HEADER RNA 17-JUL-24 9IS7 TITLE PARACANDIDIMONAS LACTEA CP GROUP II INTRON 2S STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (153-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: RESIDUES 111-140 IS MISSED IN THIS MODEL; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (582-MER); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARACANDIDIMONAS LACTEA; SOURCE 3 ORGANISM_TAXID: 2895524; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: PARACANDIDIMONAS LACTEA; SOURCE 8 ORGANISM_TAXID: 2895524; SOURCE 9 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS CRYOEM, RIBOZYME, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR L.WANG,J.H.XIE,C.ZHANG,J.ZOU,Z.HUANG,S.SHANG,X.CHEN,Y.YANG,J.LIU, AUTHOR 2 H.DONG,D.HUANG,Z.SU REVDAT 2 25-JUN-25 9IS7 1 JRNL REVDAT 1 12-FEB-25 9IS7 0 JRNL AUTH L.WANG,J.XIE,C.ZHANG,J.ZOU,Z.HUANG,S.SHANG,X.CHEN,Y.YANG, JRNL AUTH 2 J.LIU,H.DONG,D.HUANG,Z.SU JRNL TITL STRUCTURAL BASIS OF CIRCULARLY PERMUTED GROUP II INTRON JRNL TITL 2 SELF-SPLICING. JRNL REF NAT.STRUCT.MOL.BIOL. V. 32 1091 2025 JRNL REFN ESSN 1545-9985 JRNL PMID 39890981 JRNL DOI 10.1038/S41594-025-01484-X REMARK 2 REMARK 2 RESOLUTION. 2.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 2.870 REMARK 3 NUMBER OF PARTICLES : 33739 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 9IS7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 19-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1300049480. 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 : PARACANDIDIMONAS LACTEA CP REMARK 245 GROUP II INTRON 2S STATE 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 : 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 K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 C A 111 REMARK 465 C A 112 REMARK 465 U A 113 REMARK 465 G A 114 REMARK 465 C A 115 REMARK 465 G A 116 REMARK 465 C A 117 REMARK 465 C A 118 REMARK 465 G A 119 REMARK 465 C A 120 REMARK 465 A A 121 REMARK 465 A A 122 REMARK 465 C A 123 REMARK 465 G A 124 REMARK 465 U A 125 REMARK 465 G A 126 REMARK 465 C A 127 REMARK 465 A A 128 REMARK 465 G A 129 REMARK 465 G A 130 REMARK 465 C A 131 REMARK 465 C A 132 REMARK 465 A A 133 REMARK 465 G A 134 REMARK 465 C A 135 REMARK 465 A A 136 REMARK 465 G A 137 REMARK 465 U A 138 REMARK 465 C A 139 REMARK 465 U A 140 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 K A 205 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 29 O5' REMARK 620 2 A A 30 OP2 102.1 REMARK 620 3 A B 644 OP2 156.2 87.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 31 OP1 REMARK 620 2 G A 54 OP1 84.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 52 OP1 REMARK 620 2 G A 54 OP2 77.8 REMARK 620 3 G A 153 O3' 83.7 108.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 206 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 54 O6 REMARK 620 2 G A 57 OP2 105.7 REMARK 620 3 C A 58 OP2 131.4 105.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 804 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 152 OP1 REMARK 620 2 A B 355 OP2 138.9 REMARK 620 3 U B 356 OP2 67.5 95.