HEADER RNA 11-JUL-22 7YG8 TITLE CRYO-EM STRUCTURE OF TETRAHYMENA RIBOZYME CONFORMATION 5 UNDERGOING TITLE 2 THE SECOND-STEP SELF-SPLICING COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*UP*CP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-R(*CP*CP*CP*UP*C)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: RNA (387-MER); COMPND 11 CHAIN: N; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: TETRAHYMENA; SOURCE 4 ORGANISM_TAXID: 5890; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: TETRAHYMENA; SOURCE 8 ORGANISM_TAXID: 5890; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: TETRAHYMENA; SOURCE 11 ORGANISM_TAXID: 5890; SOURCE 12 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-FLUC(DELTAI); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 905932 KEYWDS TETRAHYMENA RIBOZYME, SECOND STEP OF SELF-SPLICING, CONFORMATION 5, KEYWDS 2 RNA EXPDTA ELECTRON MICROSCOPY AUTHOR S.LI,Z.P.MICHAEL,X.ZHANG,P.GREG,K.ZHANG REVDAT 1 29-MAR-23 7YG8 0 JRNL AUTH S.LI,M.Z.PALO,X.ZHANG,G.PINTILIE,K.ZHANG JRNL TITL SNAPSHOTS OF THE SECOND-STEP SELF-SPLICING OF TETRAHYMENA JRNL TITL 2 RIBOZYME REVEALED BY CRYO-EM. JRNL REF NAT COMMUN V. 14 1294 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 36928031 JRNL DOI 10.1038/S41467-023-36724-5 REMARK 2 REMARK 2 RESOLUTION. 2.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL 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) : 2.970 REMARK 3 NUMBER OF PARTICLES : 144613 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7YG8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030858. 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 : CRYO-EM STRUCTURE OF REMARK 245 TETRAHYMENA RIBOZYME REMARK 245 CONFORMATION 5 UNDERGOING THE REMARK 245 SECOND-STEP SELF-SPLICING REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.60 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 : NULL 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) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 5280.00 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: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 U B 6 REMARK 465 G N 17 REMARK 465 G N 18 REMARK 465 U N 19 REMARK 465 U N 20 REMARK 465 U N 21 REMARK 465 G N 22 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 U A 1 O5' REMARK 470 C B 1 O5' 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 O2' G N 126 O2' U N 202 2.11 REMARK 500 O2' G A 3 OP2 A N 306 2.14 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 N 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G N 257 OP1 REMARK 620 2 U N 258 OP2 75.0 REMARK 620 3 U N 305 OP2 88.7 132.2 REMARK 620 N 1 2 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 U N 258 OP1 REMARK 620 2 A N 261 OP2 102.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 304 OP1 REMARK 620 2 A N 306 OP1 70.7 REMARK 620 N 1 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 U N 307 OP2 REMARK 620 2 A N 308 OP2 66.9 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33811 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF TETRAHYMENA RIBOZYME CONFORMATION 5 UNDERGOING REMARK 900 THE SECOND-STEP SELF-SPLICING DBREF 7YG8 A 1 3 PDB 7YG8 7YG8 1 3 DBREF 7YG8 B 1 6 PDB 7YG8 7YG8 1 6 DBREF 7YG8 N 19 409 GB 10832 X54512.1 7027 7417 SEQADV 7YG8 G N 17 GB 10832 EXPRESSION TAG SEQADV 7YG8 G N 18 GB 10832 EXPRESSION TAG SEQRES 1 A 3 U C G SEQRES 1 B 6 C C C U C U SEQRES 1 N 393 G G U U U G G A G G G A A SEQRES 2 N 393 A A G U U A U C A G G C A SEQRES 3 N 393 U G C A C C U G G U A G C SEQRES 4 N 393 U A G U C U U U A A A C C SEQRES 5 N 393 A A U A G A U U G C A U C SEQRES 6 N 393 G G U U U A A A A G G C A SEQRES 7 N 393 A G A C C G U C A A A U U SEQRES 8 N 393 G C G G G A A A G G G G U SEQRES 9 N 393 C A A C A G C C G U U C A SEQRES 10 N 393 G U A C C A A G U C U C A SEQRES 11 N 393 G G G G A A A C U U U G A SEQRES 12 N 393 G A U G G C C U U G C A A SEQRES 13 N 393 A G G G U A U G G U A A U SEQRES 14 N 393 A A G C U G A C G G A C A SEQRES 15 N 393 U G G U C C U A A C C A C SEQRES 16 N 393 G C A G C C A A G U C C U SEQRES 17 N 393 A A G U C A A C A G A U C SEQRES 18 N 393 U U C U G U U G A U A U G SEQRES 19 N 393 G A U G C A G U U C A C A SEQRES 20 N 393 G A C U A A A U G U C G G SEQRES 21 N 393 U C G G G G A A G A U G U SEQRES 22 N 393 A U U C U U C U C A U A A SEQRES 23 N 393 G A U A U A G U C G G A C SEQRES 24 N 393 C U C U C C U U A A U G G SEQRES 25 N 393 G A G C U A G C G G A U G SEQRES 26 N 393 A A G U G A U G C A A C A SEQRES 27 N 393 C U G G A G C C G C U G G SEQRES 28 N 393 G A A C U A A U U U G U A SEQRES 29 N 393 U G C G A A A G U A U A U SEQRES 30 N 393 U G A U U A G U U U U G G SEQRES 31 N 393 A G U 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 HETNAM MG MAGNESIUM ION FORMUL 4 MG 5(MG 2+) LINK OP1 G N 257 MG MG N 504 1555 1555 2.34 LINK OP2 U N 258 MG MG N 504 1555 1555 2.28 LINK OP1 U N 258 MG MG N 505 1555 1555 2.36 LINK OP2 A N 261 MG MG N 505 1555 1555 2.65 LINK OP1 A N 304 MG MG N 501 1555 1555 2.13 LINK OP1 U N 305 MG MG N 503 1555 1555 2.89 LINK OP2 U N 305 MG MG N 504 1555 1555 2.46 LINK OP1 A N 306 MG MG N 501 1555 1555 2.64 LINK OP2 U N 307 MG MG N 502 1555 1555 2.81 LINK OP2 A N 308 MG MG N 502 1555 1555 2.62 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