HEADER RNA 22-JUN-21 7R6M TITLE POST-2S INTERMEDIATE OF THE TETRAHYMENA GROUP I INTRON, SYMMETRY- TITLE 2 EXPANDED MONOMER FROM A SYNTHETIC DIMERIC CONSTRUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROUP I INTRON; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LIGATED EXON MIMIC OF THE GROUP I INTRON; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: TETRAHYMENA THERMOPHILA; SOURCE 4 ORGANISM_TAXID: 5911; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: TETRAHYMENA THERMOPHILA; SOURCE 8 ORGANISM_TAXID: 5911 KEYWDS RIBOZYME, GROUP I INTRON, CATALYTIC RNA, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR F.THELOT,D.LIU,M.LIAO,P.YIN REVDAT 4 05-JUN-24 7R6M 1 REMARK REVDAT 3 01-JUN-22 7R6M 1 JRNL REVDAT 2 18-MAY-22 7R6M 1 JRNL REVDAT 1 04-MAY-22 7R6M 0 JRNL AUTH D.LIU,F.A.THELOT,J.A.PICCIRILLI,M.LIAO,P.YIN JRNL TITL SUB-3- ANGSTROM CRYO-EM STRUCTURE OF RNA ENABLED BY JRNL TITL 2 ENGINEERED HOMOMERIC SELF-ASSEMBLY. JRNL REF NAT.METHODS V. 19 576 2022 JRNL REFN ESSN 1548-7105 JRNL PMID 35501384 JRNL DOI 10.1038/S41592-022-01455-W REMARK 2 REMARK 2 RESOLUTION. 3.68 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) : 3.680 REMARK 3 NUMBER OF PARTICLES : 113548 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 7R6M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257396. 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 : POST-2S INTERMEDIATE OF REMARK 245 TETRAHYMENA GROUP I INTRON, REMARK 245 SYMMETRY-EXPANDED MONOMER FROM REMARK 245 A SYNTHETIC DIMERIC CONSTRUCT REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 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 K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4700.00 REMARK 245 ILLUMINATION MODE : OTHER 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: 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 G A 235 REMARK 465 A A 236 REMARK 465 U A 237 REMARK 465 G A 238 REMARK 465 G A 239 REMARK 465 U A 240 REMARK 465 U A 241 REMARK 465 G A 286A REMARK 465 A A 286B REMARK 465 A A 286C REMARK 465 C A 286D REMARK 465 C A 286E REMARK 465 A A 286F REMARK 465 U A 286G REMARK 465 C A 286H REMARK 465 C A 286I REMARK 465 A A 374 REMARK 465 U A 375 REMARK 465 U A 376 REMARK 465 U A 377 REMARK 465 G A 378 REMARK 465 U A 379 REMARK 465 A A 380 REMARK 465 U A 381 REMARK 465 G A 382 REMARK 465 C A 383 REMARK 465 G A 384 REMARK 465 A A 385 REMARK 465 A A 386 REMARK 465 A A 387 REMARK 465 G A 388 REMARK 465 U A 389 REMARK 465 A A 390 REMARK 465 U A 391 REMARK 465 A A 392 REMARK 465 U A 393 REMARK 465 U A 394 REMARK 465 G A 395 REMARK 465 A A 396 REMARK 465 U A 397 REMARK 465 DT B 7 REMARK 465 A B 8 REMARK 465 A B 9 REMARK 465 G B 10 REMARK 465 G B 11 REMARK 465 U B 12 REMARK 465 C B 13 REMARK 465 C B 14 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 U A 292 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 C A 45 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 C A 68 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 C A 68 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 U A 84 N1 - C2 - O2 ANGL. DEV. = 6.8 DEGREES REMARK 500 U A 84 N3 - C2 - O2 ANGL. DEV. = -7.4 DEGREES REMARK 500 U A 84 C6 - N1 - C1' ANGL. DEV. = -9.1 DEGREES REMARK 500 U A 84 C2 - N1 - C1' ANGL. DEV. = 12.6 DEGREES REMARK 500 C A 93 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 C A 124 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 C A 124 C2 - N1 - C1' ANGL. DEV. = 7.0 DEGREES REMARK 500 U A 135 C5 - C4 - O4 ANGL. DEV. = -3.9 DEGREES REMARK 500 U A 168 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 C A 242 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 C A 242 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 C A 242 N1 - C2 - O2 ANGL. DEV. = 5.8 DEGREES REMARK 500 C A 242 N3 - C2 - O2 ANGL. DEV. = -5.6 DEGREES REMARK 500 C A 242 C2 - N1 - C1' ANGL. DEV. = 8.8 DEGREES REMARK 500 C A 320 C6 - N1 - C2 ANGL. DEV. = -2.9 DEGREES REMARK 500 C A 320 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 U A 340 N1 - C2 - O2 ANGL. DEV. = 5.5 DEGREES REMARK 500 U A 340 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 U A 340 C2 - N1 - C1' ANGL. DEV. = 9.2 DEGREES REMARK 500 C A 355 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 256 OP1 REMARK 620 2 U A 273 OP1 88.