HEADER RNA 24-JUL-23 8TJX TITLE TETRAHYMENA RIBOZYME CRYO-EM SCAFFOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (440-MER); COMPND 3 CHAIN: N; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TETRAHYMENA; SOURCE 3 ORGANISM_TAXID: 5890; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-FLUC(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905932 KEYWDS RIBOZYME, SCAFFOLD, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR C.J.LANGEBERG,J.S.KIEFT REVDAT 2 22-NOV-23 8TJX 1 JRNL REVDAT 1 01-NOV-23 8TJX 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. 2.44 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) : 2.440 REMARK 3 NUMBER OF PARTICLES : 570576 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 8TJX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276119. 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 CRYO-EM REMARK 245 SCAFFOLD 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: 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 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 N 1 REMARK 465 G N 2 REMARK 465 G N 3 REMARK 465 U N 4 REMARK 465 C N 5 REMARK 465 A N 6 REMARK 465 G N 7 REMARK 465 G N 8 REMARK 465 C N 9 REMARK 465 C N 10 REMARK 465 G N 11 REMARK 465 G N 12 REMARK 465 C N 13 REMARK 465 U N 14 REMARK 465 G N 15 REMARK 465 G N 179 REMARK 465 A N 180 REMARK 465 G N 181 REMARK 465 G N 182 REMARK 465 C N 385 REMARK 465 A N 386 REMARK 465 G N 387 REMARK 465 U N 388 REMARK 465 C N 389 REMARK 465 G N 390 REMARK 465 C N 391 REMARK 465 C N 392 REMARK 465 A N 393 REMARK 465 C N 394 REMARK 465 A N 395 REMARK 465 G N 396 REMARK 465 U N 397 REMARK 465 U N 398 REMARK 465 U N 399 REMARK 465 G N 400 REMARK 465 G N 401 REMARK 465 G N 402 REMARK 465 G N 403 REMARK 465 A N 404 REMARK 465 A N 405 REMARK 465 A N 406 REMARK 465 G N 407 REMARK 465 C N 408 REMARK 465 U N 409 REMARK 465 G N 410 REMARK 465 U N 411 REMARK 465 G N 412 REMARK 465 C N 413 REMARK 465 A N 414 REMARK 465 G N 415 REMARK 465 C N 416 REMARK 465 C N 417 REMARK 465 U N 418 REMARK 465 G N 419 REMARK 465 U N 420 REMARK 465 A N 421 REMARK 465 A N 422 REMARK 465 C N 423 REMARK 465 C N 424 REMARK 465 C N 425 REMARK 465 C N 426 REMARK 465 C N 427 REMARK 465 C N 428 REMARK 465 C N 429 REMARK 465 A N 430 REMARK 465 C N 431 REMARK 465 G N 432 REMARK 465 A N 433 REMARK 465 A N 434 REMARK 465 A N 435 REMARK 465 G N 436 REMARK 465 U N 437 REMARK 465 G N 438 REMARK 465 G N 439 REMARK 465 G N 440 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 N3 A N 184 N6 A N 186 2.12 REMARK 500 O2' A N 250 O2' G N 252 2.14 REMARK 500 O2' G N 282 O2' U N 358 2.19 REMARK 500 N6 A N 112 O2' G N 127 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 G N 175 N3 - C4 - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 G N 175 C5 - C6 - O6 ANGL. DEV. = 3.6 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 N 511 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 26 OP1 REMARK 620 2 U N 43 OP1 86.6 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 27 OP1 REMARK 620 2 U N 28 OP2 85.3 REMARK 620 3 U N 75 OP2 82.2 114.2 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 C N 32 OP2 REMARK 620 2 A N 363 OP1 103.0 REMARK 620 N 1 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 71 OP1 REMARK 620 2 A N 72 OP2 80.3 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 74 OP1 REMARK 620 2 A N 76 OP1 84.9 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 77 OP2 REMARK 620 2 A N 78 OP2 70.