HEADER RNA 01-JUN-21 7EZ2 TITLE HOLO L-16 SCAI TETRAHYMENA RIBOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOLO L-16 SCAI TETRAHYMENA RIBOZYME S1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HOLO L-16 SCAI TETRAHYMENA RIBOZYME S2; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: HOLO L-16 SCAI TETRAHYMENA RIBOZYME; COMPND 12 CHAIN: N; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TETRAHYMENA THERMOPHILA; SOURCE 3 ORGANISM_TAXID: 5911; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: TETRAHYMENA THERMOPHILA; SOURCE 8 ORGANISM_TAXID: 5911; SOURCE 9 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: TETRAHYMENA THERMOPHILA; SOURCE 13 ORGANISM_TAXID: 5911; SOURCE 14 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS RNA STRUCTURE, TETRAHYMENA RIBOZYME, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR Z.SU,K.ZHANG,K.KAPPEL,B.LUO,R.DAS,W.CHIU REVDAT 3 12-JUN-24 7EZ2 1 REMARK REVDAT 2 16-FEB-22 7EZ2 1 JRNL REVDAT 1 25-AUG-21 7EZ2 0 JRNL AUTH Z.SU,K.ZHANG,K.KAPPEL,S.LI,M.Z.PALO,G.D.PINTILIE,R.RANGAN, JRNL AUTH 2 B.LUO,Y.WEI,R.DAS,W.CHIU JRNL TITL CRYO-EM STRUCTURES OF FULL-LENGTH TETRAHYMENA RIBOZYME AT JRNL TITL 2 3.1 ANGSTROM RESOLUTION. JRNL REF NATURE V. 596 603 2021 JRNL REFN ESSN 1476-4687 JRNL PMID 34381213 JRNL DOI 10.1038/S41586-021-03803-W REMARK 2 REMARK 2 RESOLUTION. 3.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CTFFIND, RELION, UCSF CHIMERA, REMARK 3 RELION, RELION, RELION, RELION, PHENIX, REMARK 3 COOT REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : NULL 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) : 3.050 REMARK 3 NUMBER OF PARTICLES : 230386 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 7EZ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022411. 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 : HOLO L-16 SCAI TETRAHYMENA REMARK 245 RIBOZYME WITH SUBSTRATES S1 AND REMARK 245 S2, AND METAL IONS. REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 5559 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 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) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, N 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 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 N 527 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 3 O2' REMARK 620 2 A N 261 O3' 121.3 REMARK 620 3 C N 262 OP1 91.2 59.6 REMARK 620 4 A N 306 OP2 100.9 107.1 165.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 526 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 6 O3' REMARK 620 2 C N 208 OP1 85.5 REMARK 620 3 A N 304 OP1 98.5 69.5 REMARK 620 4 A N 306 OP1 164.2 97.2 97.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 505 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 183 OP1 REMARK 620 2 A N 184 OP2 76.3 REMARK 620 3 A N 186 OP2 98.0 72.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 184 OP1 REMARK 620 2 A N 186 OP1 80.0 REMARK 620 3 A N 187 OP2 149.3 80.3 REMARK 620 4 G N 188 OP2 105.9 152.0 81.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 207 OP1 REMARK 620 2 C N 262 OP2 146.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 511 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 256 OP1 REMARK 620 2 U N 273 OP1 89.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 515 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G N 257 OP1 REMARK 620 2 U N 258 OP2 81.1 REMARK 620 3 U N 305 OP2 94.8 114.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 519 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 301 OP1 REMARK 620 2 A N 302 OP2 79.