HEADER RNA 06-JUN-23 8T2P TITLE 5TU-T1 - HETERODIMERIC TRIPLET POLYMERASE RIBOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (135-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (152-MER); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS POLYMERASE, RIBOZYME, HETERODIMER, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR E.K.S.MCRAE,E.KRISTOFFERSEN,I.GALLEGO,K.HANSEN,P.HOLLIGER, AUTHOR 2 E.S.ANDERSEN REVDAT 1 24-JAN-24 8T2P 0 JRNL AUTH E.K.S.MCRAE,C.J.K.WAN,E.L.KRISTOFFERSEN,K.HANSEN,E.GIANNI, JRNL AUTH 2 I.GALLEGO,J.F.CURRAN,J.ATTWATER,P.HOLLIGER,E.S.ANDERSEN JRNL TITL CRYO-EM STRUCTURE AND FUNCTIONAL LANDSCAPE OF AN RNA JRNL TITL 2 POLYMERASE RIBOZYME. JRNL REF PROC.NATL.ACAD.SCI.USA V. 121 32121 2024 JRNL REFN ESSN 1091-6490 JRNL PMID 38207080 JRNL DOI 10.1073/PNAS.2313332121 REMARK 2 REMARK 2 RESOLUTION. 5.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CRYOSPARC, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, ROSETTA, ISOLDE, REMARK 3 UCSF CHIMERAX, COOT, PHENIX, AMBER REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : MODEL WAS INITIALLY BUILT USING DRRAFTER AND REMARK 3 THEN IMPROVED USING ISOLDE IN CHIMERAX, COOT, PHENIX RSR AND REMARK 3 QRNAS. 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) : 5.000 REMARK 3 NUMBER OF PARTICLES : 86000 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 8T2P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000274939. 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 : 5TU-T1 - TRIPLET POLYMERASE REMARK 245 RIBOZYME REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 REMARK 245 SAMPLE SUPPORT DETAILS : 15MA ON A GLOQUBE PLUS REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : HETERODIMERIC COMPLEX OF TWO REMARK 245 RNA STRANDS COMPRISING A FUNCTIONAL TRIPLET POLYMERASE RIBOZYME. 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) : 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) : 6000.00 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: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 G A 1 P G A 1 OP3 -0.188 REMARK 500 G A 10 N7 G A 10 C8 -0.037 REMARK 500 G A 61 N7 G A 61 C8 -0.041 REMARK 500 C A 62 N3 C A 62 C4 -0.044 REMARK 500 A A 74 C6 A A 74 N1 -0.049 REMARK 500 A A 74 N7 A A 74 C8 -0.044 REMARK 500 A A 75 C6 A A 75 N1 -0.054 REMARK 500 A A 75 N7 A A 75 C8 -0.042 REMARK 500 C A 82 N3 C A 82 C4 -0.045 REMARK 500 G A 93 N7 G A 93 C8 -0.036 REMARK 500 C A 94 N3 C A 94 C4 -0.045 REMARK 500 G A 113 N7 G A 113 C8 -0.044 REMARK 500 G B 1 P G B 1 OP3 -0.125 REMARK 500 A B 19 C6 A B 19 N1 -0.050 REMARK 500 A B 23 C6 A B 23 N1 -0.051 REMARK 500 A B 24 C6 A B 24 N1 -0.047 REMARK 500 A B 89 C6 A B 89 N1 -0.049 REMARK 500 A B 89 N7 A B 89 C8 -0.045 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 A A 74 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A 135 C5' - C4' - O4' ANGL. DEV. = 10.6 DEGREES REMARK 500 U B 148 N3 - C4 - C5 ANGL. DEV. = -3.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-40984 RELATED DB: EMDB REMARK 900 5TU-T1 - HETERODIMERIC TRIPLET POLYMERASE RIBOZYME DBREF 8T2P A 1 135 PDB 8T2P 8T2P 1 135 DBREF 8T2P B 1 152 PDB 8T2P 8T2P 1 152 SEQRES 1 A 135 G A C C A A U C U G C C C SEQRES 2 A 135 U C A G A G C U C G A G A SEQRES 3 A 135 A C A U C U U C G G A U G SEQRES 4 A 135 C A G A G G A G G C A G G SEQRES 5 A 135 C U U C G G U G G C G C G SEQRES 6 A 135 A U A G C G C C A A C G U SEQRES 7 A 135 C C U C A A C C U C C A A SEQRES 8 A 135 U G C A U C C C A C C A C SEQRES 9 A 135 A U G A U G A U G C C U G SEQRES 10 A 135 A A G A G C C U U G G U U SEQRES 11 A 135 U U U U G SEQRES 1 B 152 G G A U C U U C U C G A U SEQRES 2 B 152 C U A A C A A A A A A G A SEQRES 3 B 152 C A A A U C U G C C A C A SEQRES 4 B 152 A A G C U U G A G A G C A SEQRES 5 B 152 U C U U C G G A U G C A G SEQRES 6 B 152 A G G C G G C A G C C U U SEQRES 7 B 152 C G G U G G C G C G A U A SEQRES 8 B 152 G C G C C A A C G U U C U SEQRES 9 B 152 C A A C U A U G A C A C G SEQRES 10 B 152 C A A A A C G C G U G C U SEQRES 11 B 152 C C G U U G A A U G G A G SEQRES 12 B 152 U U U A U C A U G 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