HEADER RNA 08-NOV-24 9KGH TITLE CRYO-EM STRUCTURE OF CIRCULAR INTRON OF THYMIDYLATE SYNTHASE (TD) GENE TITLE 2 OF BACTERIOPHAGE T4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (264-MER); COMPND 3 CHAIN: U; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 2681598; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-FLUC(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905932 KEYWDS T4 TD, GROUP I INTRON, CRYO-EM, CIRCULAR RNA, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR L.AN,S.LI,K.ZHANG REVDAT 1 12-NOV-25 9KGH 0 JRNL AUTH L.AN,S.LI,K.ZHANG JRNL TITL MECHANISTIC INSIGHTS INTO CYCLIZATION OF THE T4 TD GROUP I JRNL TITL 2 INTRON JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX, 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 172889 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 9KGH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 13-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300053497. 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 THYMIDYLATE SYNTHASE REMARK 245 (TD) GENE OF BACTERIOPHAGE T4 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 : FEI FALCON I (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2700.00 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) : 5000.00 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: U 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 U 212 C5 A U 212 N7 -0.048 REMARK 500 A U 212 N7 A U 212 C8 -0.044 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 U U 36 N1 - C2 - O2 ANGL. DEV. = 4.9 DEGREES REMARK 500 U U 36 C2 - N1 - C1' ANGL. DEV. = 9.3 DEGREES REMARK 500 C U 42 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 C U 63 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 U U 79 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 C U 98 C6 - N1 - C2 ANGL. DEV. = -3.6 DEGREES REMARK 500 C U 98 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 C U 98 N1 - C2 - O2 ANGL. DEV. = 5.8 DEGREES REMARK 500 C U 98 N3 - C2 - O2 ANGL. DEV. = -5.9 DEGREES REMARK 500 C U 98 C2 - N1 - C1' ANGL. DEV. = 6.7 DEGREES REMARK 500 C U 99 C6 - N1 - C2 ANGL. DEV. = -3.0 DEGREES REMARK 500 C U 99 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 C U 99 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 C U 117 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 C U 117 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 U U 118 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 A U 119 O3' - P - OP2 ANGL. DEV. = 7.4 DEGREES REMARK 500 U U 132 N1 - C2 - O2 ANGL. DEV. = 6.5 DEGREES REMARK 500 U U 132 N3 - C2 - O2 ANGL. DEV. = -7.0 DEGREES REMARK 500 U U 132 C2 - N1 - C1' ANGL. DEV. = 9.1 DEGREES REMARK 500 U U 140 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 U U 140 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 C U 146 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 G U 149 C4 - C5 - N7 ANGL. DEV. = 2.8 DEGREES REMARK 500 C U 180 C6 - N1 - C2 ANGL. DEV. = -3.6 DEGREES REMARK 500 C U 180 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 U U 193 N1 - C2 - O2 ANGL. DEV. = 5.3 DEGREES REMARK 500 U U 193 N3 - C2 - O2 ANGL. DEV. = -6.4 DEGREES REMARK 500 U U 193 C2 - N1 - C1' ANGL. DEV. = 9.0 DEGREES REMARK 500 C U 200 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 C U 200 N1 - C2 - O2 ANGL. DEV. = 5.9 DEGREES REMARK 500 C U 200 N3 - C2 - O2 ANGL. DEV. = -6.6 DEGREES REMARK 500 C U 200 C2 - N1 - C1' ANGL. DEV. = 9.7 DEGREES REMARK 500 G U 209 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 G U 209 N3 - C4 - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 G U 209 C6 - C5 - N7 ANGL. DEV. = 3.6 DEGREES REMARK 500 G U 209 C8 - N9 - C1' ANGL. DEV. = 9.1 DEGREES REMARK 500 G U 209 C4 - N9 - C1' ANGL. DEV. = -8.7 DEGREES REMARK 500 U U 210 N1 - C2 - O2 ANGL. DEV. = 5.1 DEGREES REMARK 500 U U 210 N3 - C2 - O2 ANGL. DEV. = -6.5 DEGREES REMARK 500 G U 211 N3 - C4 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 A U 212 C4 - C5 - N7 ANGL. DEV. = 3.2 DEGREES REMARK 500 A U 212 N9 - C4 - C5 ANGL. DEV. = -3.8 DEGREES REMARK 500 A U 212 N3 - C4 - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 A U 212 C6 - C5 - N7 ANGL. DEV. = -5.0 DEGREES REMARK 500 A U 212 N1 - C6 - N6 ANGL. DEV. = 5.6 DEGREES REMARK 500 A U 212 C5 - C6 - N6 ANGL. DEV. = -6.2 DEGREES REMARK 500 C U 213 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 C U 220 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 C U 232 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 57 ANGLE DEVIATIONS. 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 U 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A U 4 OP1 REMARK 620 2 A U 190 OP1 142.9 REMARK 620 3 A U 192 OP1 126.5 86.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG U 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A U 120 OP1 REMARK 620 2 A U 192 OP2 127.2 REMARK 620 3 G U 267 O3' 93.1 117.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG U 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U U 193 OP2 REMARK 620 2 A U 194 OP2 101.6 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62319 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF CIRCULAR INTRON OF THYMIDYLATE SYNTHASE (TD) REMARK 900 GENE OF BACTERIOPHAGE T4 DBREF 9KGH U 4 267 PDB 9KGH 9KGH 4 267 SEQRES 1 U 264 A A U U G A G G C C U G A SEQRES 2 U 264 G U A U A A G G U G A C U SEQRES 3 U 264 U A U A C U U G U A A U C SEQRES 4 U 264 U A U C U A A A C G G G G SEQRES 5 U 264 A A C C U C U C U A G U A SEQRES 6 U 264 G A C A A U C C C G U G C SEQRES 7 U 264 U A A A U U G U A G G A C SEQRES 8 U 264 U G C C C G G G U U C U A SEQRES 9 U 264 C A U A A A U G C C U A A SEQRES 10 U 264 C G A C U A U C C C U U U SEQRES 11 U 264 G G G G A G U A G G G U C SEQRES 12 U 264 A A G U G A C U C G A A A SEQRES 13 U 264 C G A U A G A C A A C U U SEQRES 14 U 264 G C U U U A A C A A G U U SEQRES 15 U 264 G G A G A U A U A G U C U SEQRES 16 U 264 G C U C U G C A U G G U G SEQRES 17 U 264 A C A U G C A G C U G G A SEQRES 18 U 264 U A U A A U U C C G G G G SEQRES 19 U 264 U A A G A U U A A C G A C SEQRES 20 U 264 C U U A U C U G A A C A U SEQRES 21 U 264 A A U G HET MG U 301 1 HET MG U 302 1 HET MG U 303 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 3(MG 2+) LINK OP1 A U 4 MG MG U 301 1555 1555 1.80 LINK OP1 A U 120 MG MG U 302 1555 1555 2.12 LINK OP1 A U 190 MG MG U 301 1555 1555 2.13 LINK OP1 A U 192 MG MG U 301 1555 1555 2.56 LINK OP2 A U 192 MG MG U 302 1555 1555 1.96 LINK OP2 U U 193 MG MG U 303 1555 1555 1.89 LINK OP2 A U 194 MG MG U 303 1555 1555 1.92 LINK O3' G U 267 MG MG U 302 1555 1555 2.17 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 TER 5623 G U 267 HETATM 5624 MG MG U 301 155.632 148.849 154.717 1.00 30.00 MG HETATM 5625 MG MG U 302 157.055 150.485 150.578 1.00 30.00 MG HETATM 5626 MG MG U 303 152.691 156.554 152.626 1.00 30.00 MG CONECT 2 5624 CONECT 2465 5625 CONECT 3964 5624 CONECT 4006 5624 CONECT 4007 5625 CONECT 4029 5626 CONECT 4049 5626 CONECT 5608 5625 CONECT 5624 2 3964 4006 CONECT 5625 2465 4007 5608 CONECT 5626 4029 4049 MASTER 216 0 3 0 0 0 0 6 5625 1 11 21 END