 2 G A 301 N7 97.6 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-74195 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF RNASE P RNA FROM GEOBACILLUS REMARK 900 STEAROTHERMOPHILUS, CONFORMER 4 DBREF 9ZGM A 1 417 GB 143442 M19021.1 1 417 SEQADV 9ZGM C A 417 GB 143442 G 417 CONFLICT 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 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 HET MG A 522 1 HET MG A 523 1 HET MG A 524 1 HET MG A 525 1 HET MG A 526 1 HET MG A 527 1 HET MG A 528 1 HET MG A 529 1 HET MG A 530 1 HET MG A 531 1 HET MG A 532 1 HET MG A 533 1 HET MG A 534 1 HET MG A 535 1 HET MG A 536 1 HET MG A 537 1 HET MG A 538 1 HET MG A 539 1 HET MG A 540 1 HET MG A 541 1 HET MG A 542 1 HET MG A 543 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 43(MG 2+) LINK O6 G A 27 MG MG A 504 1555 1555 1.98 LINK N1 A A 45 MG MG A 538 1555 1555 2.74 LINK OP2 G A 47 MG MG A 519 1555 1555 2.03 LINK OP1 A A 50 MG MG A 505 1555 1555 1.99 LINK O4 U A 56 MG MG A 540 1555 1555 2.86 LINK N7 G A 66 MG MG A 526 1555 1555 2.06 LINK OP2 A A 82 MG MG A 524 1555 1555 2.52 LINK OP1 C A 103 MG MG A 510 1555 1555 2.50 LINK OP2 C A 103 MG MG A 510 1555 1555 2.13 LINK N7 G A 113 MG MG A 532 1555 1555 2.19 LINK O6 G A 113 MG MG A 532 1555 1555 2.27 LINK N7 G A 114 MG MG A 532 1555 1555 2.63 LINK OP1 G A 139 MG MG A 528 1555 1555 1.94 LINK N1 G A 140 MG MG A 515 1555 1555 2.12 LINK N2 G A 140 MG MG A 515 1555 1555 2.17 LINK OP2 G A 140 MG MG A 528 1555 1555 1.91 LINK O2 C A 243 MG MG A 515 1555 1555 2.26 LINK N3 C A 243 MG MG A 515 1555 1555 2.15 LINK N1 C A 244 MG MG A 515 1555 1555 2.58 LINK N3 C A 244 MG MG A 515 1555 1555 2.32 LINK N7 A A 249 MG MG A 537 1555 1555 2.84 LINK OP1 A A 257 MG MG A 509 1555 1555 1.94 LINK OP2 C A 258 MG MG A 509 1555 1555 2.09 LINK N7 G A 272 MG MG A 535 1555 1555 2.41 LINK O6 G A 272 MG MG A 535 1555 1555 2.09 LINK OP1 G A 275 MG MG A 513 1555 1555 2.03 LINK O2' C A 276 MG MG A 511 1555 1555 2.62 LINK O2' A A 277 MG MG A 512 1555 1555 2.19 LINK OP1 A A 277 MG MG A 513 1555 1555 2.27 LINK N6 A A 277 MG MG A 534 1555 1555 2.30 LINK OP2 C A 278 MG MG A 512 1555 1555 2.01 LINK OP2 G A 288 MG MG A 523 1555 1555 2.03 LINK OP2 U A 293 MG MG A 502 1555 1555 2.38 LINK N7 G A 294 MG MG A 502 1555 1555 2.56 LINK O6 G A 298 MG MG A 541 1555 1555 2.31 LINK O6 G A 299 MG MG A 522 1555 1555 2.04 LINK OP2 A A 300 MG MG A 517 1555 1555 2.22 LINK N7 G A 301 MG MG A 517 1555 1555 2.20 LINK OP1 A A 330 MG MG A 512 1555 1555 2.49 LINK OP2 G A 331 MG MG A 512 1555 1555 1.95 LINK OP2 A A 332 MG MG A 533 1555 1555 2.85 LINK OP2 A A 339 MG MG A 530 1555 1555 2.92 LINK OP2 C A 386 MG MG A 501 1555 1555 1.95 LINK N7 A A 387 MG MG A 516 1555 1555 2.83 LINK O6 G A 388 MG MG A 527 1555 1555 2.10 LINK OP2 A A 390 MG MG A 505 1555 1555 2.06 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 569 8967 CONECT 956 9001 CONECT 985 8982 CONECT 1051 8968 CONECT 1194 9003 CONECT 1402 8989 CONECT 1732 8987 CONECT 2177 8973 CONECT 2178 8973 CONECT 2404 8995 CONECT 2407 8995 CONECT 2427 8995 CONECT 2948 8991 CONECT 2972 8991 CONECT 2988 8978 CONECT 2990 8978 CONECT 5204 8978 CONECT 5205 8978 CONECT 5222 8978 CONECT 5225 8978 CONECT 5329 9000 CONECT 5493 8972 CONECT 5516 8972 CONECT 5827 8998 CONECT 5830 8998 CONECT 5883 8976 CONECT 5915 8974 CONECT 5926 8976 CONECT 5935 8975 CONECT 5942 8997 CONECT 5949 8975 CONECT 6156 8986 CONECT 6268 8965 CONECT 6300 8965 CONECT 6390 9004 CONECT 6413 8985 CONECT 6421 8980 CONECT 6455 8980 CONECT 7073 8975 CONECT 7096 8975 CONECT 7119 8996 CONECT 7271 8993 CONECT 8282 8964 CONECT 8314 8979 CONECT 8339 8990 CONECT 8369 8968 CONECT 8964 8282 CONECT 8965 6268 6300 CONECT 8967 569 CONECT 8968 1051 8369 CONECT 8972 5493 5516 CONECT 8973 2177 2178 CONECT 8974 5915 CONECT 8975 5935 5949 7073 7096 CONECT 8976 5883 5926 CONECT 8978 2988 2990 5204 5205 CONECT 8978 5222 5225 CONECT 8979 8314 CONECT 8980 6421 6455 CONECT 8982 985 CONECT 8985 6413 CONECT 8986 6156 CONECT 8987 1732 CONECT 8989 1402 CONECT 8990 8339 CONECT 8991 2948 2972 CONECT 8993 7271 CONECT 8995 2404 2407 2427 CONECT 8996 7119 CONECT 8997 5942 CONECT 8998 5827 5830 CONECT 9000 5329 CONECT 9001 956 CONECT 9003 1194 CONECT 9004 6390 MASTER 212 0 43 0 0 0 0 6 9005 1 75 33 END