HEADER RNA 01-FEB-23 8I7N TITLE THE TET-S1 STATE OF G264A MUTATED TETRAHYMENA GROUP I INTRON WITH 6NT TITLE 2 3'/5'-EXON AND 2-AMINOPURINE NUCLEOSIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THE TET-S1 STATE MOLECULE OF CO-TRANSCRIPTIONAL FOLDED COMPND 3 G264A MUTATED TETRAHYMENA GROUP I INTRON WITH 6NT 3'/5'-EXON AND 2- COMPND 4 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 8I7N 1 REMARK REVDAT 1 29-MAR-23 8I7N 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. 2.98 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) : 2.980 REMARK 3 NUMBER OF PARTICLES : 953401 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 8I7N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300035080. 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 6NT 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 524 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U N -1 O3' REMARK 620 2 C N 208 OP1 71.8 REMARK 620 3 A N 304 OP1 120.5 92.0 REMARK 620 4 A N 306 OP1 145.3 88.9 87.9 REMARK 620 N 1 2 3 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 183 OP1 REMARK 620 2 A N 184 OP2 78.9 REMARK 620 3 A N 186 OP2 96.5 79.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 184 OP1 REMARK 620 2 A N 186 OP1 90.4 REMARK 620 3 A N 187 OP2 168.9 86.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 207 OP1 REMARK 620 2 C N 262 OP2 121.1 REMARK 620 N 1 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 85.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 514 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G N 257 OP1 REMARK 620 2 U N 258 OP2 84.4 REMARK 620 3 U N 305 OP2 88.6 120.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 518 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 301 OP1 REMARK 620 2 A N 302 OP2 80.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 525 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U N 307 OP2 REMARK 620 2 A N 308 OP2 75.7 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34670 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-34671 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-35223 RELATED DB: EMDB REMARK 900 G264A MUTANT TETRAHYMENA GROUP I INTRON WITH 6NT 3'/5'-EXON CO- REMARK 900 TRANSCRIBED WITH 2-AMINOPURINE NUCLEOSIDE. DBREF 8I7N N -6 413 GB JN547815 JN547815.1 2852 3269 SEQADV 8I7N A N 264 GB JN547815 G 3120 ENGINEERED MUTATION SEQRES 1 N 418 C U C U C U A A A U A G C SEQRES 2 N 418 A A U A U U U A C C U U U SEQRES 3 N 418 G G A G G G A A A A G U U SEQRES 4 N 418 A U C A G G C A U G C A C SEQRES 5 N 418 C U G G U A G C U A G U C SEQRES 6 N 418 U U U A A A C C A A U A G SEQRES 7 N 418 A U U G C A U C G G U U U SEQRES 8 N 418 A A A A G G C A A G A C C SEQRES 9 N 418 G U C A A A U U G C G G G SEQRES 10 N 418 A A A G G G G U C A A C A SEQRES 11 N 418 G C C G U U C A G U A C C SEQRES 12 N 418 A A G U C U C A G G G G A SEQRES 13 N 418 A A C U U U G A G A U G G SEQRES 14 N 418 C C U U G C A A A G G G U SEQRES 15 N 418 A U G G U A A U A A G C U SEQRES 16 N 418 G A C G G A C A U G G U C SEQRES 17 N 418 C U A A C C A C G C A G C SEQRES 18 N 418 C A A G U C C U A A G U C SEQRES 19 N 418 A A C A G A U C U U C U G SEQRES 20 N 418 U U G A U A U G G A U G C SEQRES 21 N 418 A G U U C A C A A A C U A SEQRES 22 N 418 A A U G U C G G U C G G G SEQRES 23 N 418 G A A G A U G U A U U C U SEQRES 24 N 418 U C U C A U A A G A U A U SEQRES 25 N 418 A G U C G G A C C U C U C SEQRES 26 N 418 C U U A A U G G G A G C U SEQRES 27 N 418 A G C G G A U G A A G U G SEQRES 28 N 418 A U G C A A C A C U G G A SEQRES 29 N 418 G C C G C U G G G A A C U SEQRES 30 N 418 A A U U U G U A U G C G A SEQRES 31 N 418 A A G U A U A U U G A U U SEQRES 32 N 418 A G U U U U G G A G U A C SEQRES 33 N 418 U C HET MG N 501 1 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 SPD N 528 10 HET OJI N 529 19 HETNAM MG MAGNESIUM ION HETNAM SPD SPERMIDINE HETNAM OJI (2R,3R,4S,5R)-2-(2-AZANYLPURIN-9-YL)-5-(HYDROXYMETHYL) HETNAM 2 OJI OXOLANE-3,4-DIOL HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 2 MG 27(MG 2+) FORMUL 29 SPD C7 H19 N3 FORMUL 30 OJI C10 H13 N5 O4 LINK O3' U N -1 MG MG N 524 1555 1555 2.91 LINK OP1 A N 28 MG MG N 526 1555 1555 2.44 LINK O6 G N 148 MG MG N 509 1555 1555 2.85 LINK O6 G N 164 MG MG N 507 1555 1555 2.77 LINK OP2 A N 171 MG MG N 520 1555 1555 2.60 LINK OP2 A N 172 MG MG N 521 1555 1555 2.25 LINK OP1 A N 183 MG MG N 505 1555 1555 2.23 LINK OP1 A N 184 MG MG N 504 1555 1555 1.98 LINK OP2 A N 184 MG MG N 505 1555 1555 2.43 LINK OP1 A N 186 MG MG N 504 1555 1555 2.04 LINK OP2 A N 186 MG MG N 505 1555 1555 2.52 LINK OP2 A N 187 MG MG N 504 1555 1555 2.04 LINK O6 G N 188 MG MG N 506 1555 1555 2.16 LINK OP1 A N 207 MG MG N 502 1555 1555 2.10 LINK OP1 C N 208 MG MG N 524 1555 1555 2.28 LINK OP1 A N 256 MG MG N 511 1555 1555 2.45 LINK OP1 G N 257 MG MG N 514 1555 1555 2.34 LINK OP2 U N 258 MG MG N 514 1555 1555 2.31 LINK OP1 U N 258 MG MG N 515 1555 1555 2.36 LINK OP1 U N 259 MG MG N 516 1555 1555 2.35 LINK OP2 C N 262 MG MG N 502 1555 1555 2.29 LINK OP1 U N 273 MG MG N 511 1555 1555 2.30 LINK OP1 A N 301 MG MG N 518 1555 1555 2.20 LINK OP2 A N 302 MG MG N 518 1555 1555 2.58 LINK OP1 A N 304 MG MG N 524 1555 1555 2.13 LINK OP2 U N 305 MG MG N 514 1555 1555 2.30 LINK OP1 U N 305 MG MG N 517 1555 1555 2.64 LINK OP1 A N 306 MG MG N 524 1555 1555 2.04 LINK OP2 U N 307 MG MG N 525 1555 1555 2.70 LINK OP2 A N 308 MG MG N 525 1555 1555 2.41 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