HEADER RNA 03-NOV-22 8HD7 TITLE THE INTERMEDIATE PRE-TET-S1 STATE OF G264A MUTATED TETRAHYMENA GROUP I TITLE 2 INTRON WITH 6NT 3'/5'-EXON AND 2-AMINOPURINE NUCLEOSIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THE INTERMEDIATE PRE-TET-S1 STATE MOLECULE OF CO- COMPND 3 TRANSCRIPTIONAL FOLDED G264A MUTANT TETRAHYMENA GROUP I INTRON WITH COMPND 4 6NT 3'/5'-EXON AND 2-AMINOPURINE NUCLEOSIDE; COMPND 5 CHAIN: N; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TETRAHYMENA THERMOPHILA; SOURCE 3 ORGANISM_TAXID: 5911; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS CATALYTIC RNA, G264A MUTATED TETRAHYMENA GROUP I INTRON, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR B.LUO,C.ZHANG,X.LING,S.MUKHERJEE,G.JIA,J.XIE,X.JIA,L.LIU,E.F.BAULIN, AUTHOR 2 Y.LUO,L.JIANG,H.DONG,X.WEI,J.M.BUJNICKI,Z.SU REVDAT 2 03-JUL-24 8HD7 1 REMARK REVDAT 1 29-MAR-23 8HD7 0 JRNL AUTH B.LUO,C.ZHANG,X.LING,S.MUKHERJEE,G.JIA,J.XIE,X.JIA,L.LIU, JRNL AUTH 2 E.F.BAULIN,Y.LUO,L.JIANG,H.DONG,X.WEI,J.M.BUJNICKI,Z.SU JRNL TITL CRYO-EM REVEALS DYNAMICS OF TETRAHYMENA GROUP I INTRON JRNL TITL 2 SELF-SPLICING JRNL REF NAT CATAL 2023 JRNL REFN ESSN 2520-1158 JRNL DOI 10.1038/S41929-023-00934-3 REMARK 2 REMARK 2 RESOLUTION. 3.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EMAN2, EPU, RELION, CTFFIND, UCSF REMARK 3 CHIMERA, PHENIX, COOT, RELION, RELION, REMARK 3 RELION, RELION REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 3.520 REMARK 3 NUMBER OF PARTICLES : 111196 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 8HD7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1300033093. 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 : CO-TRANSCRIPTIONAL FOLDED G264A REMARK 245 MUTATED TETRAHYMENA GROUP I REMARK 245 INTRON WITH 6-NT 3'/5'-EXON AND REMARK 245 2-AMINOPURINE NUCLEOSIDE 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 : 7.00 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 K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3700.00 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) : 5500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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: N 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 MG N 508 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G N 164 O6 REMARK 620 2 A N 178 OP2 75.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 506 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 183 OP1 REMARK 620 2 A N 184 OP2 77.8 REMARK 620 3 A N 186 OP2 91.8 74.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 505 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 184 OP1 REMARK 620 2 A N 187 OP2 95.6 REMARK 620 3 G N 188 OP2 133.1 83.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 207 OP1 REMARK 620 2 C N 262 OP1 147.9 REMARK 620 3 C N 262 OP2 123.7 70.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 511 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 256 OP1 REMARK 620 2 U N 273 OP1 109.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 515 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G N 257 OP1 REMARK 620 2 U N 258 OP2 69.5 REMARK 620 3 U N 305 OP2 104.6 126.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 519 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 301 OP1 REMARK 620 2 A N 302 OP2 93.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 526 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 304 OP1 REMARK 620 2 A N 306 OP1 76.