HEADER RNA 15-JUL-24 9G4I TITLE GROUP II INTRON ASSEMBLY INTERMEDIATE DOMAIN 1 AND 2 "PARTLY OPEN" TITLE 2 STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROUP IIC INTRON; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: OCEANOBACILLUS IHEYENSIS; SOURCE 4 ORGANISM_TAXID: 182710 KEYWDS RNA FOLDING, PROTEIN-FREE RNA CRYO-EM, RIBOZYME, METALLOENZYMES, KEYWDS 2 SPLICING, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR S.S.JADHAV,M.MARCIA REVDAT 1 05-NOV-25 9G4I 0 JRNL AUTH S.S.JADHAV,M.MAIORCA,T.MULVANEY,M.TOPF,M.MARCIA JRNL TITL SEQUENTIAL ASSEMBLY OF THE CATALYTIC STRUCTURE OF A LARGE JRNL TITL 2 MULTIDOMAIN RNA VISUALIZED BY CRYO-ELECTRON MICROSCOPY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, PHENIX, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, ERRASER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 4FAQ REMARK 3 REFINEMENT SPACE : REAL 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) : 4.610 REMARK 3 NUMBER OF PARTICLES : 41652 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 9G4I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1292140332. 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 : GROUP IIC INTRON REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.50 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 3807.00 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: 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 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 G A -6 REMARK 465 G A -5 REMARK 465 G A 1 REMARK 465 U A 2 REMARK 465 G A 3 REMARK 465 U A 4 REMARK 465 G A 5 REMARK 465 C A 6 REMARK 465 U A 84 REMARK 465 A A 105 REMARK 465 A A 106 REMARK 465 G A 107 REMARK 465 C A 116 REMARK 465 G A 179 REMARK 465 A A 207 REMARK 465 U A 235 REMARK 465 G A 236 REMARK 465 A A 237 REMARK 465 A A 260 REMARK 465 C A 261 REMARK 465 A A 287 REMARK 465 G A 288 REMARK 465 C A 289 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 G A -4 P OP1 OP2 REMARK 470 C A 7 P OP1 OP2 REMARK 470 C A 85 P OP1 OP2 REMARK 470 G A 108 P OP1 OP2 REMARK 470 G A 117 P OP1 OP2 REMARK 470 C A 180 P OP1 OP2 REMARK 470 A A 208 P OP1 OP2 REMARK 470 U A 238 P OP1 OP2 REMARK 470 C A 262 P OP1 OP2 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 G A -4 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 G A -4 N3 - C4 - C5 ANGL. DEV. = -3.1 DEGREES REMARK 500 A A -1 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A -1 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 C A 8 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 A A 12 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 A A 12 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 A A 12 N1 - C6 - N6 ANGL. DEV. = -6.2 DEGREES REMARK 500 C A 19 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 A A 20 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 A A 20 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 20 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 C A 23 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 A A 25 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 A A 25 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 A A 25 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 A A 25 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 A A 27 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 A A 27 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 A A 27 N1 - C6 - N6 ANGL. DEV. = -6.8 DEGREES REMARK 500 A A 33 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 A A 33 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 33 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 A A 35 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 A A 35 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 U A 37 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 C A 39 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 C A 40 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 A A 42 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 42 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 A A 43 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 A A 43 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 