HEADER RNA 03-DEC-25 9ZHV TITLE CRYO-EM STRUCTURE OF RNASE P RNA FROM GEOBACILLUS STEAROTHERMOPHILUS, TITLE 2 CONFORMER 41 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 9ZHV 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 41 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERAX, COOT, CRYOSPARC, CRYOSPARC, REMARK 3 PHENIX 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 66889 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 9ZHV 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_1000302641. 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 IN AIR 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 N3 C A 152 O4 U A 175 2.14 REMARK 500 O4 U A 124 O6 G A 127 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 G A 203 O3' - P - OP2 ANGL. DEV. = -23.7 DEGREES REMARK 500 G A 203 O3' - P - OP1 ANGL. DEV. = -21.5 DEGREES REMARK 500 G A 203 OP1 - P - OP2 ANGL. DEV. = 11.8 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 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 50 OP1 REMARK 620 2 A A 389 OP1 93.0 REMARK 620 3 A A 390 OP2 87.8 90.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 529 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 50 OP2 REMARK 620 2 G A 51 N7 125.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 507 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 103 OP1 REMARK 620 2 C A 103 OP2 72.0 REMARK 620 N 1 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 G A 139 OP2 REMARK 620 2 G A 139 O5' 77.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 506 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 257 OP1 REMARK 620 2 A A 257 OP2 74.6 REMARK 620 3 C A 258 OP2 90.4 98.8 REMARK 620 N 1 2 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 G A 275 OP1 REMARK 620 2 A A 277 OP1 94.4 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 277 O2' REMARK 620 2 C A 278 OP2 87.5 REMARK 620 3 A A 330 OP1 94.7 93.7 REMARK 620 4 G A 331 OP2 93.5 179.0 86.5 REMARK 620 N 1 2 3 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 U A 293 OP2 REMARK 620 2 G A 294 N7 77.9 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 300 OP2 REMARK 620 2 G A 301 N7 101.6 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-74250 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF RNASE P RNA FROM GEOBACILLUS REMARK 900 STEAROTHERMOPHILUS, CONFORMER 41 DBREF 9ZHV A 1 417 GB 143442 M19021.1 1 417 SEQADV 9ZHV U A 126 GB 143442 C 126 CONFLICT SEQADV 9ZHV 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 U 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 HETNAM MG MAGNESIUM ION FORMUL 2 MG 35(MG 2+) FORMUL 37 HOH *2(H2 O) LINK OP2 G A 47 MG MG A 514 1555 1555 2.95 LINK OP1 A A 50 MG MG A 503 1555 1555 1.95 LINK OP2 A A 50 MG MG A 529 1555 1555 2.87 LINK N7 G A 51 MG MG A 529 1555 1555 2.00 LINK N7 G A 71 MG MG A 513 1555 1555 2.08 LINK OP2 A A 82 MG MG A 519 1555 1555 2.36 LINK OP1 C A 103 MG MG A 507 1555 1555 2.09 LINK OP2 C A 103 MG MG A 507 1555 1555 2.27 LINK OP2 G A 139 MG MG A 533 1555 1555 2.06 LINK O5' G A 139 MG MG A 533 1555 1555 1.95 LINK OP1 A A 257 MG MG A 506 1555 1555 1.90 LINK OP2 A A 257 MG MG A 506 1555 1555 2.29 LINK OP2 C A 258 MG MG A 506 1555 1555 2.24 LINK OP1 G A 275 MG MG A 510 1555 1555 2.12 LINK O2 C A 276 MG MG A 508 1555 1555 2.05 LINK O2' A A 277 MG MG A 509 1555 1555 2.11 LINK OP1 A A 277 MG MG A 510 1555 1555 2.20 LINK OP2 C A 278 MG MG A 509 1555 1555 2.04 LINK OP2 U A 293 MG MG A 501 1555 1555 2.73 LINK N7 G A 294 MG MG A 501 1555 1555 2.76 LINK O6 G A 299 MG MG A 517 1555 1555 1.95 LINK OP2 A A 300 MG MG A 512 1555 1555 2.06 LINK N7 G A 301 MG MG A 512 1555 1555 2.04 LINK OP1 A A 330 MG MG A 509 1555 1555 2.17 LINK OP2 G A 331 MG MG A 509 1555 1555 1.93 LINK OP2 G A 335 MG MG A 524 1555 1555 2.46 LINK OP1 A A 389 MG MG A 503 1555 1555 2.95 LINK OP2 A A 389 MG MG A 522 1555 1555 2.91 LINK OP2 A A 390 MG MG A 503 1555 1555 1.91 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 985 8977 CONECT 1051 8966 CONECT 1052 8992 CONECT 1086 8992 CONECT 1508 8976 CONECT 1732 8982 CONECT 2177 8970 CONECT 2178 8970 CONECT 2949 8996 CONECT 2950 8996 CONECT 5493 8969 CONECT 5494 8969 CONECT 5516 8969 CONECT 5883 8973 CONECT 5919 8971 CONECT 5926 8973 CONECT 5935 8972 CONECT 5949 8972 CONECT 6268 8964 CONECT 6300 8964 CONECT 6413 8980 CONECT 6421 8975 CONECT 6455 8975 CONECT 7073 8972 CONECT 7096 8972 CONECT 7183 8987 CONECT 8346 8966 CONECT 8347 8985 CONECT 8369 8966 CONECT 8964 6268 6300 CONECT 8966 1051 8346 8369 CONECT 8969 5493 5494 5516 CONECT 8970 2177 2178 CONECT 8971 5919 CONECT 8972 5935 5949 7073 7096 CONECT 8973 5883 5926 CONECT 8975 6421 6455 CONECT 8976 1508 CONECT 8977 985 CONECT 8980 6413 CONECT 8982 1732 CONECT 8985 8347 CONECT 8987 7183 CONECT 8992 1052 1086 CONECT 8996 2949 2950 MASTER 230 0 35 0 0 0 0 6 8999 1 45 33 END