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 527 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U N 307 OP2 REMARK 620 2 A N 308 OP2 89.0 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-31385 RELATED DB: EMDB REMARK 900 APO L-21 SCAI TETRAHYMENA RIBOZYME REMARK 900 RELATED ID: EMD-34671 RELATED DB: EMDB REMARK 900 TET6_A264_2 DBREF 8HD7 N -6 414 GB JN547815 JN547815.1 2852 3270 SEQADV 8HD7 A N 264 GB JN547815 G 3120 ENGINEERED MUTATION SEQRES 1 N 419 C U C U C U A A A U A G C SEQRES 2 N 419 A A U A U U U A C C U U U SEQRES 3 N 419 G G A G G G A A A A G U U SEQRES 4 N 419 A U C A G G C A U G C A C SEQRES 5 N 419 C U G G U A G C U A G U C SEQRES 6 N 419 U U U A A A C C A A U A G SEQRES 7 N 419 A U U G C A U C G G U U U SEQRES 8 N 419 A A A A G G C A A G A C C SEQRES 9 N 419 G U C A A A U U G C G G G SEQRES 10 N 419 A A A G G G G U C A A C A SEQRES 11 N 419 G C C G U U C A G U A C C SEQRES 12 N 419 A A G U C U C A G G G G A SEQRES 13 N 419 A A C U U U G A G A U G G SEQRES 14 N 419 C C U U G C A A A G G G U SEQRES 15 N 419 A U G G U A A U A A G C U SEQRES 16 N 419 G A C G G A C A U G G U C SEQRES 17 N 419 C U A A C C A C G C A G C SEQRES 18 N 419 C A A G U C C U A A G U C SEQRES 19 N 419 A A C A G A U C U U C U G SEQRES 20 N 419 U U G A U A U G G A U G C SEQRES 21 N 419 A G U U C A C A A A C U A SEQRES 22 N 419 A A U G U C G G U C G G G SEQRES 23 N 419 G A A G A U G U A U U C U SEQRES 24 N 419 U C U C A U A A G A U A U SEQRES 25 N 419 A G U C G G A C C U C U C SEQRES 26 N 419 C U U A A U G G G A G C U SEQRES 27 N 419 A G C G G A U G A A G U G SEQRES 28 N 419 A U G C A A C A C U G G A SEQRES 29 N 419 G C C G C U G G G A A C U SEQRES 30 N 419 A A U U U G U A U G C G A SEQRES 31 N 419 A A G U A U A U U G A U U SEQRES 32 N 419 A G U U U U G G A G U A C SEQRES 33 N 419 U C G HET SPD N 501 10 HET MG N 502 1 HET MG N 503 1 HET MG N 504 1 HET MG N 505 1 HET MG N 506 1 HET MG N 507 1 HET MG N 508 1 HET MG N 509 1 HET MG N 510 1 HET MG N 511 1 HET MG N 512 1 HET MG N 513 1 HET MG N 514 1 HET MG N 515 1 HET MG N 516 1 HET MG N 517 1 HET MG N 518 1 HET MG N 519 1 HET MG N 520 1 HET MG N 521 1 HET MG N 522 1 HET MG N 523 1 HET MG N 524 1 HET MG N 525 1 HET MG N 526 1 HET MG N 527 1 HET MG N 528 1 HETNAM SPD SPERMIDINE HETNAM MG MAGNESIUM ION HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 2 SPD C7 H19 N3 FORMUL 3 MG 27(MG 2+) LINK O6 G N 91 MG MG N 528 1555 1555 2.67 LINK O6 G N 116 MG MG N 504 1555 1555 2.96 LINK O6 G N 164 MG MG N 508 1555 1555 2.54 LINK OP2 A N 171 MG MG N 522 1555 1555 2.49 LINK OP2 A N 172 MG MG N 523 1555 1555 2.61 LINK OP2 A N 178 MG MG N 508 1555 1555 2.24 LINK OP1 A N 183 MG MG N 506 1555 1555 2.38 LINK OP1 A N 184 MG MG N 505 1555 1555 2.32 LINK OP2 A N 184 MG MG N 506 1555 1555 2.17 LINK OP2 A N 186 MG MG N 506 1555 1555 2.61 LINK OP2 A N 187 MG MG N 505 1555 1555 2.71 LINK OP2 G N 188 MG MG N 505 1555 1555 2.98 LINK OP1 A N 207 MG MG N 503 1555 1555 2.91 LINK OP2 G N 212 MG MG N 514 1555 1555 2.01 LINK OP1 A N 256 MG MG N 511 1555 1555 2.12 LINK OP1 G N 257 MG MG N 515 1555 1555 2.42 LINK OP2 U N 258 MG MG N 515 1555 1555 2.63 LINK OP1 U N 258 MG MG N 516 1555 1555 2.23 LINK OP1 U N 259 MG MG N 517 1555 1555 2.15 LINK OP1 C N 262 MG MG N 503 1555 1555 2.16 LINK OP2 C N 262 MG MG N 503 1555 1555 2.28 LINK OP1 U N 273 MG MG N 511 1555 1555 2.60 LINK OP1 A N 301 MG MG N 519 1555 1555 2.20 LINK OP2 A N 302 MG MG N 519 1555 1555 1.93 LINK OP1 A N 304 MG MG N 526 1555 1555 2.46 LINK OP2 U N 305 MG MG N 515 1555 1555 2.27 LINK OP1 U N 305 MG MG N 518 1555 1555 2.02 LINK OP1 A N 306 MG MG N 526 1555 1555 