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 512 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 257 OP1 REMARK 620 2 U A 258 OP2 95.8 REMARK 620 3 U A 305 OP2 87.4 90.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 513 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 262 OP1 REMARK 620 2 A A 306 OP2 89.9 REMARK 620 3 G A 414 O2' 126.5 76.5 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-24282 RELATED DB: EMDB REMARK 900 POST-2S INTERMEDIATE OF THE TETRAHYMENA GROUP I INTRON, SYMMETRY- REMARK 900 EXPANDED MONOMER FROM A SYNTHETIC DIMERIC CONSTRUCT DBREF 7R6M A 21 414 GB V01416 V01416.1 72 465 DBREF 7R6M B 1 14 PDB 7R6M 7R6M 1 14 SEQADV 7R6M G A 232 GB V01416 C 283 CONFLICT SEQADV 7R6M G A 235 GB V01416 A 284 CONFLICT SEQADV 7R6M A A 236 GB V01416 G 285 CONFLICT SEQADV 7R6M U A 237 GB V01416 A 286 CONFLICT SEQADV 7R6M G A 238 GB V01416 U 287 CONFLICT SEQADV 7R6M G A 239 GB V01416 C 288 CONFLICT SEQADV 7R6M A GB V01416 U 292 DELETION SEQADV 7R6M A GB V01416 G 293 DELETION SEQADV 7R6M A A 284 GB V01416 INSERTION SEQADV 7R6M G A 285 GB V01416 INSERTION SEQADV 7R6M A A 286C GB V01416 U 338 CONFLICT SEQADV 7R6M C A 286D GB V01416 G 339 CONFLICT SEQADV 7R6M C A 286E GB V01416 U 340 CONFLICT SEQADV 7R6M C A 286H GB V01416 INSERTION SEQADV 7R6M C A 286I GB V01416 INSERTION SEQRES 1 A 396 U G G A G G G A A A A G U SEQRES 2 A 396 U A U C A G G C A U G C A SEQRES 3 A 396 C C U G G U A G C U A G U SEQRES 4 A 396 C U U U A A A C C A A U A SEQRES 5 A 396 G A U U G C A U C G G U U SEQRES 6 A 396 U A A A A G G C A A G A C SEQRES 7 A 396 C G U C A A A U U G C G G SEQRES 8 A 396 G A A A G G G G U C A A C SEQRES 9 A 396 A G C C G U U C A G U A C SEQRES 10 A 396 C A A G U C U C A G G G G SEQRES 11 A 396 A A A C U U U G A G A U G SEQRES 12 A 396 G C C U U G C A A A G G G SEQRES 13 A 396 U A U G G U A A U A A G C SEQRES 14 A 396 U G A C G G A C A U G G U SEQRES 15 A 396 C C U A A C C A C G C A G SEQRES 16 A 396 C C A A G U C C U A A G U SEQRES 17 A 396 C A A G G A U G G U U C U SEQRES 18 A 396 U G A U A U G G A U G C A SEQRES 19 A 396 G U U C A C A G A C U A A SEQRES 20 A 396 A U G U C G G U C G G G G SEQRES 21 A 396 A A G A G A A C C A U C C SEQRES 22 A 396 U C U U C U C A U A A G A SEQRES 23 A 396 U A U A G U C G G A C C U SEQRES 24 A 396 C U C C U U A A U G G G A SEQRES 25 A 396 G C U A G C G G A U G A A SEQRES 26 A 396 G U G A U G C A A C A C U SEQRES 27 A 396 G G A G C C G C U G G G A SEQRES 28 A 396 A C U A A U U U G U A U G SEQRES 29 A 396 C G A A A G U A U A U U G SEQRES 30 A 396 A U U A G U U U U G G A G SEQRES 31 A 396 U A C U C G SEQRES 1 B 14 C U C U C DT DT A A G G U C SEQRES 2 B 14 C HET MG A 501 1 HET MG A 502 1 HET MG A 503 1 HET MG A 504 1 HET MG A 505 1 HET MG A 506 1 HET MG A 507 1 HET MG A 508 1 HET MG A 509 1 HET MG A 510 1 HET MG A 511 1 HET MG A 512 1 HET MG A 513 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 13(MG 2+) LINK O6 G A 164 MG MG A 502 1555 1555 2.02 LINK O6 G A 188 MG MG A 509 1555 1555 2.01 LINK OP1 A A 256 MG MG A 503 1555 1555 2.53 LINK OP1 G A 257 MG MG A 512 1555 1555 2.06 LINK OP1 U A 258 MG MG A 504 1555 1555 2.01 LINK OP2 U A 258 MG MG A 512 1555 1555 2.09 LINK OP1 U A 259 MG MG A 505 1555 1555 2.04 LINK OP1 C A 262 MG MG A 513 1555 1555 2.09 LINK OP1 U A 273 MG MG A 503 1555 1555 2.05 LINK OP1 U A 305 MG MG A 506 1555 1555 2.13 LINK OP2 U A 305 MG MG A 512 1555 1555 2.03 LINK OP2 A A 306 MG MG A 513 1555 1555 2.61 LINK O2' G A 414 MG MG A 513 1555 1555 2.81 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