HEADER RNA 14-MAY-22 7XSL TITLE MISFOLDED TETRAHYMENA RIBOZYME CONFORMATION 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (388-MER); COMPND 3 CHAIN: N; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TETRAHYMENA THERMOPHILA; SOURCE 3 ORGANISM_TAXID: 5911; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS MISFOLDED TETRAHYMENA RIBOZYME, TOPOLOGICAL CROSSING, CRYO-EM, KEYWDS 2 REFOLDING, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR S.LI,M.PALO,G.PINTILIE,X.ZHANG,Z.SU,K.KAPPEL,W.CHIU,K.ZHANG,R.DAS REVDAT 2 05-OCT-22 7XSL 1 JRNL REVDAT 1 03-AUG-22 7XSL 0 JRNL AUTH S.LI,M.Z.PALO,G.PINTILIE,X.ZHANG,Z.SU,K.KAPPEL,W.CHIU, JRNL AUTH 2 K.ZHANG,R.DAS JRNL TITL TOPOLOGICAL CROSSING IN THE MISFOLDED TETRAHYMENA RIBOZYME JRNL TITL 2 RESOLVED BY CRYO-EM. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 46119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 36067294 JRNL DOI 10.1073/PNAS.2209146119 REMARK 2 REMARK 2 RESOLUTION. 3.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EMAN2, EPU, CTFFIND, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC 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) : 3.840 REMARK 3 NUMBER OF PARTICLES : 431156 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7XSL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1300029519. 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 : MISFOLDED TETRAHYMENA RIBOZYME REMARK 245 CONFORMATION 2 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 : 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 : 42382 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) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2800.00 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) : 5130.00 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 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 G N 22 O5' 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 O3' G N 331 O2' U N 402 1.94 REMARK 500 O2' U N 182 OP2 G N 188 1.95 REMARK 500 OP1 U N 33 O2' C N 298 2.08 REMARK 500 O2 U N 106 O2' U N 258 2.10 REMARK 500 O2' A N 113 N6 A N 207 2.11 REMARK 500 OP1 C N 208 O2' A N 306 2.15 REMARK 500 O2' U N 56 N7 A N 95 2.16 REMARK 500 N4 C N 109 O2 U N 259 2.18 REMARK 500 N1 A N 79 O6 G N 349 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 C N 99 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 U N 271 N3 - C4 - O4 ANGL. DEV. = -5.5 DEGREES REMARK 500 U N 271 C5 - C4 - O4 ANGL. DEV. = 3.8 DEGREES REMARK 500 A N 306 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33426 RELATED DB: EMDB REMARK 900 MISFOLDED TETRAHYMENA RIBOZYME CONFORMATION 2 DBREF 7XSL N 22 409 GB 10832 X54512.1 7030 7417 SEQRES 1 N 388 G G A G G G A A A A G U U SEQRES 2 N 388 A U C A G G C A U G C A C SEQRES 3 N 388 C U G G U A G C U A G U C SEQRES 4 N 388 U U U A A A C C A A U A G SEQRES 5 N 388 A U U G C A U C G G U U U SEQRES 6 N 388 A A A A G G C A A G A C C SEQRES 7 N 388 G U C A A A U U G C G G G SEQRES 8 N 388 A A A G G G G U C A A C A SEQRES 9 N 388 G C C G U U C A G U A C C SEQRES 10 N 388 A A G U C U C A G G G G A SEQRES 11 N 388 A A C U U U G A G A U G G SEQRES 12 N 388 C C U U G C A A A G G G U SEQRES 13 N 388 A U G G U A A U A A G C U SEQRES 14 N 388 G A C G G A C A U G G U C SEQRES 15 N 388 C U A A C C A C G C A G C SEQRES 16 N 388 C A A G U C C U A A G U C SEQRES 17 N 388 A A C A G A U C U U C U G SEQRES 18 N 388 U U G A U A U G G A U G C SEQRES 19 N 388 A G U U C A C A G A C U A SEQRES 20 N 388 A A U G U C G G U C G G G SEQRES 21 N 388 G A A G A U G U A U U C U SEQRES 22 N 388 U C U C A U A A G A U A U SEQRES 23 N 388 A G U C G G A C C U C U C SEQRES 24 N 388 C U U A A U G G G A G C U SEQRES 25 N 388 A G C G G A U G A A G U G SEQRES 26 N 388 A U G C A A C A C U G G A SEQRES 27 N 388 G C C G C U G G G A A C U SEQRES 28 N 388 A A U U U G U A U G C G A SEQRES 29 N 388 A A G U A U A U U G A U U SEQRES 30 N 388 A G U U U U G G A G U 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