HEADER RNA 10-MAR-25 9M79 TITLE FOCUSED ASYMMETRIC UNIT OF UCC118 ROOL RNA AT 1.96-ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UCC118 ROOL RNA MONOMER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LIGILACTOBACILLUS SALIVARIUS UCC118; SOURCE 3 ORGANISM_TAXID: 362948; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-FLUC(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905932 KEYWDS NATURAL RNA-ONLY MULTIMER, CRYO-EM, OLIGOMER, ROOL., RNA EXPDTA ELECTRON MICROSCOPY AUTHOR S.ZHANG,R.YI,L.AN,S.LI,K.ZHANG REVDAT 2 29-OCT-25 9M79 1 JRNL REVDAT 1 10-SEP-25 9M79 0 JRNL AUTH S.ZHANG,R.YI,L.AN,J.LIU,X.YAO,S.LI,K.ZHANG JRNL TITL STRUCTURAL INSIGHTS INTO HIGHER-ORDER NATURAL RNA-ONLY JRNL TITL 2 MULTIMERS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 32 2012 2025 JRNL REFN ESSN 1545-9985 JRNL PMID 40770114 JRNL DOI 10.1038/S41594-025-01650-1 REMARK 2 REMARK 2 RESOLUTION. 1.96 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) : 1.960 REMARK 3 NUMBER OF PARTICLES : 568717 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 9M79 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 11-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057309. 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 : UCC118 ROOL RNA MONOMER 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 : 36386 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1300.00 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) : 3000.00 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 1 REMARK 465 G A 2 REMARK 465 U A 342 REMARK 465 U A 343 REMARK 465 A A 344 REMARK 465 C A 345 REMARK 465 A A 346 REMARK 465 U A 347 REMARK 465 U A 348 REMARK 465 A A 349 REMARK 465 A A 350 REMARK 465 C A 351 REMARK 465 U A 352 REMARK 465 G A 353 REMARK 465 G A 354 REMARK 465 A A 355 REMARK 465 A A 356 REMARK 465 C A 357 REMARK 465 A A 358 REMARK 465 U A 359 REMARK 465 U A 360 REMARK 465 G A 361 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 31 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 C A 31 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 A A 72 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 C A 104 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 U A 178 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 U A 178 N3 - C2 - O2 ANGL. DEV. = -6.2 DEGREES REMARK 500 U A 178 C2 - N1 - C1' ANGL. DEV. = 8.4 DEGREES REMARK 500 C A 203 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 C A 203 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 C A 203 C2 - N1 - C1' ANGL. DEV. = 7.2 DEGREES REMARK 500 C A 210 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES REMARK 500 C A 210 N1 - C2 - O2 ANGL. DEV. = 4.8 DEGREES REMARK 500 C A 210 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 C A 210 C2 - N1 - C1' ANGL. DEV. = 9.6 DEGREES REMARK 500 U A 258 N1 - C2 - O2 ANGL. DEV. = 5.7 DEGREES REMARK 500 U A 258 N3 - C2 - O2 ANGL. DEV. = -6.0 DEGREES REMARK 500 U A 258 C2 - N1 - C1' ANGL. DEV. = 9.0 DEGREES REMARK 500 A A 304 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 A A 304 C3' - O3' - P ANGL. DEV. = 9.4 DEGREES REMARK 500 G A 387 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 U A 396 N1 - C2 - O2 ANGL. DEV. = 5.1 DEGREES REMARK 500 U A 396 N3 - C2 - O2 ANGL. DEV. = -6.8 DEGREES REMARK 500 U A 396 C2 - N1 - C1' ANGL. DEV. = 8.8 DEGREES REMARK 500 U A 473 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 U A 473 N1 - C2 - O2 ANGL. DEV. = 6.5 DEGREES REMARK 500 U A 473 N3 - C2 - O2 ANGL. DEV. = -6.5 DEGREES REMARK 500 U A 473 C2 - N1 - C1' ANGL. DEV. = 9.0 DEGREES REMARK 500 C A 485 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 C A 485 N1 - C2 - O2 ANGL. DEV. = 4.6 DEGREES REMARK 500 C A 485 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 C A 485 C2 - N1 - C1' ANGL. DEV. = 7.5 DEGREES REMARK 500 C A 504 C6 - N1 - C2 ANGL. DEV. = -3.1 DEGREES REMARK 500 C A 504 N1 - C2 - O2 ANGL. DEV. = 5.2 DEGREES REMARK 500 C A 504 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 C A 504 C2 - N1 - C1' ANGL. DEV. = 9.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-63679 RELATED DB: EMDB REMARK 900 FOCUSED ASYMMETRIC UNIT OF UCC118 ROOL RNA AT 1.96-ANGSTROM REMARK 900 RESOLUTION DBREF1 9M79 A 1 520 GB CP000234.1 DBREF2 9M79 A 90821902 178792 178273 SEQADV 9M79 G A 2 GB 90821902 U 78791 CONFLICT SEQRES 1 A 520 G G A C C G A U G A A G C SEQRES 2 A 520 U A G U G G A U G A G G U SEQRES 3 A 520 G U G A C A A G C C G C C SEQRES 4 A 520 U A G C C A U A C G A C U SEQRES 5 A 520 C U U A A U A A C U A C U SEQRES 6 A 520 A U G A C G A A A U A U A SEQRES 7 A 520 C G G A U A C G U U U A U SEQRES 8 A 520 U U U U U C U A A U U U C SEQRES 9 A 520 C A C U U G G G U A G U A SEQRES 10 A 520 C U A A U U G G G A G C A SEQRES 11 A 520 A C G A A A A A A G U U G SEQRES 12 A 520 U G U A G A G A G A A G C SEQRES 13 A 520 A A G G G G A C U C A U A SEQRES 14 A 520 U C U G A A A C U A A G A SEQRES 15 A 520 C A C U U G C C G U C A G SEQRES 16 A 520 G G A U U C G C A A U A U SEQRES 17 A 520 G C C A U C U U C A G U U SEQRES 18 A 520 A A U U A A G G C U G A U SEQRES 19 A 520 U A C C U U A G G A A C C SEQRES 20 A 520 A A A A G A A G A A U A U SEQRES 21 A 520 C A A C U A A G A A U U C SEQRES 22 A 520 G U G U C G U G A A G U U SEQRES 23 A 520 G U G G U G A C G C A A C SEQRES 24 A 520 U A U A A C U G A C G A G SEQRES 25 A 520 U A A G G U U U G A G U A SEQRES 26 A 520 G C C A A A A U C G A C A SEQRES 27 A 520 A U C U U A C A U U A A C SEQRES 28 A 520 U G G A A C A U U G C A C SEQRES 29 A 520 A U G U U U G G U G A A A SEQRES 30 A 520 A U U G G A U A G G A A A SEQRES 31 A 520 A G A U C U A U G C C C U SEQRES 32 A 520 G A A C U U G A A A U G C SEQRES 33 A 520 G G A C U A G G U C G U G SEQRES 34 A 520 G A A G U U G C U A G C C SEQRES 35 A 520 A U G A U G U G C U A G U SEQRES 36 A 520 C U G A U U C A G U A G U SEQRES 37 A 520 C U A A U A A G U C C A G SEQRES 38 A 520 A U A C A A G A G U A U C SEQRES 39 A 520 C C A C G U A A G C C A A SEQRES 40 A 520 U A C G C G U C G G U U 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 MASTER 179 0 0 0 0 0 0 610633 1 0 40 END