HEADER RNA 07-JAN-25 9LEL TITLE FOCUSED ASYMMETRIC UNIT OF SAG-18RS21-TRNASER GOLLD RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAG-18RS21-TRNASER GOLLD RNA; COMPND 3 CHAIN: J; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS AGALACTIAE 18RS21; SOURCE 3 ORGANISM_TAXID: 342613; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-FLUC(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905932 KEYWDS NATURAL RNA NANOCAGES; LARGE RNA; CRYO-EM; GOLLD RNA, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR K.ZHANG,S.LI REVDAT 2 29-OCT-25 9LEL 1 JRNL REVDAT 1 10-SEP-25 9LEL 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. 2.98 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) : 2.980 REMARK 3 NUMBER OF PARTICLES : 129692 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 9LEL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 11-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1300055501. 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 : FOCUSED ASYMMETRIC UNIT OF SAG REMARK 245 -18RS21-TRNASER GOLLD RNA 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 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) : 4600.00 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: J 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 J -1 REMARK 465 G J 0 REMARK 465 G J 62 REMARK 465 A J 63 REMARK 465 U J 64 REMARK 465 A J 65 REMARK 465 C J 66 REMARK 465 A J 67 REMARK 465 C J 68 REMARK 465 G J 69 REMARK 465 A J 70 REMARK 465 A J 71 REMARK 465 A J 72 REMARK 465 A J 73 REMARK 465 C J 74 REMARK 465 A J 75 REMARK 465 A J 76 REMARK 465 U J 77 REMARK 465 G J 78 REMARK 465 C J 79 REMARK 465 U J 80 REMARK 465 A J 81 REMARK 465 U J 82 REMARK 465 U J 83 REMARK 465 U J 84 REMARK 465 G J 85 REMARK 465 U J 86 REMARK 465 U J 87 REMARK 465 G J 88 REMARK 465 A J 89 REMARK 465 A J 90 REMARK 465 A J 91 REMARK 465 A J 92 REMARK 465 U J 93 REMARK 465 A J 94 REMARK 465 U J 95 REMARK 465 U J 96 REMARK 465 G J 97 REMARK 465 G J 98 REMARK 465 A J 99 REMARK 465 A J 100 REMARK 465 U J 101 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 A J 4 C5 A J 4 C6 -0.066 REMARK 500 A J 4 C5 A J 4 N7 -0.040 REMARK 500 G J 20 C5 G J 20 N7 -0.053 REMARK 500 G J 20 C8 G J 20 N9 -0.050 REMARK 500 G J 37 C4 G J 37 C5 -0.047 REMARK 500 G J 37 C6 G J 37 N1 -0.045 REMARK 500 A J 39 N3 A J 39 C4 -0.043 REMARK 500 A J 39 C5 A J 39 N7 -0.042 REMARK 500 A J 39 N9 A J 39 C4 -0.037 REMARK 500 A J 40 N3 A J 40 C4 -0.048 REMARK 500 A J 40 C4 A J 40 C5 -0.057 REMARK 500 A J 40 C6 A J 40 N1 -0.046 REMARK 500 A J 40 C5 A J 40 N7 -0.041 REMARK 500 A J 40 N9 A J 40 C4 -0.039 REMARK 500 A J 109 C5 A J 109 C6 -0.054 REMARK 500 A J 109 C5 A J 109 N7 -0.044 REMARK 500 A J 109 C8 A J 109 N9 -0.051 REMARK 500 C J 129 N1 C J 129 C6 -0.041 REMARK 500 G J 130 N1 G J 130 C2 -0.049 REMARK 500 G J 130 C4 G J 130 C5 -0.055 REMARK 500 G J 130 C6 G J 130 N1 -0.048 REMARK 500 G J 130 C5 G J 130 N7 -0.040 REMARK 500 A J 131 N3 A J 131 C4 -0.039 REMARK 500 A J 131 C5 A