HEADER RNA 03-DEC-25 9ZHF TITLE CRYO-EM STRUCTURE OF RNASE P RNA FROM GEOBACILLUS STEAROTHERMOPHILUS, TITLE 2 CONFORMER 29 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE P RNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 4 ORGANISM_TAXID: 1422 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 9ZHF 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 29 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, 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 : 57.000 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) : 2.880 REMARK 3 NUMBER OF PARTICLES : 97395 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 9ZHF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1000302610. 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 : 2.70 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 : 165000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : THE ALIGNMENT PROCEDURE WAS REMARK 245 PERFORMED USING THE EPU SOFTWARE UTILIZING ITS AUTOFOCUS AND REMARK 245 AUTO-TUNING FUNCTIONS FOR INITIAL MICROSCOPE ALIGNMENT. THIS WAS REMARK 245 FOLLOWED BY MANUAL FINE-TUNING ADJUSTMENTS OF THE BEAM SHIFT, REMARK 245 STIGMATION, AND FOCUS CONTROLS TO ENSURE OPTIMAL IMAGE QUALITY. REMARK 245 GRID SQUARES WERE SCREENED SYSTEMATICALLY, ENSURING THE REMARK 245 SELECTION OF AREAS WITH APPROPRIATE ICE THICKNESS AND PARTICLE REMARK 245 DISTRIBUTION. IMAGE SHIFT CALIBRATION AND EUCENTRIC HEIGHT REMARK 245 ADJUSTMENT WERE PERFORMED WITHIN EPU TO MAINTAIN BEAM ALIGNMENT REMARK 245 DURING DATA ACQUISITION 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 N2 G A 117 O2 C A 134 2.12 REMARK 500 O2 U A 120 N2 G A 131 2.17 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 389 OP1 116.8 REMARK 620 3 A A 390 OP2 84.6 129.9 REMARK 620 4 HOH A 601 O 128.0 103.4 94.4 REMARK 620 N 1 2 3 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 83 N7 REMARK 620 2 G A 83 O6 75.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 522 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 84 O4 REMARK 620 2 G A 85 O6 63.2 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 102 OP2 REMARK 620 2 C A 103 OP2 79.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 527 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 139 OP1 REMARK 620 2 G A 139 OP2 58.3 REMARK 620 N 1 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 94.6 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 85.1 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 276 O2 REMARK 620 2 U A 333 O4 121.7 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 82.2 REMARK 620 3 A A 330 OP1 85.4 90.8 REMARK 620 4 G A 331 OP2 81.5 163.3 84.1 REMARK 620 N 1 2 3 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 A A 300 OP2 REMARK 620 2 G A 301 N7 91.5 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-74232 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF RNASE P RNA FROM GEOBACILLUS REMARK 900 STEAROTHERMOPHILUS, CONFORMER 29 DBREF 9ZHF A 1 416 GB 143442 M19021.1 1 416 SEQADV 9ZHF C A 417 GB 143442 EXPRESSION TAG 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+) FORMUL 45 HOH *(H2 O) LINK OP2 G A 14 MG MG A 517 1555 1555 1.93 LINK OP1 A A 50 MG MG A 505 1555 1555 1.97 LINK N7 G A 65 MG MG A 524 1555 1555 2.10 LINK N7 G A 71 MG MG A 516 1555 1555 1.97 LINK N7 G A 83 MG MG A 532 1555 1555 2.11 LINK O6 G A 83 MG MG A 532 1555 1555 2.85 LINK O4 U A 84 MG MG A 522 1555 1555 2.53 LINK O6 G A 85 MG MG A 522 1555 1555 2.65 LINK O2' G A 85 MG MG A 539 1555 1555 2.05 LINK OP2 C A 102 MG MG A 510 1555 1555 2.83 LINK OP2 C A 103 MG MG A 510 1555 1555 2.03 LINK O2' A A 137 MG MG A 538 1555 1555 2.04 LINK OP1 G A 139 MG MG A 527 1555 1555 2.33 LINK OP2 G A 139 MG MG A 527 1555 1555 2.85 LINK OP1 A A 257 MG MG A 509 1555 1555 2.13 LINK OP2 C A 258 MG MG A 509 1555 1555 2.04 LINK OP1 G A 275 MG MG A 513 1555 1555 1.97 LINK O2 C A 276 MG MG A 511 1555 1555 2.12 LINK O2' A A 277 MG MG A 512 1555 1555 2.39 LINK OP1 A A 277 MG MG A 513 1555 1555 2.21 LINK N6 A A 277 MG MG A 531 1555 1555 2.07 LINK OP2 C A 278 MG MG A 512 1555 1555 2.07 LINK OP2 G A 288 MG MG A 521 1555 1555 2.91 LINK O6 G A 289 MG MG A 530 1555 1555 2.61 LINK N7 G A 294 MG MG A 502 1555 1555 1.92 LINK O6 G A 299 MG MG A 520 1555 1555 2.41 LINK OP2 A A 300 MG MG A 515 1555 1555 2.08 LINK N7 G A 301 MG MG A 515 1555 1555 2.65 LINK OP1 A A 330 MG MG A 512 1555 1555 2.18 LINK OP2 G A 331 MG MG A 512 1555 1555 2.06 LINK O4 U A 333 MG MG A 511 1555 1555 2.30 LINK OP2 C A 386 MG MG A 501 1555 1555 2.10 LINK OP1 A A 389 MG MG A 505 1555 1555 2.05 LINK OP2 A A 390 MG MG A 505 1555 1555 2.06 LINK O4 U A 393 MG MG A 537 1555 1555 2.73 LINK MG MG A 505 O HOH A 601 1555 1555 1.83 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 275 8980 CONECT 1051 8968 CONECT 1379 8987 CONECT 1508 8979 CONECT 1766 8995 CONECT 1769 8995 CONECT 1792 8985 CONECT 1805 9002 CONECT 1812 8985 CONECT 2158 8973 CONECT 2178 8973 CONECT 2915 9001 CONECT 2948 8990 CONECT 2949 8990 CONECT 5493 8972 CONECT 5516 8972 CONECT 5883 8976 CONECT 5919 8974 CONECT 5926 8976 CONECT 5935 8975 CONECT 5942 8994 CONECT 5949 8975 CONECT 6156 8984 CONECT 6194 8993 CONECT 6300 8965 CONECT 6413 8983 CONECT 6421 8978 CONECT 6455 8978 CONECT 7073 8975 CONECT 7096 8975 CONECT 7156 8974 CONECT 8282 8964 CONECT 8346 8968 CONECT 8369 8968 CONECT 8448 9000 CONECT 8964 8282 CONECT 8965 6300 CONECT 8968 1051 8346 8369 9007 CONECT 8972 5493 5516 CONECT 8973 2158 2178 CONECT 8974 5919 7156 CONECT 8975 5935 5949 7073 7096 CONECT 8976 5883 5926 CONECT 8978 6421 6455 CONECT 8979 1508 CONECT 8980 275 CONECT 8983 6413 CONECT 8984 6156 CONECT 8985 1792 1812 CONECT 8987 1379 CONECT 8990 2948 2949 CONECT 8993 6194 CONECT 8994 5942 CONECT 8995 1766 1769 CONECT 9000 8448 CONECT 9001 2915 CONECT 9002 1805 CONECT 9007 8968 MASTER 212 0 43 0 0 0 0 6 9006 1 58 33 END