43 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 C A 44 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 A A 49 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 A A 49 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 A A 49 N1 - C6 - N6 ANGL. DEV. = -6.8 DEGREES REMARK 500 A A 50 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 A A 50 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 A A 50 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 C A 53 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 A A 54 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 A A 54 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 54 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 A A 56 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 A A 56 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 56 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 A A 57 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 A A 57 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 A A 57 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 285 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 G A 10 0.06 SIDE CHAIN REMARK 500 A A 20 0.10 SIDE CHAIN REMARK 500 G A 21 0.07 SIDE CHAIN REMARK 500 U A 24 0.06 SIDE CHAIN REMARK 500 A A 25 0.13 SIDE CHAIN REMARK 500 G A 30 0.05 SIDE CHAIN REMARK 500 G A 32 0.07 SIDE CHAIN REMARK 500 A A 33 0.07 SIDE CHAIN REMARK 500 C A 40 0.06 SIDE CHAIN REMARK 500 A A 43 0.07 SIDE CHAIN REMARK 500 G A 48 0.06 SIDE CHAIN REMARK 500 A A 50 0.06 SIDE CHAIN REMARK 500 A A 57 0.11 SIDE CHAIN REMARK 500 A A 60 0.08 SIDE CHAIN REMARK 500 A A 63 0.09 SIDE CHAIN REMARK 500 A A 72 0.10 SIDE CHAIN REMARK 500 G A 90 0.06 SIDE CHAIN REMARK 500 G A 92 0.06 SIDE CHAIN REMARK 500 C A 102 0.08 SIDE CHAIN REMARK 500 U A 103 0.07 SIDE CHAIN REMARK 500 G A 108 0.05 SIDE CHAIN REMARK 500 A A 109 0.16 SIDE CHAIN REMARK 500 G A 111 0.06 SIDE CHAIN REMARK 500 G A 113 0.06 SIDE CHAIN REMARK 500 G A 118 0.07 SIDE CHAIN REMARK 500 A A 122 0.07 SIDE CHAIN REMARK 500 U A 125 0.09 SIDE CHAIN REMARK 500 U A 126 0.06 SIDE CHAIN REMARK 500 C A 127 0.06 SIDE CHAIN REMARK 500 U A 132 0.07 SIDE CHAIN REMARK 500 A A 140 0.06 SIDE CHAIN REMARK 500 A A 143 0.07 SIDE CHAIN REMARK 500 U A 146 0.07 SIDE CHAIN REMARK 500 U A 150 0.13 SIDE CHAIN REMARK 500 A A 166 0.06 SIDE CHAIN REMARK 500 U A 176 0.06 SIDE CHAIN REMARK 500 A A 186 0.06 SIDE CHAIN REMARK 500 A A 187 0.09 SIDE CHAIN REMARK 500 A A 189 0.07 SIDE CHAIN REMARK 500 C A 190 0.06 SIDE CHAIN REMARK 500 A A 192 0.06 SIDE CHAIN REMARK 500 U A 198 0.07 SIDE CHAIN REMARK 500 A A 208 0.07 SIDE CHAIN REMARK 500 A A 215 0.06 SIDE CHAIN REMARK 500 A A 217 0.08 SIDE CHAIN REMARK 500 A A 231 0.07 SIDE CHAIN REMARK 500 A A 240 0.05 SIDE CHAIN REMARK 500 A A 245 0.06 SIDE CHAIN REMARK 500 A A 249 0.06 SIDE CHAIN REMARK 500 G A 252 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 57 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-51040 RELATED DB: EMDB REMARK 900 GROUP II INTRON ASSEMBLY INTERMEDIATE DOMAIN 1 AND 2 DBREF 9G4I A -6 289 PDB 9G4I 9G4I -6 289 SEQRES 1 A 296 G G G U U A U G U G U G C SEQRES 2 A 296 C C G G C A U G G G U G C SEQRES 3 A 296 A G U C U A U A G G G U G SEQRES 4 A 296 A G A G U C C C G A A C U SEQRES 5 A 296 G U G A A G G C A G A A G SEQRES 6 A 296 U A A C A G U U A G C C U SEQRES 7 A 296 A A C G C A A G G G U G U SEQRES 8 A 296 C C G U G G C G A C A U G SEQRES 9 A 296 G A A U C U G A A G G A A SEQRES 10 A 296 G C G G A C G G C A A A C SEQRES 11 A 296 C U U C G G U C U G A G G SEQRES 12 A 296 A A C A C G A A C U U C A SEQRES 13 A 296 U A U G A G G C U A G G U SEQRES 14 A 296 A U C A A U G G A U G A G SEQRES 15 A 296 U U U G C A U A A C A A A SEQRES 16 A 296 A C A A A G U C C U U U C SEQRES 17 A 296 U G C C A A A G U U G G U SEQRES 18 A 296 A C A G A G U A A A U G A SEQRES 19 A 296 A G C A G A U U G A U G A SEQRES 20 A 296 A G G G A A A G A C U G C SEQRES 21 A 296 A U U C U U A C C C G G G SEQRES 22 A 296 G A G G U C U G G A A A C SEQRES 23 A 296 A G A A G U C A G C 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 5846 C A 286 MASTER 282 0 0 0 0 0 0 6 5845 1 0 23 END