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 528 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U N 307 OP2 REMARK 620 2 A N 308 OP2 94.3 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-31385 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-31386 RELATED DB: EMDB REMARK 900 HOLO L16 SCAI TETRAHYMENA RIBOZYME DBREF 7EZ2 A 1 8 PDB 7EZ2 7EZ2 1 8 DBREF 7EZ2 B 1 6 PDB 7EZ2 7EZ2 1 6 DBREF 7EZ2 N 17 408 PDB 7EZ2 7EZ2 17 408 SEQRES 1 A 8 U C G SSU A A C C SEQRES 1 B 6 C C C U C U SEQRES 1 N 392 G G U U U G G A G G G A A SEQRES 2 N 392 A A G U U A U C A G G C A SEQRES 3 N 392 U G C A C C U G G U A G C SEQRES 4 N 392 U A G U C U U U A A A C C SEQRES 5 N 392 A A U A G A U U G C A U C SEQRES 6 N 392 G G U U U A A A A G G C A SEQRES 7 N 392 A G A C C G U C A A A U U SEQRES 8 N 392 G C G G G A A A G G G G U SEQRES 9 N 392 C A A C A G C C G U U C A SEQRES 10 N 392 G U A C C A A G U C U C A SEQRES 11 N 392 G G G G A A A C U U U G A SEQRES 12 N 392 G A U G G C C U U G C A A SEQRES 13 N 392 A G G G U A U G G U A A U SEQRES 14 N 392 A A G C U G A C G G A C A SEQRES 15 N 392 U G G U C C U A A C C A C SEQRES 16 N 392 G C A G C C A A G U C C U SEQRES 17 N 392 A A G U C A A C A G A U C SEQRES 18 N 392 U U C U G U U G A U A U G SEQRES 19 N 392 G A U G C A G U U C A C A SEQRES 20 N 392 G A C U A A A U G U C G G SEQRES 21 N 392 U C G G G G A A G A U G U SEQRES 22 N 392 A U U C U U C U C A U A A SEQRES 23 N 392 G A U A U A G U C G G A C SEQRES 24 N 392 C U C U C C U U A A U G G SEQRES 25 N 392 G A G C U A G C G G A U G SEQRES 26 N 392 A A G U G A U G C A A C A SEQRES 27 N 392 C U G G A G C C G C U G G SEQRES 28 N 392 G A A C U A A U U U G U A SEQRES 29 N 392 U G C G A A A G U A U A U SEQRES 30 N 392 U G A U U A G U U U U G G SEQRES 31 N 392 A G HET SSU A 4 20 HET MG N 501 1 HET MG N 502 1 HET MG N 503 1 HET MG N 504 1 HET MG N 505 1 HET MG N 506 1 HET MG N 507 1 HET MG N 508 1 HET MG N 509 1 HET MG N 510 1 HET MG N 511 1 HET MG N 512 1 HET MG N 513 1 HET MG N 514 1 HET MG N 515 1 HET MG N 516 1 HET MG N 517 1 HET MG N 518 1 HET MG N 519 1 HET MG N 520 1 HET MG N 521 1 HET MG N 522 1 HET MG N 523 1 HET MG N 524 1 HET MG N 525 1 HET MG N 526 1 HET MG N 527 1 HET MG N 528 1 HET MG N 529 1 HET MG N 530 1 HET MG N 531 1 HETNAM SSU URIDINE-5'-PHOSPHOROTHIOATE HETNAM MG MAGNESIUM ION HETSYN SSU SP-SULFUR-SUBSTITUTED URIDINE FORMUL 1 SSU C9 H13 N2 O8 P S FORMUL 4 MG 31(MG 2+) LINK O3' G A 3 P SSU A 4 1555 1555 1.61 LINK O3' SSU A 4 P A A 5 1555 1555 1.61 LINK O2' G A 3 MG MG N 527 1555 1555 1.99 LINK O3' U B 6 MG MG N 526 1555 1555 2.32 LINK OP1 A N 28 MG MG N 530 1555 1555 2.25 LINK OP1 A N 94 MG MG N 529 1555 1555 2.76 LINK OP2 G N 150 MG MG N 510 1555 1555 2.33 LINK O6 G N 164 MG MG N 507 1555 1555 2.50 LINK OP2 A N 171 MG MG N 522 1555 1555 2.75 LINK OP2 A N 172 MG MG N 523 1555 1555 2.49 LINK OP1 A N 183 MG MG N 505 1555 1555 2.30 LINK OP1 A N 184 MG MG N 504 1555 1555 1.86 LINK OP2 A N 184 MG MG N 505 1555 1555 2.11 LINK OP1 A N 186 MG MG N 504 1555 1555 2.21 LINK OP2 A N 186 MG MG N 505 1555 1555 2.50 LINK OP2 A N 187 MG MG N 504 1555 1555 1.81 LINK OP2 G N 188 MG MG N 504 1555 1555 2.29 LINK O6 G N 188 MG MG N 506 1555 1555 1.96 LINK OP1 A N 207 MG MG N 502 1555 1555 1.98 LINK OP1 C N 208 MG MG N 526 1555 1555 2.21 LINK OP1 A N 256 MG MG N 511 1555 1555 2.51 LINK OP1 G N 257 MG MG N 515 1555 1555 2.34 LINK OP2 U N 258 MG MG N 515 1555 1555 2.28 LINK OP1 U N 258 MG MG N 516 1555 1555 2.57 LINK OP1 U N 259 MG MG N 517 1555 1555 2.68 LINK O3' A N 261 MG MG N 527 1555 1555 2.85 LINK OP2 C N 262 MG MG N 502 1555 1555 2.10 LINK OP1 C N 262 MG MG N 527 1555 1555 1.82 LINK OP1 U N 273 MG MG N 511 1555 1555 2.54 LINK O6 G N 280 MG MG N 521 1555 1555 2.96 LINK OP1 A N 301 MG MG N 519 1555 1555 2.32 LINK OP2 A N 302 MG MG N 519 1555 1555 2.45 LINK OP1 A N 304 MG MG N 526 1555 1555 2.60 LINK OP2 U N 305 MG MG N 515 1555 1555 2.47 LINK OP1 U N 305 MG MG N 518 1555 1555 2.65 LINK OP1 A N 306 MG MG N 526 1555 1555 2.21 LINK OP2 A N 306 MG MG N 527 1555 1555 1.89 LINK OP2 U N 307 MG MG N 528 1555 1555 2.26 LINK OP2 A N 308 MG MG N 528 1555 1555 2.28 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