HEADER RNA 11-JAN-24 8XTP TITLE COMAMONAS TESTOSTERONI KF-1 CIRCULARLY PERMUTED GROUP II INTRON POST- TITLE 2 2S STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (595-MER); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (133-MER); COMPND 7 CHAIN: A; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: COMAMONAS TESTOSTERONI KF-1; SOURCE 3 ORGANISM_TAXID: 399795; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: COMAMONAS TESTOSTERONI KF-1; SOURCE 8 ORGANISM_TAXID: 399795; 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.R.HUANG,S.T.SHANG,X.Y.CHEN,Y.YANG, AUTHOR 2 J.LIU,H.H.DONG,D.M.HUANG,Z.M.SU REVDAT 3 23-JUL-25 8XTP 1 REMARK REVDAT 2 25-JUN-25 8XTP 1 JRNL REVDAT 1 12-FEB-25 8XTP 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. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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) : 2.900 REMARK 3 NUMBER OF PARTICLES : 59466 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 8XTP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 17-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300044183. 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 : COMAMONAS TESTOSTERONI KF-1 REMARK 245 CIRCULARLY PERMUTED GROUP II REMARK 245 INTRON POST-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) : 6400.00 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: B, 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 K B 901 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 222 OP1 REMARK 620 2 C B 223 OP2 71.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 926 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 262 OP1 REMARK 620 2 C B 620 OP1 81.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 912 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 366 O3' REMARK 620 2 G B 417 OP2 82.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 910 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 523 OP2 REMARK 620 2 G B 568 OP2 77.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 909 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 557 OP2 REMARK 620 2 U B 558 O4 91.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 911 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 566 OP1 REMARK 620 2 G B 568 OP1 78.1 REMARK 620 3 C B 569 OP2 177.8 102.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 934 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 629 OP1 REMARK 620 2 A B 630 OP2 83.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 201 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 696 O6 REMARK 620 2 A A 60 OP2 105.4 REMARK 620 3 G A 61 OP2 128.8 86.1 REMARK 620 4 G A 83 OP1 157.6 90.5 66.8 REMARK 620 5 G A 83 O5' 116.7 133.2 83.2 43.7 REMARK 620 6 G A 83 O4' 67.4 167.1 106.8 93.8 50.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 60 OP1 REMARK 620 2 G A 61 OP1 123.4 REMARK 620 3 G A 61 OP2 80.6 53.0 REMARK 620 4 G A 83 OP1 95.5 111.2 88.1 REMARK 620 5 U A 133 O3' 71.8 105.2 122.9 142.2 REMARK 620 6 U A 133 O2' 59.6 165.3 137.4 81.7 61.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 205 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 62 OP1 REMARK 620 2 G A 80 OP2 166.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 81 OP1 REMARK 620 2 G A 83 OP2 81.