HEADER RNA 24-JUL-23 8TJV TITLE TETRAHYMENA RIBOZYME SCAFFOLDED FLUORIDE RIBOSWITCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (417-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA PETROPHILA, TETRAHYMENA; SOURCE 3 ORGANISM_TAXID: 93929, 5890; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-FLUC(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905932 KEYWDS RIBOZYME, XRRNA, SCAFFOLD, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR C.J.LANGEBERG,J.S.KIEFT REVDAT 2 22-NOV-23 8TJV 1 JRNL REVDAT 1 01-NOV-23 8TJV 0 JRNL AUTH C.J.LANGEBERG,J.S.KIEFT JRNL TITL A GENERALIZABLE SCAFFOLD-BASED APPROACH FOR STRUCTURE JRNL TITL 2 DETERMINATION OF RNAS BY CRYO-EM. JRNL REF NUCLEIC ACIDS RES. V. 51 E100 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37791881 JRNL DOI 10.1093/NAR/GKAD784 REMARK 2 REMARK 2 RESOLUTION. 2.99 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) : 2.990 REMARK 3 NUMBER OF PARTICLES : 238627 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 8TJV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276110. 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 : TETRAHYMENA RIBOZYME SCAFFOLDED REMARK 245 FLUORIDE RIBOSWITCH 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 5000.00 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: 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 G A 191 REMARK 465 G A 192 REMARK 465 A A 193 REMARK 465 G A 194 REMARK 465 G A 195 REMARK 465 G A 196 REMARK 465 A A 197 REMARK 465 A A 198 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 MG MG A 502 MG MG A 503 1.53 REMARK 500 MG MG A 501 MG MG A 503 1.61 REMARK 500 MG MG A 503 F F A 504 1.70 REMARK 500 OP1 U A 406 F F A 504 1.89 REMARK 500 O6 G A 161 O2 U A 176 2.13 REMARK 500 OP2 U A 7 F F A 504 2.16 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 K A 505 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 5 OP1 REMARK 620 2 A A 6 OP1 92.2 REMARK 620 3 A A 6 O5' 122.3 46.9 REMARK 620 4 A A 6 O3' 165.7 86.9 66.4 REMARK 620 5 U A 7 OP1 112.5 71.3 92.9 53.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 6 OP1 REMARK 620 2 U A 7 OP1 97.5 REMARK 620 3 U A 7 OP2 83.4 61.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 6 OP2 REMARK 620 2 U A 7 OP2 98.8 REMARK 620 3 U A 406 OP1 163.9 86.7 REMARK 620 4 G A 407 OP2 84.5 150.5 98.2 REMARK 620 N 1 2 3 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 6 OP1 REMARK 620 2 A A 6 OP2 70.0 REMARK 620 3 U A 7 OP2 114.0 79.6 REMARK 620 4 U A 406 OP1 165.9 95.9 61.9 REMARK 620 5 G A 407 OP2 102.1 72.8 122.9 72.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 516 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 39 OP1 REMARK 620 2 U A 56 OP1 86.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 520 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 40 OP1 REMARK 620 2 U A 41 OP2 88.7 REMARK 620 3 U A 88 OP2 87.7 128.9 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 C A 45 OP2 REMARK 620 2 A A 376 OP1 144.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 524 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 84 OP1 REMARK 620 2 A A 85 OP2 85.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 531 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 87 OP1 REMARK 620 2 A A 89 OP1 79.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 532 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 90 OP2 REMARK 620 2 A A 91 OP2 81.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 528 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 341 OP2 REMARK 620 2 A A 342 OP2 80.4 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 A A 352 OP1 REMARK 620 2 A A 353 OP2 86.5 REMARK 620 3 A A 355 OP2 97.3 77.