J 131 C6 -0.075 REMARK 500 A J 131 C5 A J 131 N7 -0.051 REMARK 500 A J 131 N9 A J 131 C4 -0.069 REMARK 500 A J 132 C4 A J 132 C5 -0.048 REMARK 500 A J 132 C6 A J 132 N1 -0.046 REMARK 500 A J 132 C5 A J 132 N7 -0.041 REMARK 500 A J 133 C5 A J 133 N7 -0.038 REMARK 500 G J 134 C4 G J 134 C5 -0.043 REMARK 500 G J 134 C5 G J 134 N7 -0.039 REMARK 500 G J 136 C4 G J 136 C5 -0.045 REMARK 500 G J 138 C4 G J 138 C5 -0.048 REMARK 500 U J 140 N1 U J 140 C2 -0.058 REMARK 500 U J 140 C2 U J 140 N3 -0.042 REMARK 500 U J 214 C5 U J 214 C6 -0.054 REMARK 500 A J 215 N1 A J 215 C2 -0.062 REMARK 500 A J 215 C2 A J 215 N3 -0.054 REMARK 500 A J 215 C5 A J 215 C6 -0.094 REMARK 500 A J 215 N9 A J 215 C4 0.065 REMARK 500 G J 218 C5 G J 218 N7 -0.074 REMARK 500 A J 246 C4 A J 246 C5 -0.049 REMARK 500 A J 246 C5 A J 246 N7 -0.041 REMARK 500 G J 247 N1 G J 247 C2 -0.051 REMARK 500 G J 247 C4 G J 247 C5 -0.051 REMARK 500 G J 247 C8 G J 247 N9 -0.044 REMARK 500 U J 248 C4 U J 248 C5 -0.067 REMARK 500 A J 249 N3 A J 249 C4 -0.040 REMARK 500 A J 249 C4 A J 249 C5 -0.058 REMARK 500 REMARK 500 THIS ENTRY HAS 143 BOND DEVIATIONS. 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 J 1 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 G J 2 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 G J 2 N3 - C4 - C5 ANGL. DEV. = 3.7 DEGREES REMARK 500 G J 2 C4 - C5 - C6 ANGL. DEV. = -5.2 DEGREES REMARK 500 G J 2 N3 - C4 - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 G J 2 C6 - C5 - N7 ANGL. DEV. = 5.6 DEGREES REMARK 500 G J 2 N1 - C6 - O6 ANGL. DEV. = -4.9 DEGREES REMARK 500 G J 2 C8 - N9 - C1' ANGL. DEV. = 14.8 DEGREES REMARK 500 G J 2 C4 - N9 - C1' ANGL. DEV. = -16.1 DEGREES REMARK 500 G J 2 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES REMARK 500 A J 4 C4 - C5 - N7 ANGL. DEV. = 4.5 DEGREES REMARK 500 A J 4 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 A J 4 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 A J 4 N9 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 A J 4 C6 - C5 - N7 ANGL. DEV. = -5.7 DEGREES REMARK 500 A J 4 N1 - C6 - N6 ANGL. DEV. = 6.1 DEGREES REMARK 500 A J 4 C5 - C6 - N6 ANGL. DEV. = -6.2 DEGREES REMARK 500 G J 5 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 G J 6 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 U J 16 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 U J 16 N3 - C2 - O2 ANGL. DEV. = -5.7 DEGREES REMARK 500 U J 19 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 U J 22 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 A J 29 O4' - C1' - N9 ANGL. DEV. = 8.8 DEGREES REMARK 500 A J 29 C8 - N9 - C1' ANGL. DEV. = 10.9 DEGREES REMARK 500 A J 40 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 C J 43 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 C J 53 C2 - N1 - C1' ANGL. DEV. = 7.3 DEGREES REMARK 500 U J 59 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 U J 59 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 U J 59 C5 - C4 - O4 ANGL. DEV. = -5.8 DEGREES