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 202 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 83 O6 REMARK 620 2 G A 86 OP2 139.2 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38646 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF INTRON 4 DBREF1 8XTP B 220 814 GB CP140157.1 DBREF2 8XTP B 2637094706 1901452 1902046 DBREF1 8XTP A 1 133 GB CP140157.1 DBREF2 8XTP A 2637094706 1901233 1901365 SEQRES 1 B 595 G G G C G A C C G U G A A SEQRES 2 B 595 A C G G C G C U G G G C A SEQRES 3 B 595 G G A A A U G G C C C A G SEQRES 4 B 595 U G A C C U G G U C A A U SEQRES 5 B 595 G G U G A A A G U C G G U SEQRES 6 B 595 G A A A G A C C G A C C G SEQRES 7 B 595 G U G G G G C G U A U C G SEQRES 8 B 595 A A A G A G C G C A A C A SEQRES 9 B 595 C C U G C C G C A C A G G SEQRES 10 B 595 A U G G C U U C U G A G G SEQRES 11 B 595 U A C C G G U G A C G G U SEQRES 12 B 595 A C A G A A C G C G G A G SEQRES 13 B 595 G G G A A A C C U G G A A SEQRES 14 B 595 G C G A G G G C A C C U C SEQRES 15 B 595 G G G A A A C C G G G G G SEQRES 16 B 595 U C G A U G C A U A G C U SEQRES 17 B 595 C A A A C C U G U A A C G SEQRES 18 B 595 G C A C C A G U G G A G G SEQRES 19 B 595 G U G C U G U G C G G A G SEQRES 20 B 595 C A A C G U G G A G C C A SEQRES 21 B 595 C A G G C A U G A A G C C SEQRES 22 B 595 G U G G U U C G U A G U C SEQRES 23 B 595 G A U G A G A C A A G C G SEQRES 24 B 595 G U G A G U A A G G G A A SEQRES 25 B 595 G G G C U G C G A A C A U SEQRES 26 B 595 C G C C U C C C C G A A A SEQRES 27 B 595 U C C A A G G A A A G C C SEQRES 28 B 595 G A A A G G C U A G C C G SEQRES 29 B 595 C U U U G U U G A G A C A SEQRES 30 B 595 G U G G C G C C A C G U U SEQRES 31 B 595 G C G C A U U A G C C G U SEQRES 32 B 595 G A C C U A A A C G G G G SEQRES 33 B 595 A A C C U C U U G G C C G SEQRES 34 B 595 U A C C G A C U C G G G U SEQRES 35 B 595 G G C A C C G G U C G G G SEQRES 36 B 595 C U C G A U G G C U C A A SEQRES 37 B 595 G A G G G G G A G A U G U SEQRES 38 B 595 G A U G A U U A G G G U U SEQRES 39 B 595 U G A C C C G U G A U G C SEQRES 40 B 595 G A U A C G A C C G A A G SEQRES 41 B 595 C A U C C G G G G A G C U SEQRES 42 B 595 G U C U G A C G A A G A G SEQRES 43 B 595 U C G G C A G C A G U G G SEQRES 44 B 595 G U U U G G C G A C C C G SEQRES 45 B 595 C U C C G A A A G U C G C SEQRES 46 B 595 A A G C G U U U G C SEQRES 1 A 133 C C G G G G C G C C A C C SEQRES 2 A 133 C C G G A A G U G A U G C SEQRES 3 A 133 G A G U C G C C A A C U C SEQRES 4 A 133 G C A U C A C A A G C A A SEQRES 5 A 133 A C G C U G U A G C C G C SEQRES 6 A 133 G U G C C U C U A A U A G SEQRES 7 A 133 G G C U G G C G C G G U U SEQRES 8 A 133 G C G A A G G G C G C U G SEQRES 9 A 133 G U G A G U G C A A C U C SEQRES 10 A 133 U C A C C U U C G A C C C SEQRES 11 A 133 A A U HET K B 901 1 HET K B 902 1 HET MG B 903 1 HET MG B 904 1 HET MG B 905 1 HET MG B 906 1 HET MG B 907 1 HET MG B 908 1 HET MG B 909 1 HET MG B 910 1 HET MG B 911 1 HET MG B 912 1 HET MG B 913 1 HET MG B 914 1 HET MG B 915 1 HET MG B 916 1 HET MG B 917 1 HET MG B 918 1 HET MG B 919 1 HET MG B 920 1 HET MG B 921 1 HET MG B 922 1 HET MG B 923 1 HET MG B 924 1 HET MG B 925 1 HET MG B 926 1 HET MG B 927 1 HET MG B 928 1 HET MG B 929 1 HET MG B 930 1 HET MG B 931 1 HET MG B 932 1 HET MG B 933 1 HET MG B 934 1 HET MG B 935 1 HET SPD B 936 10 HET K A 201 1 HET K A 202 1 HET MG A 203 1 HET MG A 204 1 HET MG A 205 1 HET MG A 206 1 HET MG A 207 1 HETNAM K POTASSIUM ION HETNAM MG MAGNESIUM ION HETNAM SPD SPERMIDINE HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 3 K 4(K 1+) FORMUL 5 MG 38(MG 2+) FORMUL 38 SPD C7 H19 