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 826 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 155 O6 REMARK 620 2 G B 158 OP2 130.5 REMARK 620 3 A B 642 OP1 70.3 124.8 REMARK 620 4 A B 642 OP2 120.4 101.0 54.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 809 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 455 OP2 REMARK 620 2 G B 508 OP2 70.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 824 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 579 OP1 REMARK 620 2 G B 580 OP2 75.8 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-60833 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF INTRON 5 DBREF 9IS7 A 1 153 PDB 9IS7 9IS7 1 153 DBREF 9IS7 B 154 735 PDB 9IS7 9IS7 154 735 SEQRES 1 A 153 A G C A G G C G C C A C C SEQRES 2 A 153 U G C U G C G G A A C C G SEQRES 3 A 153 C U G A A G C C G C G U G SEQRES 4 A 153 C C U C U A A C A G G G C SEQRES 5 A 153 U G G C G C G G C U A C G SEQRES 6 A 153 A A G G G C G C U G G G G SEQRES 7 A 153 G U G G G A A C C A C C U SEQRES 8 A 153 C C U U C G A C C C A A U SEQRES 9 A 153 C C A U G G C C U G C G C SEQRES 10 A 153 C G C A A C G U G C A G G SEQRES 11 A 153 C C A G C A G U C U C C A SEQRES 12 A 153 C G A C A A G G A G SEQRES 1 B 582 G G G C G A C U A C G A A SEQRES 2 B 582 A C G G G C C U G G G U A SEQRES 3 B 582 G G A A A U G A C C C A G SEQRES 4 B 582 U G A C C C U G A C A G U SEQRES 5 B 582 U U G G G A A A G U C G G SEQRES 6 B 582 U G A A A G C C C G A C C SEQRES 7 B 582 C U C G G G G C C U A G C SEQRES 8 B 582 G A A A G U G G G C G A C SEQRES 9 B 582 G A G U G C A A C A C C U SEQRES 10 B 582 G G A G G C U G A G G G C SEQRES 11 B 582 G U C A G U G A U G G C G SEQRES 12 B 582 U C A G G C A U G C G G G SEQRES 13 B 582 A G A A A U C U A G G C A SEQRES 14 B 582 U G C U G G C A C C U A U SEQRES 15 B 582 C G A A A G A U G G G G C SEQRES 16 B 582 C G C U G G A U A G C U C SEQRES 17 B 582 A A U C A G G U A A A G G SEQRES 18 B 582 C A C C G U U C A G G U G SEQRES 19 B 582 C U G U G U U G A G G C A SEQRES 20 B 582 U A G G A A G G C A G G G SEQRES 21 B 582 C C G C A G U C G C G G U SEQRES 22 B 582 A A G C A A G C A G C G U SEQRES 23 B 582 U G A A G C G C A U C G G SEQRES 24 B 582 C A G U A C C G C A U C C SEQRES 25 B 582 G U U A U G G A A C C U U SEQRES 26 B 582 G G G A G C G A G A A A C SEQRES 27 B 582 C C U G G A A A C G G G G SEQRES 28 B 582 G U A G G G U C A G A G A SEQRES 29 B 582 C C U A G A U A A A U C C SEQRES 30 B 582 G A U G U G G C C G A G C SEQRES 31 B 582 U G G C U G U C G U U C G SEQRES 32 B 582 A U G C C G U A G U A C U SEQRES 33 B 582 G A C U G U C U A A G U A SEQRES 34 B 582 G G G A A G G U C U C G G SEQRES 35 B 582 C A G A U C G U G G G G G SEQRES 36 B 582 U G G C A C C C U G C G A SEQRES 37 B 582 A A U U A U C U G C C A A SEQRES 38 B 582 G A C U G G G A G A U G G SEQRES 39 B 582 C U U G A G U A G U G C C SEQRES 40 B 582 G C C G C G C G A G C G G SEQRES 41 B 582 U G G G C A G