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 509 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 353 OP1 REMARK 620 2 A A 355 OP1 86.9 REMARK 620 3 A A 356 OP2 171.1 84.4 REMARK 620 4 G A 357 OP2 100.8 171.0 87.9 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-41312 RELATED DB: EMDB REMARK 900 TETRAHYMENA RIBOZYME SCAFFOLDED FLUORIDE RIBOSWITCH DBREF 8TJV A 1 28 PDB 8TJV 8TJV 1 28 DBREF 8TJV A 29 397 PDB 8TJV 8TJV 29 397 DBREF 8TJV A 398 417 PDB 8TJV 8TJV 398 417 SEQRES 1 A 417 G G G C G A U G A G G C C SEQRES 2 A 417 C G C C C A A A C U G C C SEQRES 3 A 417 C U A U A U G G A U G C A SEQRES 4 A 417 G U U C A C A G A C U A A SEQRES 5 A 417 A U G U C G G U C G G G G SEQRES 6 A 417 A A G A U G U A U U C U U SEQRES 7 A 417 C U C A U A A G A U A U A SEQRES 8 A 417 G U C G G A C C U C U C C SEQRES 9 A 417 U U A A U G G G A G C U A SEQRES 10 A 417 G C G G A U G A A G U G A SEQRES 11 A 417 U G C A A C A C U G G A G SEQRES 12 A 417 C C G C U G G G A A C U A SEQRES 13 A 417 A U U U G U A U G C G A A SEQRES 14 A 417 A G U A U A U U G A U U A SEQRES 15 A 417 G U U U U G G A G G A G G SEQRES 16 A 417 G A A A A G U U A U C A G SEQRES 17 A 417 G C A U G C A C C U G G U SEQRES 18 A 417 A G C U A G U C U U U A A SEQRES 19 A 417 A C C A A U A G A U U G C SEQRES 20 A 417 A U C G G U U U A A A A G SEQRES 21 A 417 G C A A G A C C G U C A A SEQRES 22 A 417 A U U G C G G G A A A G G SEQRES 23 A 417 G G U C A A C A G C C G U SEQRES 24 A 417 U C A G U A C C A A G U C SEQRES 25 A 417 U C A G G G G A A A C U U SEQRES 26 A 417 U G A G A U G G C C U U G SEQRES 27 A 417 C A A A G G G U A U G G U SEQRES 28 A 417 A A U A A G C U G A C G G SEQRES 29 A 417 A C A U G G U C C U A A C SEQRES 30 A 417 C A C G C A G C C A A G U SEQRES 31 A 417 C C U A A G U A G G G C U SEQRES 32 A 417 G A U G G C C U C U A C U SEQRES 33 A 417 G HET MG A 501 1 HET MG A 502 1 HET MG A 503 1 HET F A 504 1 HET K 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 HET MG A 514 1 HET MG A 515 1 HET MG A 516 1 HET MG A 517 1 HET MG A 518 1 HET MG A 519 1 HET MG A 520 1 HET MG A 521 1 HET MG A 522 1 HET MG A 523 1 HET MG A 524 1 HET MG A 525 1 HET MG A 526 1 HET MG A 527 1 HET MG A 528 1 HET MG A 529 1 HET MG A 530 1 HET MG A 531 1 HET MG A 532 1 HETNAM MG MAGNESIUM ION HETNAM F FLUORIDE ION HETNAM K POTASSIUM ION FORMUL 2 MG 30(MG 2+) FORMUL 5 F F 1- FORMUL 6 K K 1+ LINK OP1 G A 5 K K A 505 1555 1555 2.71 LINK OP1 A A 6 MG MG A 501 1555 1555 2.64 LINK OP2 A A 6 MG MG A 502 1555 1555 2.01 LINK OP1 A A 6 MG MG A 503 1555 1555 2.02 LINK OP2 A A 6 MG MG A 503 1555 1555 2.43 LINK OP1 A A 6 K K A 505 1555 1555 3.32 LINK O5' A A 6 K K A 505 1555 1555 2.84 LINK O3' A A 6 K K A 505 1555 1555 2.72 LINK OP1 U A 7 MG MG A 501 1555 1555 2.14 LINK OP2 U A 7 MG MG A 501 1555 1555 2.77 LINK OP2 U A 7 MG MG A 502 1555 1555 1.96 LINK OP2 U A 7 MG MG A 503 1555 1555 2.27 LINK OP1 U A 7 K K A 505 1555 1555 2.83 LINK OP1 A A 39 MG MG A 516 1555 1555 2.35 LINK OP1 G A 40 MG MG A 520 1555 1555 2.27 LINK OP2 U A 41 MG MG A 520 1555 1555 2.01 LINK OP1 U A 41 MG MG A 521 1555 1555 2.23 LINK OP1 U A 42 MG MG A 522 1555 1555 2.21 LINK OP2 C A 45 MG MG A 507 1555 1555 2.16 LINK OP1 U A 56 MG MG A 516 1555 1555 2.48 LINK OP1 A A 84 MG MG A 524 1555 1555 2.12 LINK OP2 A A 85 MG MG A 524 1555 1555 2.30 LINK OP1 A A 87 MG MG A 531 1555 1555 2.17 LINK OP2 U A 88 MG MG A 520 1555 1555 2.01 LINK OP1 U A 88 MG MG A 523 1555 1555 2.24 LINK OP1 A A 89 MG MG A 531 1555 1555 2.08 LINK OP2 U A 90 MG MG A 532 1555 1555 2.24 LINK OP2 A A 91 MG MG A 532 1555 1555 2.07 LINK O6 G A 333 MG MG A 512 1555 1555 2.13 LINK OP2 A A 340 MG MG A 527 1555 1555 2.16 LINK OP2 A A 341 MG MG A 528 1555 1555 2.14 LINK OP2 A A 342 MG MG A 528 1555 1555 2.40 LINK OP1 A A 352 MG MG A 510 1555 1555 1.99 LINK OP1 A A 353 MG MG A 509 1555 1555 1.94 LINK OP2 A A 353 MG MG A 510 1555 1555 2.21 LINK OP1 A A 355 MG MG A 509 1555 1555 1.98 LINK OP2 A A 355 MG MG A 510 1555 1555 2.47 LINK OP2 A A 356 MG MG A 509 1555 1555 1.98 LINK OP2 G A 357 MG MG A 509 1555 1555 2.17 LINK O6 G A 357 MG MG A 511 1555 1555 2.25 LINK OP1 A A 376 MG MG A 507 1555 1555 1.96 LINK OP1 U A 406 MG MG A 502 1555 1555 2.01 LINK OP1 U A 406 MG MG A 503 1555 1555 2.91 LINK OP2 G A 407 MG MG A 502 1555 1555 1.98 LINK OP2 G A 407 MG MG A 503 1555 1555 2.06 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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