HEADER RNA 26-OCT-24 9K9K TITLE CRYO-EM STRUCTURE OF CIRCULAR INTRON OF ANABAENA TRNA(LEU) PRECURSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (249-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANABAENA; SOURCE 3 ORGANISM_TAXID: 1163; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-FLUC(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905932 KEYWDS ANABAENA TRNA(LEU) PRECURSOR, SELF-FOLDING, SPLICING, CYCLIZATION, KEYWDS 2 CRYO-EM, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR X.ZHANG,S.LI,K.ZHANG REVDAT 1 22-APR-26 9K9K 0 JRNL AUTH X.ZHANG,S.LI,K.ZHANG JRNL TITL SELF-SPLICING AND CYCLIZATION MECHANISMS OF THE FULL-LENGTH JRNL TITL 2 ANABAENA PRE-TRNA JRNL REF NAT.CHEM.BIOL. 2026 JRNL REFN ESSN 1552-4469 JRNL DOI 10.1038/S41589-026-02205-1 REMARK 2 REMARK 2 RESOLUTION. 3.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, 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) : 3.450 REMARK 3 NUMBER OF PARTICLES : 130650 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 9K9K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 29-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300053029. 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 CIRCULAR REMARK 245 INTRON OF ANABAENA TRNA(LEU) REMARK 245 PRECURSOR REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.20 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2800.00 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) : 5800.00 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 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 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 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 35 OP1 REMARK 620 2 U A 119 OP1 104.3 REMARK 620 3 A A 231 OP1 100.3 86.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 118 OP1 REMARK 620 2 G A 188 OP2 102.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 234 OP2 REMARK 620 2 A A 235 OP2 70.5 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62192 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF CIRCULAR INTRON OF ANABAENA TRNA(LEU) PRECURSOR DBREF 9K9K A 35 283 PDB 9K9K 9K9K 35 283 SEQRES 1 A 249 A A A U A A U U G A G C C SEQRES 2 A 249 U U A G A G A A G A A A U SEQRES 3 A 249 U C U U U A A G U G G A U SEQRES 4 A 249 G C U C U C A A A C U C A SEQRES 5 A 249 G G G A A A C C U A A A U SEQRES 6 A 249 C U A G C U A U A G A C A SEQRES 7 A 249 A G G C A A U C C U G A G SEQRES 8 A 249 C C A A G C C G A A G U A SEQRES 9 A 249 G U A A U U A G U A A G U SEQRES 10 A 249 U A A C A A C A G A U A A SEQRES 11 A 249 C U U A C A G C U A G U C SEQRES 12 A 249 G G A A G G U G C A G A G SEQRES 13 A 249 A C U C G A C G G G A G C SEQRES 14 A 249 U A C C C U A A C G U C A SEQRES 15 A 249 A G A C G A G G G U A A A SEQRES 16 A 249 G A G A G A G U C C A A U SEQRES 17 A 249 U C U C A A A G C C A A U SEQRES 18 A 249 A G G C A G U A G C G A A SEQRES 19 A 249 A G C U G C G G G A G A A SEQRES 20 A 249 U G HET MG A 301 1 HET MG A 302 1 HET MG A 303 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 3(MG 2+) LINK OP1 A A 35 MG MG A 301 1555 1555 2.14 LINK OP1 A A 118 MG MG A 302 1555 1555 2.45 LINK OP1 U A 119 MG MG A 301 1555 1555 2.23 LINK OP2 G A 188 MG MG A 302 1555 1555 2.32 LINK OP1 A A 231 MG MG A 301 1555 1555 2.15 LINK OP2 G A 234 MG MG A 303 1555 1555 2.80 LINK OP2 A A 235 MG MG A 303 1555 1555 2.45 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 2 5352 CONECT 1776 5353 CONECT 1798 5352 CONECT 3277 5353 CONECT 4206 5352 CONECT 4274 5354 CONECT 4297 5354 CONECT 5352 2 1798 4206 CONECT 5353 1776 3277 CONECT 5354 4274 4297 MASTER 126 0 3 0 0 0 0 6 5353 1 10 20 END