HEADER RNA 03-DEC-25 9ZH7 TITLE CRYO-EM STRUCTURE OF RNASE P RNA FROM GEOBACILLUS STEAROTHERMOPHILUS, TITLE 2 CONFORMER 22 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 9ZH7 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 22 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.89 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 : RIGID BODY 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) : 2.890 REMARK 3 NUMBER OF PARTICLES : 84306 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 9ZH7 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_1000302587. 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 317 O2 U A 320 2.19 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 C A 152 O4' - C1' - N1 ANGL. DEV. = 5.0 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 505 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 50 OP1 REMARK 620 2 A A 389 OP1 95.8 REMARK 620 3 A A 390 OP2 84.8 96.8 REMARK 620 4 HOH A 601 O 171.9 82.7 87.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 533 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 81 O2' REMARK 620 2 G A 83 N7 146.3 REMARK 620 3 G A 83 O6 105.9 67.8 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 113 N7 REMARK 620 2 G A 113 O6 95.4 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 A A 137 O4' REMARK 620 2 A A 240 N6 86.8 REMARK 620 3 A A 240 N1 103.3 54.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 525 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 139 OP1 REMARK 620 2 G A 140 OP2 89.3 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 92.9 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 83.4 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 88.2 REMARK 620 3 A A 330 OP1 87.6 79.7 REMARK 620 4 G A 331 OP2 97.0 156.3 77.5 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 OP1 REMARK 620 2 U A 293 OP2 61.3 REMARK 620 3 U A 293 O5' 52.1 59.6 REMARK 620 4 G A 294 N7 137.7 91.8 86.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 520 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 298 O6 REMARK 620 2 G A 299 O6 82.9 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 A A 300 OP2 REMARK 620 2 G A 301 N7 113.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 385 OP1 REMARK 620 2 C A 386 OP2 99.3 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-74224 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF RNASE P RNA FROM GEOBACILLUS REMARK 900 STEAROTHERMOPHILUS, CONFORMER 22 DBREF 9ZH7 A 1 417 GB 143442 M19021.1 1 417 SEQADV 9ZH7 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+) FORMUL 45 HOH *(H2 O) LINK N7 G A 46 MG MG A 507 1555 1555 2.99 LINK OP2 G A 47 MG MG A 517 1555 1555 2.07 LINK OP1 A A 50 MG MG A 505 1555 1555 1.84 LINK OP2 C A 53 MG MG A 540 1555 1555 2.69 LINK O2' U A 81 MG MG A 533 1555 1555 2.74 LINK OP2 A A 82 MG MG A 522 1555 1555 2.58 LINK N7 G A 83 MG MG A 533 1555 1555 2.66 LINK O6 G A 83 MG MG A 533 1555 1555 2.82 LINK OP2 C A 103 MG MG A 510 1555 1555 1.97 LINK N7 G A 113 MG MG A 528 1555 1555 1.98 LINK O6 G A 113 MG MG A 528 1555 1555 2.20 LINK O4' A A 137 MG MG A 527 1555 1555 1.95 LINK OP1 G A 139 MG MG A 525 1555 1555 1.95 LINK OP2 G A 140 MG MG A 525 1555 1555 2.05 LINK N6 A A 240 MG MG A 527 1555 1555 2.22 LINK N1 A A 240 MG MG A 527 1555 1555 2.74 LINK N7 A A 255 MG MG A 538 1555 1555 2.41 LINK OP1 A A 257 MG MG A 509 1555 1555 2.09 LINK OP2 C A 258 MG MG A 509 1555 1555 1.99 LINK O2' U A 270 MG MG A 530 1555 1555 2.58 LINK OP1 G A 275 MG MG A 513 1555 1555 2.08 LINK O2 C A 276 MG MG A 529 1555 1555 2.44 LINK O2' A A 277 MG MG A 512 1555 1555 2.05 LINK OP1 A A 277 MG MG A 513 1555 1555 2.19 LINK OP2 C A 278 MG MG A 512 1555 1555 2.06 LINK OP2 G A 288 MG MG A 521 1555 1555 2.35 LINK OP1 U A 293 MG MG A 502 1555 1555 2.84 LINK OP2 U A 293 MG MG A 502 1555 1555 1.97 LINK O5' U A 293 MG MG A 502 1555 1555 2.81 LINK N7 G A 294 MG MG A 502 1555 1555 2.99 LINK O6 G A 298 MG MG A 520 1555 1555 2.86 LINK O6 G A 299 MG MG A 520 1555 1555 1.99 LINK OP2 A A 300 MG MG A 515 1555 1555 2.01 LINK N7 G A 301 MG MG A 515 1555 1555 2.07 LINK OP1 A A 330 MG MG A 512 1555 1555 2.53 LINK OP2 G A 331 MG MG A 512 1555 1555 2.04 LINK OP1 A A 385 MG MG A 501 1555 1555 2.60 LINK OP2 C A 386 MG MG A 501 1555 1555 2.06 LINK OP1 A A 389 MG MG A 505 1555 1555 2.69 LINK OP2 A A 390 MG MG A 505 1555 1555 2.10 LINK MG MG A 505 O HOH A 601 1555 1555 1.82 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 974 8970 CONECT 985 8980 CONECT 1051 8968 CONECT 1117 9003 CONECT 1720 8996 CONECT 1732 8985 CONECT 1766 8996 CONECT 1769 8996 CONECT 2178 8973 CONECT 2404 8991 CONECT 2407 8991 CONECT 2911 8990 CONECT 2948 8988 CONECT 2972 8988 CONECT 5143 8990 CONECT 5144 8990 CONECT 5462 9001 CONECT 5493 8972 CONECT 5516 8972 CONECT 5781 8993 CONECT 5883 8976 CONECT 5919 8992 CONECT 5926 8976 CONECT 5935 8975 CONECT 5949 8975 CONECT 6156 8984 CONECT 6267 8965 CONECT 6268 8965 CONECT 6269 8965 CONECT 6300 8965 CONECT 6390 8983 CONECT 6413 8983 CONECT 6421 8978 CONECT 6455 8978 CONECT 7073 8975 CONECT 7096 8975 CONECT 8259 8964 CONECT 8282 8964 CONECT 8346 8968 CONECT 8369 8968 CONECT 8964 8259 8282 CONECT 8965 6267 6268 6269 6300 CONECT 8968 1051 8346 8369 9007 CONECT 8970 974 CONECT 8972 5493 5516 CONECT 8973 2178 CONECT 8975 5935 5949 7073 7096 CONECT 8976 5883 5926 CONECT 8978 6421 6455 CONECT 8980 985 CONECT 8983 6390 6413 CONECT 8984 6156 CONECT 8985 1732 CONECT 8988 2948 2972 CONECT 8990 2911 5143 5144 CONECT 8991 2404 2407 CONECT 8992 5919 CONECT 8993 5781 CONECT 8996 1720 1766 1769 CONECT 9001 5462 CONECT 9003 1117 CONECT 9007 8968 MASTER 239 0 43 0 0 0 0 6 9006 1 62 33 END