HEADER RNA 28-MAY-25 9V7Q TITLE CRYO-EM STRUCTURES OF THE AZOARCUS PRE-TRNA(ILE) INTRON CONFORMATION TITLE 2 AFTER THE CYCLIZATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (203-MER); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AZOARCUS OLEARIUS; SOURCE 3 ORGANISM_TAXID: 418699; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-FLUC(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905932 KEYWDS AZOARCUS PRE-TRNA(ILE), SELF-SPLICING, CIRCULAR INTRON, RNA KEYWDS 2 STRUCTURE, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR Y.HONG,J.LIU,X.ZHANG,J.LIU,S.LI,K.ZHANG REVDAT 1 25-MAR-26 9V7Q 0 JRNL AUTH Y.HONG,J.LIU,X.ZHANG,J.LIU,S.LI,K.ZHANG JRNL TITL PRE-SPLICING CONFORMATION AND STEPWISE CIRCULARIZATION OF A JRNL TITL 2 GROUP I INTRON IN AZOARCUS PRE-TRNA JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL DOI 10.1038/S41467-026-70747-Y REMARK 2 REMARK 2 RESOLUTION. 3.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, PHENIX, CRYOSPARC, REMARK 3 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) : 3.270 REMARK 3 NUMBER OF PARTICLES : 335306 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 9V7Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 30-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300059673. 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 STRUCTURES OF THE REMARK 245 AZOARCUS PRE-TRNA(ILE) INTRON REMARK 245 CONFORMATION AFTER THE REMARK 245 CYCLIZATION REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL 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 : 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) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 5950.00 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: B 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 A B 173 C5 A B 173 N7 -0.038 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 C B 13 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 C B 28 C6 - N1 - C2 ANGL. DEV. = -4.1 DEGREES REMARK 500 C B 28 C5 - C6 - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 C B 28 C2 - N1 - C1' ANGL. DEV. = 8.6 DEGREES REMARK 500 C B 59 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 C B 72 C6 - N1 - C2 ANGL. DEV. = -3.1 DEGREES REMARK 500 C B 72 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 C B 72 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 C B 72 C2 - N1 - C1' ANGL. DEV. = 8.2 DEGREES REMARK 500 C B 94 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 C B 99 C6 - N1 - C2 ANGL. DEV. = -3.6 DEGREES REMARK 500 C B 99 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 C B 143 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 C B 145 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 C B 177 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 C B 196 C6 - N1 - C2 ANGL. DEV. = -2.4 DEGREES REMARK 500 C B 196 N1 - C2 - O2 ANGL. DEV. = 4.1 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 B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 3 OP2 REMARK 620 2 C B 87 OP1 92.1 REMARK 620 3 G B 169 OP1 160.1 95.9 REMARK 620 4 A B 171 OP1 81.4 75.6 83.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 306 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 3 OP2 REMARK 620 2 G B 127 OP1 146.8 REMARK 620 3 A B 171 OP2 108.3 75.9 REMARK 620 4 G B 205 O3' 108.5 75.8 143.0 REMARK 620 5 G B 205 O2' 107.6 104.4 96.9 67.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 86 OP1 REMARK 620 2 G B 127 OP2 80.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 123 OP1 REMARK 620 2 C B 170 OP2 74.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 172 OP2 REMARK 620 2 A B 173 OP2 74.5 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U6B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A SELF-SPLICING GROUP I INTRON WITH BOTH EXONS REMARK 900 RELATED ID: EMD-64821 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURES OF THE AZOARCUS PRE-TRNA(ILE) INTRON REMARK 900 CONFORMATION AFTER THE CYCLIZATION DBREF 9V7Q B 3 205 GB 70997234 DQ103524.1 3 205 SEQRES 1 B 203 U U C G A U G U G C C U U SEQRES 2 B 203 G C G C C G G G A A A C C SEQRES 3 B 203 A C G C A A G G G A U G G SEQRES 4 B 203 U G U C A A A U U C G G C SEQRES 5 B 203 G A A A C C U A A G C G C SEQRES 6 B 203 C C G C C C G G G C G U A SEQRES 7 B 203 U G G C A A C G C C G A G SEQRES 8 B 203 C C A A G C U U C G G C G SEQRES 9 B 203 C C U G C G C C G A U G A SEQRES 10 B 203 A G G U G U A G A G A C U SEQRES 11 B 203 A G A C G G C A C C C A C SEQRES 12 B 203 C U A A G G C A A A C G C SEQRES 13 B 203 U A U G G U G A A G G C A SEQRES 14 B 203 U A G U C C A G G G A G U SEQRES 15 B 203 G G C G A A A G U C A C A SEQRES 16 B 203 C A A A C C G G HET MG B 301 1 HET MG B 302 1 HET MG B 303 1 HET MG B 304 1 HET MG B 305 1 HET MG B 306 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 6(MG 2+) LINK OP2 U B 3 MG MG B 301 1555 1555 1.89 LINK OP2 U B 3 MG MG B 306 1555 1555 1.78 LINK OP1 A B 86 MG MG B 302 1555 1555 2.34 LINK OP1 C B 87 MG MG B 301 1555 1555 2.22 LINK OP1 U B 123 MG MG B 304 1555 1555 2.34 LINK OP2 G B 127 MG MG B 302 1555 1555 2.18 LINK OP1 G B 127 MG MG B 306 1555 1555 2.59 LINK OP1 G B 169 MG MG B 301 1555 1555 1.85 LINK OP2 C B 170 MG MG B 304 1555 1555 2.27 LINK OP1 C B 170 MG MG B 305 1555 1555 2.78 LINK OP1 A B 171 MG MG B 301 1555 1555 2.42 LINK OP2 A B 171 MG MG B 306 1555 1555 1.84 LINK OP2 U B 172 MG MG B 303 1555 1555 2.26 LINK OP2 A B 173 MG MG B 303 1555 1555 2.49 LINK O3' G B 205 MG MG B 306 1555 1555 1.72 LINK O2' G B 205 MG MG B 306 1555 1555 2.66 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 3 4361 4366 CONECT 1779 4362 CONECT 1801 4361 CONECT 2572 4364 CONECT 2657 4366 CONECT 2658 4362 CONECT 3561 4361 CONECT 3584 4365 CONECT 3585 4364 CONECT 3604 4361 CONECT 3605 4366 CONECT 3627 4363 CONECT 3647 4363 CONECT 4345 4366 CONECT 4347 4366 CONECT 4361 3 1801 3561 3604 CONECT 4362 1779 2658 CONECT 4363 3627 3647 CONECT 4364 2572 3585 CONECT 4365 3584 CONECT 4366 3 2657 3605 4345 CONECT 4366 4347 MASTER 201 0 6 0 0 0 0 6 4365 1 22 16 END