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG N 523 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A N 328 OP2 REMARK 620 2 A N 329 OP2 102.3 REMARK 620 N 1 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 339 OP1 REMARK 620 2 A N 340 OP2 78.4 REMARK 620 3 A N 342 OP2 91.1 76.8 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 340 OP1 REMARK 620 2 A N 342 OP1 91.6 REMARK 620 3 A N 343 OP2 174.8 88.4 REMARK 620 4 G N 344 OP2 87.9 159.0 94.0 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-41313 RELATED DB: EMDB REMARK 900 TETRAHYMENA RIBOZYME CRYO-EM SCAFFOLD DBREF 8TJX N 1 440 PDB 8TJX 8TJX 1 440 SEQRES 1 N 440 G G G U C A G G C C G G C SEQRES 2 N 440 U G A U A U G G A U G C A SEQRES 3 N 440 G U U C A C A G A C U A A SEQRES 4 N 440 A U G U C G G U C G G G G SEQRES 5 N 440 A A G A U G U A U U C U U SEQRES 6 N 440 C U C A U A A G A U A U A SEQRES 7 N 440 G U C G G A C C U C U C C SEQRES 8 N 440 U U A A U G G G A G C U A SEQRES 9 N 440 G C G G A U G A A G U G A SEQRES 10 N 440 U G C A A C A C U G G A G SEQRES 11 N 440 C C G C U G G G A A C U A SEQRES 12 N 440 A U U U G U A U G C G A A SEQRES 13 N 440 A G U A U A U U G A U U A SEQRES 14 N 440 G U U U U G G A G G A G G SEQRES 15 N 440 G A A A A G U U A U C A G SEQRES 16 N 440 G C A U G C A C C U G G U SEQRES 17 N 440 A G C U A G U C U U U A A SEQRES 18 N 440 A C C A A U A G A U U G C SEQRES 19 N 440 A U C G G U U U A A A A G SEQRES 20 N 440 G C A A G A C C G U C A A SEQRES 21 N 440 A U U G C G G G A A A G G SEQRES 22 N 440 G G U C A A C A G C C G U SEQRES 23 N 440 U C A G U A C C A A G U C SEQRES 24 N 440 U C A G G G G A A A C U U SEQRES 25 N 440 U G A G A U G G C C U U G SEQRES 26 N 440 C A A A G G G U A U G G U SEQRES 27 N 440 A A U A A G C U G A C G G SEQRES 28 N 440 A C A U G G U C C U A A C SEQRES 29 N 440 C A C G C A G C C A A G U SEQRES 30 N 440 C C U A A G U C A G U C G SEQRES 31 N 440 C C A C A G U U U G G G G SEQRES 32 N 440 A A A G C U G U G C A G C SEQRES 33 N 440 C U G U A A C C C C C C C SEQRES 34 N 440 A C G A A A G U G G G 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 HETNAM MG MAGNESIUM ION FORMUL 2 MG 27(MG 2+) LINK OP1 A N 26 MG MG N 511 1555 1555 2.17 LINK OP1 G N 27 MG MG N 515 1555 1555 2.22 LINK OP2 U N 28 MG MG N 515 1555 1555 2.13 LINK OP1 U N 28 MG MG N 516 1555 1555 2.02 LINK OP1 U N 29 MG MG N 517 1555 1555 2.27 LINK OP2 C N 32 MG MG N 502 1555 1555 2.25 LINK OP1 U N 43 MG MG N 511 1555 1555 2.25 LINK OP1 A N 71 MG MG N 519 1555 1555 2.05 LINK OP2 A N 72 MG MG N 519 1555 1555 2.32 LINK OP1 A N 74 MG MG N 526 1555 1555 2.09 LINK OP2 U N 75 MG MG N 515 1555 1555 2.01 LINK OP1 U N 75 MG MG N 518 1555 1555 2.46 LINK OP1 A N 76 MG MG N 526 1555 1555 1.98 LINK OP2 U N 77 MG MG N 527 1555 1555 2.41 LINK OP2 A N 78 MG MG N 527 1555 1555 2.32 LINK O6 G N 304 MG MG N 509 1555 1555 2.03 LINK OP2 G N 305 MG MG N 510 1555 1555 2.04 LINK O6 G N 320 MG MG N 507 1555 1555 2.69 LINK OP2 A N 327 MG MG N 522 1555 1555 2.39 LINK OP2 A N 328 MG MG N 523 1555 1555 1.98 LINK OP2 A N 329 MG MG N 523 1555 1555 2.17 LINK OP1 A N 339 MG MG N 505 1555 1555 2.07 LINK OP1 A N 340 MG MG N 504 1555 1555 1.87 LINK OP2 A N 340 MG MG N 505 1555 1555 2.30 LINK OP1 A N 342 MG MG N 504 1555 1555 1.99 LINK OP2 A N 342 MG MG N 505 1555 1555 2.24 LINK OP2 A N 343 MG MG N 504 1555 1555 1.92 LINK OP2 G N 344 MG MG N 504 1555 1555 2.52 LINK O6 G N 344 MG MG N 506 1555 1555 1.97 LINK OP1 A N 363 MG MG N 502 1555 1555 2.25 LINK OP2 A N 370 MG MG N 514 1555 1555 2.88 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