REMARK 500 G J 60 N3 - C4 - C5 ANGL. DEV. = -4.9 DEGREES REMARK 500 G J 60 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 G J 60 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 G J 60 N3 - C4 - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 G J 60 C6 - C5 - N7 ANGL. DEV. = -4.8 DEGREES REMARK 500 G J 60 C8 - N9 - C1' ANGL. DEV. = -7.8 DEGREES REMARK 500 G J 60 C4 - N9 - C1' ANGL. DEV. = 11.0 DEGREES REMARK 500 C J 61 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 C J 61 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 C J 113 C6 - N1 - C2 ANGL. DEV. = -2.9 DEGREES REMARK 500 C J 113 N1 - C2 - O2 ANGL. DEV. = 5.9 DEGREES REMARK 500 C J 113 N3 - C2 - O2 ANGL. DEV. = -7.0 DEGREES REMARK 500 C J 113 C2 - N1 - C1' ANGL. DEV. = 9.0 DEGREES REMARK 500 C J 118 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 C J 118 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 C J 118 C2 - N1 - C1' ANGL. DEV. = 7.6 DEGREES REMARK 500 C J 120 N1 - C2 - O2 ANGL. DEV. = 5.0 DEGREES REMARK 500 C J 120 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 A J 131 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 203 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-63028 RELATED DB: EMDB REMARK 900 FOCUSED ASYMMETRIC UNIT OF SAG-18RS21-TRNASER GOLLD RNA DBREF 9LEL J -1 474 PDB 9LEL 9LEL -1 474 SEQRES 1 J 476 G G A G U A G G C G U U G SEQRES 2 J 476 C G C A U U U U G U U G C SEQRES 3 J 476 U C A A A A G G C G A C G SEQRES 4 J 476 A A A C G C A A G G C A A SEQRES 5 J 476 U G C A C G U C U G C G A SEQRES 6 J 476 U A C A C G A A A A C A A SEQRES 7 J 476 U G C U A U U U G U U G A SEQRES 8 J 476 A A A U A U U G G A A U A SEQRES 9 J 476 A A G C A A A A G U C A U SEQRES 10 J 476 U G C C C G U C G C A A A SEQRES 11 J 476 C G A A A G U G U G C U U SEQRES 12 J 476 C G G U A G C U A G G C U SEQRES 13 J 476 A C C U G C U A G A G U C SEQRES 14 J 476 U C G C A A G G A U A A U SEQRES 15 J 476 A G C A A A G U C A A A G SEQRES 16 J 476 A G U A A A G C A G C U U SEQRES 17 J 476 A G A C C U U U A G C G G SEQRES 18 J 476 G G U U U U C G U U A A U SEQRES 19 J 476 U G A A A A A U G G C U U SEQRES 20 J 476 A G U A G U U U G C G G C SEQRES 21 J 476 G U A A C G A G U G G U U SEQRES 22 J 476 A G C G A U A C U A A C C SEQRES 23 J 476 G C G C A U G G U U G U U SEQRES 24 J 476 A C U U G A A G G G A U U SEQRES 25 J 476 U G A G U G G A U A A A A SEQRES 26 J 476 A A C U A A A A C A U A A SEQRES 27 J 476 G G U U U U G A A A G A C SEQRES 28 J 476 A A C U G A C U A A A C G SEQRES 29 J 476 U G U A A U C U C A G C G SEQRES 30 J 476 U A U U U G C A U U U G G SEQRES 31 J 476 A A A G U U A C U C A A G SEQRES 32 J 476 U G G U U U A A G A G G A SEQRES 33 J 476 C A G G U U G C U A C C U SEQRES 34 J 476 U G U U A G G C G U G U A SEQRES 35 J 476 A A A G C G U G C G U G G SEQRES 36 J 476 G U U C G A A U C C U A C SEQRES 37 J 476 A C U U U C U A 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 TER 9281 A J 474 MASTER 286 0 0 0 0 0 0 6 9280 1 0 37 END