A C C A U G SEQRES 42 B 582 G G G G C A G A C U U G C SEQRES 43 B 582 U G G A U G U U C C U A U SEQRES 44 B 582 C G G C G A A A G A G C C SEQRES 45 B 582 A A G C G G U A A C HET MG A 201 1 HET MG A 202 1 HET MG A 203 1 HET MG A 204 1 HET K A 205 1 HET K A 206 1 HET MG B 801 1 HET MG B 802 1 HET MG B 803 1 HET MG B 804 1 HET MG B 805 1 HET MG B 806 1 HET MG B 807 1 HET MG B 808 1 HET MG B 809 1 HET MG B 810 1 HET MG B 811 1 HET MG B 812 1 HET MG B 813 1 HET MG B 814 1 HET MG B 815 1 HET MG B 816 1 HET MG B 817 1 HET MG B 818 1 HET MG B 819 1 HET MG B 820 1 HET MG B 821 1 HET MG B 822 1 HET MG B 823 1 HET MG B 824 1 HET MG B 825 1 HET K B 826 1 HET K B 827 1 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION FORMUL 3 MG 29(MG 2+) FORMUL 7 K 4(K 1+) LINK O5' G A 29 K K A 205 1555 1555 3.38 LINK OP2 A A 30 K K A 205 1555 1555 2.75 LINK OP1 A A 31 MG MG A 201 1555 1555 2.75 LINK OP1 C A 52 MG MG A 202 1555 1555 2.35 LINK OP1 G A 54 MG MG A 201 1555 1555 2.72 LINK OP2 G A 54 MG MG A 202 1555 1555 2.36 LINK O6 G A 54 K K A 206 1555 1555 2.68 LINK OP2 G A 57 K K A 206 1555 1555 2.66 LINK OP2 C A 58 K K A 206 1555 1555 3.23 LINK OP1 A A 152 MG MG B 804 1555 1555 2.70 LINK O3' G A 153 MG MG A 202 1555 1555 2.82 LINK K K A 205 OP2 A B 644 1555 1555 2.69 LINK O6 G B 155 K K B 826 1555 1555 2.63 LINK OP2 G B 158 K K B 826 1555 1555 2.64 LINK OP2 A B 166 MG MG B 814 1555 1555 2.80 LINK OP1 U B 199 MG MG B 820 1555 1555 2.72 LINK OP2 G B 274 MG MG B 823 1555 1555 2.71 LINK OP2 G B 350 MG MG B 811 1555 1555 2.73 LINK OP2 A B 355 MG MG B 804 1555 1555 2.90 LINK OP2 U B 356 MG MG B 804 1555 1555 2.75 LINK OP2 C B 359 MG MG B 803 1555 1555 2.71 LINK OP2 G B 455 MG MG B 809 1555 1555 2.80 LINK OP2 C B 459 MG MG B 818 1555 1555 2.73 LINK OP1 U B 506 MG MG B 810 1555 1555 2.72 LINK OP2 G B 508 MG MG B 809 1555 1555 2.86 LINK OP1 A B 579 MG MG B 824 1555 1555 2.74 LINK OP2 G B 580 MG MG B 824 1555 1555 2.71 LINK OP1 A B 642 K K B 826 1555 1555 2.88 LINK OP2 A B 642 K K B 826 1555 1555 2.66 LINK OP1 A B 694 MG MG B 816 1555 1555 2.86 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 60115190 CONECT 62315190 CONECT 64415186 CONECT 109315187 CONECT 113315186 CONECT 113415187 CONECT 114915191 CONECT 120015191 CONECT 122315191 CONECT 259315195 CONECT 262215187 CONECT 267815217 CONECT 272915217 CONECT 290115205 CONECT 361115211 CONECT 523115214 CONECT 687515202 CONECT 698415195 CONECT 700615195 CONECT 707115194 CONECT 914115200 CONECT 922615209 CONECT1024015201 CONECT1028315200 CONECT1179815215 CONECT1182115215 CONECT1315815217 CONECT1315915217 CONECT1320415190 CONECT1428815207 CONECT15186 644 1133 CONECT15187 1093 1134 2622 CONECT15190 601 62313204 CONECT15191 1149 1200 1223 CONECT15194 7071 CONECT15195 2593 6984 7006 CONECT15200 914110283 CONECT1520110240 CONECT15202 6875 CONECT15205 2901 CONECT1520714288 CONECT15209 9226 CONECT15211 3611 CONECT15214 5231 CONECT152151179811821 CONECT15217 2678 27291315813159 MASTER 200 0 33 0 0 0 0 615216 2 46 57 END