HEADER RNA 22-JUN-21 7R6N TITLE EXON-FREE STATE OF THE TETRAHYMENA GROUP I INTRON, SYMMETRY-EXPANDED TITLE 2 MONOMER FROM A SYNTHETIC TRIMERIC CONSTRUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROUP I INTRON; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: TETRAHYMENA THERMOPHILA; SOURCE 4 ORGANISM_TAXID: 5911 KEYWDS RIBOZYME, CATALYTIC RNA, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR F.THELOT,D.LIU,M.LIAO,P.YIN REVDAT 4 05-JUN-24 7R6N 1 REMARK REVDAT 3 01-JUN-22 7R6N 1 JRNL REVDAT 2 18-MAY-22 7R6N 1 JRNL REVDAT 1 04-MAY-22 7R6N 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. 4.10 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) : 4.100 REMARK 3 NUMBER OF PARTICLES : 85596 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 7R6N 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_1000257399. 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 : EXON-FREE STATE OF TETRAHYMENA REMARK 245 GROUP I INTRON, SYMMETRY- REMARK 245 EXPANDED MONOMER FROM A REMARK 245 SYNTHETIC TRIMERIC 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 U A 21 REMARK 465 G A 22 REMARK 465 G A 23 REMARK 465 A A 24 REMARK 465 G A 25 REMARK 465 A A 232A REMARK 465 G A 232B REMARK 465 G A 232C REMARK 465 A A 232D REMARK 465 U A 232E REMARK 465 G A 232F REMARK 465 G A 232G REMARK 465 U A 232H REMARK 465 U A 232I REMARK 465 C A 232J REMARK 465 U A 232K REMARK 465 U A 287 REMARK 465 G A 288 REMARK 465 U A 289 REMARK 465 A A 290 REMARK 465 U A 291 REMARK 465 C A 379 REMARK 465 A A 380 REMARK 465 G A 381 REMARK 465 U A 382 REMARK 465 G A 383 REMARK 465 A A 384 REMARK 465 A A 385 REMARK 465 C A 386 REMARK 465 C A 387 REMARK 465 A A 388 REMARK 465 U A 389 REMARK 465 C A 390 REMARK 465 C A 391 REMARK 465 A A 392 REMARK 465 C A 393 REMARK 465 U A 394 REMARK 465 G A 395 REMARK 465 A A 396 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 37 C2 - N1 - C1' ANGL. DEV. = 7.5 DEGREES REMARK 500 C A 60 C2 - N1 - C1' ANGL. DEV. = 7.4 DEGREES REMARK 500 U A 86 C2 - N1 - C1' ANGL. DEV. = 7.4 DEGREES REMARK 500 C A 93 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 C A 93 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 C A 124 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 U A 168 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 U A 168 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 U A 168 C2 - N1 - C1' ANGL. DEV. = 8.3 DEGREES REMARK 500 G A 188 C4 - N9 - C1' ANGL. DEV. = 8.3 DEGREES REMARK 500 C A 223 C6 - N1 - C2 ANGL. DEV. = -2.8 DEGREES REMARK 500 C A 223 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 C A 223 C2 - N1 - C1' ANGL. DEV. = 6.8 DEGREES REMARK 500 U A 258 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 C A 260 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 C A 260 N1 - C2 - O2 ANGL. DEV. = 6.0 DEGREES REMARK 500 C A 260 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 C A 260 C2 - N1 - C1' ANGL. DEV. = 9.6 DEGREES REMARK 500 A A 263 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 U A 273 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 U A 292 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 U A 397 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 U A 397 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 U A 398 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 C A 411 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 C A 411 C2 - N1 - C1' ANGL. DEV. = 7.2 DEGREES REMARK 500 U A 412 C2 - N1 - C1' ANGL. DEV. = 7.9 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 511 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 168 OP2 REMARK 620 2 G A 188 O6 126.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 508 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 208 OP1 REMARK 620 2 A A 304 OP1 109.3 REMARK 620 3 A A 306 OP1 85.2 76.