N3 LINK OP1 G B 222 K K B 901 1555 1555 2.89 LINK OP2 C B 223 K K B 901 1555 1555 2.72 LINK OP1 A B 225 MG MG B 903 1555 1555 2.89 LINK OP2 A B 232 MG MG B 917 1555 1555 2.49 LINK OP1 C B 262 MG MG B 926 1555 1555 2.44 LINK OP1 U B 264 MG MG B 930 1555 1555 2.30 LINK OP2 G B 339 MG MG B 919 1555 1555 2.50 LINK O4 U B 343 MG MG B 916 1555 1555 2.77 LINK O3' G B 366 MG MG B 912 1555 1555 2.87 LINK OP2 G B 417 MG MG B 912 1555 1555 2.51 LINK OP2 U B 423 MG MG B 905 1555 1555 2.55 LINK OP2 C B 426 MG MG B 904 1555 1555 2.26 LINK OP2 G B 523 MG MG B 910 1555 1555 2.52 LINK OP2 A B 526 MG MG B 928 1555 1555 2.92 LINK OP2 A B 557 MG MG B 909 1555 1555 2.38 LINK O4 U B 558 MG MG B 909 1555 1555 2.30 LINK OP1 A B 566 MG MG B 911 1555 1555 2.18 LINK OP2 G B 568 MG MG B 910 1555 1555 2.30 LINK OP1 G B 568 MG MG B 911 1555 1555 2.41 LINK OP2 C B 569 MG MG B 911 1555 1555 2.07 LINK OP1 C B 620 MG MG B 926 1555 1555 2.62 LINK OP1 A B 629 MG MG B 934 1555 1555 2.71 LINK OP2 A B 630 MG MG B 934 1555 1555 2.35 LINK O6 G B 696 K K A 201 1555 1555 3.09 LINK O6 G B 704 MG MG B 918 1555 1555 2.75 LINK OP2 A B 708 MG MG B 927 1555 1555 2.55 LINK OP2 C B 726 MG MG B 921 1555 1555 2.41 LINK OP2 A A 60 K K A 201 1555 1555 2.87 LINK OP1 A A 60 MG MG A 203 1555 1555 2.55 LINK OP2 G A 61 K K A 201 1555 1555 2.76 LINK OP1 G A 61 MG MG A 203 1555 1555 2.81 LINK OP2 G A 61 MG MG A 203 1555 1555 2.85 LINK OP1 C A 62 MG MG A 205 1555 1555 2.46 LINK OP2 G A 80 MG MG A 205 1555 1555 2.13 LINK OP1 C A 81 MG MG A 204 1555 1555 2.74 LINK OP1 G A 83 K K A 201 1555 1555 3.50 LINK O5' G A 83 K K A 201 1555 1555 3.16 LINK O4' G A 83 K K A 201 1555 1555 3.31 LINK O6 G A 83 K K A 202 1555 1555 2.35 LINK OP1 G A 83 MG MG A 203 1555 1555 2.14 LINK OP2 G A 83 MG MG A 204 1555 1555 2.57 LINK OP2 G A 86 K K A 202 1555 1555 2.42 LINK O3' U A 133 MG MG A 203 1555 1555 2.53 LINK O2' U A 133 MG MG A 203 1555 1555 2.69 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 4815665 CONECT 7215665 CONECT 11415667 CONECT 26515681 CONECT 91615690 CONECT 95615694 CONECT 257715683 CONECT 267815680 CONECT 316315676 CONECT 427215676 CONECT 440215669 CONECT 446715668 CONECT 656015674 CONECT 662515692 CONECT 729115673 CONECT 732815673 CONECT 748415675 CONECT 752815675 CONECT 752915674 CONECT 755215675 CONECT 863915690 CONECT 882915698 CONECT 885215698 CONECT1029015710 CONECT1046315682 CONECT1053315691 CONECT1092015685 CONECT1408715712 CONECT1408815710 CONECT1410915712 CONECT141101571015712 CONECT1413215714 CONECT1451415714 CONECT1453615713 CONECT145761571015712 CONECT1457715713 CONECT1457815710 CONECT1458115710 CONECT1459215711 CONECT1464315711 CONECT1565215712 CONECT1565415712 CONECT15665 48 72 CONECT15667 114 CONECT15668 4467 CONECT15669 4402 CONECT15673 7291 7328 CONECT15674 6560 7529 CONECT15675 7484 7528 7552 CONECT15676 3163 4272 CONECT15680 2678 CONECT15681 265 CONECT1568210463 CONECT15683 2577 CONECT1568510920 CONECT15690 916 8639 CONECT1569110533 CONECT15692 6625 CONECT15694 956 CONECT15698 8829 8852 CONECT1570015701 CONECT157011570015702 CONECT157021570115703 CONECT157031570215704 CONECT157041570315705 CONECT157051570415706 CONECT157061570515707 CONECT157071570615708 CONECT157081570715709 CONECT1570915708 CONECT1571010290140881411014576 CONECT157101457814581 CONECT157111459214643 CONECT1571214087141091411014576 CONECT157121565215654 CONECT157131453614577 CONECT157141413214514 MASTER 195 0 43 0 0 0 0 615714 2 77 57 END