2.33 LINK OP2 U N 307 MG MG N 527 1555 1555 2.86 LINK OP2 A N 308 MG MG N 527 1555 1555 2.19 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 8947 G N 414 HETATM 8948 N1 SPD N 501 110.070 105.702 112.104 1.00 90.21 N HETATM 8949 C2 SPD N 501 110.624 105.482 113.426 1.00 90.21 C HETATM 8950 C3 SPD N 501 109.665 104.647 114.269 1.00 90.21 C HETATM 8951 C4 SPD N 501 109.493 103.231 113.726 1.00 90.21 C HETATM 8952 C5 SPD N 501 108.257 102.546 114.304 1.00 90.21 C HETATM 8953 N6 SPD N 501 108.170 101.170 113.852 1.00 90.21 N HETATM 8954 C7 SPD N 501 108.817 100.303 114.818 1.00 90.21 C HETATM 8955 C8 SPD N 501 108.318 98.869 114.655 1.00 90.21 C HETATM 8956 C9 SPD N 501 109.005 97.905 115.618 1.00 90.21 C HETATM 8957 N10 SPD N 501 108.347 96.611 115.590 1.00 90.21 N HETATM 8958 MG MG N 502 101.640 95.697 80.363 0.77 41.37 MG HETATM 8959 MG MG N 503 106.788 88.851 89.039 1.00119.59 MG HETATM 8960 MG MG N 504 116.475 96.464 78.731 0.87115.04 MG HETATM 8961 MG MG N 505 88.495 102.484 71.382 1.00 85.12 MG HETATM 8962 MG MG N 506 87.578 106.085 75.907 0.85 68.12 MG HETATM 8963 MG MG N 507 93.925 110.931 74.908 0.81 67.36 MG HETATM 8964 MG MG N 508 78.851 119.403 71.704 0.84102.88 MG HETATM 8965 MG MG N 509 75.758 111.106 79.471 0.78100.31 MG HETATM 8966 MG MG N 510 60.296 108.232 88.204 0.80126.90 MG HETATM 8967 MG MG N 511 94.046 103.740 104.670 0.88 55.33 MG HETATM 8968 MG MG N 512 93.500 103.185 116.099 1.00 81.12 MG HETATM 8969 MG MG N 513 79.217 98.391 93.958 0.84 83.58 MG HETATM 8970 MG MG N 514 95.322 102.146 90.856 1.00 83.69 MG HETATM 8971 MG MG N 515 97.509 95.347 95.577 0.89 63.52 MG HETATM 8972 MG MG N 516 97.288 90.259 96.908 0.89 49.15 MG HETATM 8973 MG MG N 517 95.308 86.139 91.557 0.90 72.41 MG HETATM 8974 MG MG N 518 101.320 97.959 97.867 0.83 72.97 MG HETATM 8975 MG MG N 519 104.004 100.546 108.252 0.87 73.15 MG HETATM 8976 MG MG N 520 97.520 105.995 101.810 1.00 78.85 MG HETATM 8977 MG MG N 521 96.440 117.183 121.200 0.88 89.23 MG HETATM 8978 MG MG N 522 91.737 114.705 82.454 0.88 87.99 MG HETATM 8979 MG MG N 523 87.316 124.784 82.772 0.85 80.43 MG HETATM 8980 MG MG N 524 100.641 123.787 82.290 0.86117.36 MG HETATM 8981 MG MG N 525 107.853 72.434 95.977 1.00112.74 MG HETATM 8982 MG MG N 526 107.970 91.393 96.223 0.91 86.65 MG HETATM 8983 MG MG N 527 106.129 83.177 100.059 0.86 89.19 MG HETATM 8984 MG MG N 528 111.085 101.655 131.181 1.00110.55 MG CONECT 2034 8984 CONECT 2576 8960 CONECT 3607 8964 CONECT 3738 8978 CONECT 3760 8979 CONECT 3893 8964 CONECT 4000 8962 CONECT 4022 8961 CONECT 4023 8962 CONECT 4065 8962 CONECT 4087 8961 CONECT 4109 8961 CONECT 4514 8959 CONECT 4619 8970 CONECT 5552 8967 CONECT 5574 8971 CONECT 5597 8972 CONECT 5598 8971 CONECT 5617 8973 CONECT 5679 8959 CONECT 5680 8959 CONECT 5914 8967 CONECT 6508 8975 CONECT 6531 8975 CONECT 6575 8982 CONECT 6597 8974 CONECT 6598 8971 CONECT 6617 8982 CONECT 6640 8983 CONECT 6660 8983 CONECT 8948 8949 CONECT 8949 8948 8950 CONECT 8950 8949 8951 CONECT 8951 8950 8952 CONECT 8952 8951 8953 CONECT 8953 8952 8954 CONECT 8954 8953 8955 CONECT 8955 8954 8956 CONECT 8956 8955 8957 CONECT 8957 8956 CONECT 8959 4514 5679 5680 CONECT 8960 2576 CONECT 8961 4022 4087 4109 CONECT 8962 4000 4023 4065 CONECT 8964 3607 3893 CONECT 8967 5552 5914 CONECT 8970 4619 CONECT 8971 5574 5598 6598 CONECT 8972 5597 CONECT 8973 5617 CONECT 8974 6597 CONECT 8975 6508 6531 CONECT 8978 3738 CONECT 8979 3760 CONECT 8982 6575 6617 CONECT 8983 6640 6660 CONECT 8984 2034 MASTER 175 0 28 0 0 0 0 6 8983 1 57 33 END