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 256 OP1 REMARK 620 2 U A 273 OP1 115.8 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 84.2 REMARK 620 3 U A 305 OP2 142.7 133.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 507 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 301 OP1 REMARK 620 2 A A 302 OP2 92.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 510 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 307 OP2 REMARK 620 2 A A 308 OP2 99.6 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-24283 RELATED DB: EMDB REMARK 900 EXON-FREE STATE OF THE TETRAHYMENA GROUP I INTRON, SYMMETRY- REMARK 900 EXPANDED MONOMER FROM A SYNTHETIC TRIMERIC CONSTRUCT DBREF 7R6N A 21 414 GB V01416 V01416.1 72 465 SEQADV 7R6N G A 232B GB V01416 INSERTION SEQADV 7R6N G A 232F GB V01416 INSERTION SEQADV 7R6N G A 232G GB V01416 C 288 CONFLICT SEQADV 7R6N C A 379 GB V01416 U 427 CONFLICT SEQADV 7R6N A A 380 GB V01416 U 428 CONFLICT SEQADV 7R6N A GB V01416 A 431 DELETION SEQADV 7R6N A GB V01416 U 432 DELETION SEQADV 7R6N A GB V01416 G 433 DELETION SEQADV 7R6N A GB V01416 C 434 DELETION SEQADV 7R6N C A 386 GB V01416 INSERTION SEQADV 7R6N C A 387 GB V01416 A 438 CONFLICT SEQADV 7R6N A A 388 GB V01416 G 439 CONFLICT SEQADV 7R6N C A 390 GB V01416 A 441 CONFLICT SEQADV 7R6N C A 391 GB V01416 U 442 CONFLICT SEQADV 7R6N C A 393 GB V01416 U 444 CONFLICT SEQRES 1 A 393 U G G A G G G A A A A G U SEQRES 2 A 393 U A U C A G G C A U G C A SEQRES 3 A 393 C C U G G U A G C U A G U SEQRES 4 A 393 C U U U A A A C C A A U A SEQRES 5 A 393 G A U U G C A U C G G U U SEQRES 6 A 393 U A A A A G G C A A G A C SEQRES 7 A 393 C G U C A A A U U G C G G SEQRES 8 A 393 G A A A G G G G U C A A C SEQRES 9 A 393 A G C C G U U C A G U A C SEQRES 10 A 393 C A A G U C U C A G G G G SEQRES 11 A 393 A A A C U U U G A G A U G SEQRES 12 A 393 G C C U U G C A A A G G G SEQRES 13 A 393 U A U G G U A A U A A G C SEQRES 14 A 393 U G A C G G A C A U G G U SEQRES 15 A 393 C C U A A C C A C G C A G SEQRES 16 A 393 C C A A G U C C U A A G U SEQRES 17 A 393 C A A C A G G A U G G U U SEQRES 18 A 393 C U G U U G A U A U G G A SEQRES 19 A 393 U G C A G U U C A C A G A SEQRES 20 A 393 C U A A A U G U C G G U C SEQRES 21 A 393 G G G G A A G A U G U A U SEQRES 22 A 393 U C U U C U C A U A A G A SEQRES 23 A 393 U A U A G U C G G A C C U SEQRES 24 A 393 C U C C U U A A U G G G A SEQRES 25 A 393 G C U A G C G G A U G A A SEQRES 26 A 393 G U G A U G C A A C A C U SEQRES 27 A 393 G G A G C C G C U G G G A SEQRES 28 A 393 A C U A A U C A G U G A A SEQRES 29 A 393 C C A U C C A C U G A U U SEQRES 30 A 393 A G U U U U G G A G U A C SEQRES 31 A 393 U C G 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 HETNAM MG MAGNESIUM ION FORMUL 2 MG 12(MG 2+) LINK O6 G A 164 MG MG A 501 1555 1555 2.09 LINK OP2 U A 168 MG MG A 511 1555 1555 2.99 LINK OP2 A A 171 MG MG A 502 1555 1555 2.06 LINK O6 G A 188 MG MG A 511 1555 1555 2.10 LINK OP1 C A 208 MG MG A 508 1555 1555 2.90 LINK OP1 A A 256 MG MG A 504 1555 1555 2.15 LINK OP1 G A 257 MG MG A 512 1555 1555 2.08 LINK OP1 U A 258 MG MG A 505 1555 1555 2.09 LINK OP2 U A 258 MG MG A 512 1555 1555 2.18 LINK OP1 U A 259 MG MG A 506 1555 1555 2.09 LINK OP1 U A 273 MG MG A 504 1555 1555 2.15 LINK OP1 A A 301 MG MG A 507 1555 1555 2.07 LINK OP2 A A 302 MG MG A 507 1555 1555 2.11 LINK OP1 A A 304 MG MG A 508 1555 1555 2.12 LINK OP1 U A 305 MG MG A 509 1555 1555 2.04 LINK OP2 U A 305 MG MG A 512 1555 1555 2.07 LINK OP1 A A 306 MG MG A 508 1555 1555 2.56 LINK OP2 U A 307 MG MG A 510 1555 1555 2.09 LINK OP2 A A 308 MG MG A 510 1555 1555 2.18 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