HEADER RNA 03-DEC-25 9ZGV TITLE CRYO-EM STRUCTURE OF RNASE P RNA FROM GEOBACILLUS STEAROTHERMOPHILUS, TITLE 2 CONFORMER 14 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 9ZGV 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 14 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.93 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 : 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) : 2.930 REMARK 3 NUMBER OF PARTICLES : 81394 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 9ZGV 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_1000302566. 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 N3 C A 152 O4 U A 175 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. = -23.1 DEGREES REMARK 500 G A 203 O3' - P - OP1 ANGL. DEV. = -21.9 DEGREES REMARK 500 G A 203 OP1 - P - OP2 ANGL. DEV. = 11.6 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 88.3 REMARK 620 3 A A 390 OP2 80.7 104.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 543 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 74 OP1 REMARK 620 2 A A 74 OP2 75.5 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 U A 81 O2' REMARK 620 2 G A 83 N7 143.8 REMARK 620 N 1 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 136 O2' REMARK 620 2 A A 137 O2' 133.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 523 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 139 OP1 REMARK 620 2 G A 140 OP2 109.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 508 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 257 OP1 REMARK 620 2 A A 257 OP2 78.6 REMARK 620 3 C A 258 OP2 100.9 95.6 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 G A 272 N7 REMARK 620 2 G A 272 O6 99.8 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 G A 275 OP1 REMARK 620 2 A A 277 OP1 85.8 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 C A 276 O2 REMARK 620 2 U A 333 O4 130.9 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 A A 277 O2' REMARK 620 2 C A 278 OP2 82.8 REMARK 620 3 A A 330 OP1 83.6 83.9 REMARK 620 4 G A 331 OP2 84.2 161.8 82.1 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 288 O6 REMARK 620 2 G A 289 O6 72.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 514 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 300 OP2 REMARK 620 2 G A 301 N7 109.1 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-74204 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF RNASE P RNA FROM GEOBACILLUS REMARK 900 STEAROTHERMOPHILUS, CONFORMER 14 DBREF 9ZGV A 1 417 GB 143442 M19021.1 1 417 SEQADV 9ZGV 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 N1 A A 45 MG MG A 531 1555 1555 2.71 LINK N7 G A 46 MG MG A 507 1555 1555 2.09 LINK OP2 G A 47 MG MG A 516 1555 1555 2.34 LINK N1 A A 48 MG MG A 527 1555 1555 2.81 LINK OP1 A A 50 MG MG A 505 1555 1555 2.19 LINK N7 A A 55 MG MG A 540 1555 1555 2.39 LINK O6 G A 66 MG MG A 522 1555 1555 2.01 LINK OP1 A A 74 MG MG A 543 1555 1555 2.07 LINK OP2 A A 74 MG MG A 543 1555 1555 2.10 LINK O2' U A 81 MG MG A 533 1555 1555 2.83 LINK N7 G A 83 MG MG A 533 1555 1555 2.86 LINK O2' G A 136 MG MG A 525 1555 1555 2.97 LINK O2' A A 137 MG MG A 525 1555 1555 2.42 LINK OP1 G A 139 MG MG A 523 1555 1555 1.96 LINK OP2 G A 140 MG MG A 523 1555 1555 1.99 LINK N7 A A 249 MG MG A 530 1555 1555 2.04 LINK OP2 A A 255 MG MG A 541 1555 1555 2.63 LINK OP1 A A 257 MG MG A 508 1555 1555 2.02 LINK OP2 A A 257 MG MG A 508 1555 1555 2.02 LINK OP2 C A 258 MG MG A 508 1555 1555 2.22 LINK N7 G A 272 MG MG A 529 1555 1555 2.06 LINK O6 G A 272 MG MG A 529 1555 1555 1.91 LINK OP1 G A 275 MG MG A 512 1555 1555 2.03 LINK O2' C A 276 MG MG A 510 1555 1555 2.98 LINK O2 C A 276 MG MG A 535 1555 1555 2.11 LINK O2' A A 277 MG MG A 511 1555 1555 2.44 LINK OP1 A A 277 MG MG A 512 1555 1555 2.16 LINK N6 A A 277 MG MG A 528 1555 1555 2.09 LINK OP2 C A 278 MG MG A 511 1555 1555 1.99 LINK O6 G A 288 MG MG A 532 1555 1555 2.90 LINK O6 G A 289 MG MG A 519 1555 1555 2.53 LINK O6 G A 289 MG MG A 532 1555 1555 2.97 LINK N7 G A 294 MG MG A 502 1555 1555 2.86 LINK O6 G A 299 MG MG A 518 1555 1555 1.96 LINK OP2 A A 300 MG MG A 514 1555 1555 2.04 LINK N7 G A 301 MG MG A 514 1555 1555 2.10 LINK OP1 A A 330 MG MG A 511 1555 1555 2.40 LINK OP2 G A 331 MG MG A 511 1555 1555 2.02 LINK O4 U A 333 MG MG A 535 1555 1555 2.59 LINK OP2 C A 386 MG MG A 501 1555 1555 2.50 LINK OP1 A A 389 MG MG A 505 1555 1555 2.80 LINK OP2 A A 390 MG MG A 505 1555 1555 2.00 LINK O4 U A 393 MG MG A 538 1555 1555 2.73 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 956 8994 CONECT 974 8970 CONECT 985 8979 CONECT 1024 8990 CONECT 1051 8968 CONECT 1169 9003 CONECT 1405 8985 CONECT 1563 9006 CONECT 1564 9006 CONECT 1720 8996 CONECT 1766 8996 CONECT 2892 8988 CONECT 2915 8988 CONECT 2948 8986 CONECT 2972 8986 CONECT 5329 8993 CONECT 5450 9004 CONECT 5493 8971 CONECT 5494 8971 CONECT 5516 8971 CONECT 5827 8992 CONECT 5830 8992 CONECT 5883 8975 CONECT 5915 8973 CONECT 5919 8998 CONECT 5926 8975 CONECT 5935 8974 CONECT 5942 8991 CONECT 5949 8974 CONECT 6171 8995 CONECT 6194 8982 8995 CONECT 6300 8965 CONECT 6413 8981 CONECT 6421 8977 CONECT 6455 8977 CONECT 7073 8974 CONECT 7096 8974 CONECT 7156 8998 CONECT 8282 8964 CONECT 8346 8968 CONECT 8369 8968 CONECT 8448 9001 CONECT 8964 8282 CONECT 8965 6300 CONECT 8968 1051 8346 8369 CONECT 8970 974 CONECT 8971 5493 5494 5516 CONECT 8973 5915 CONECT 8974 5935 5949 7073 7096 CONECT 8975 5883 5926 CONECT 8977 6421 6455 CONECT 8979 985 CONECT 8981 6413 CONECT 8982 6194 CONECT 8985 1405 CONECT 8986 2948 2972 CONECT 8988 2892 2915 CONECT 8990 1024 CONECT 8991 5942 CONECT 8992 5827 5830 CONECT 8993 5329 CONECT 8994 956 CONECT 8995 6171 6194 CONECT 8996 1720 1766 CONECT 8998 5919 7156 CONECT 9001 8448 CONECT 9003 1169 CONECT 9004 5450 CONECT 9006 1563 1564 MASTER 237 0 43 0 0 0 0 6 9005 1 69 33 END