HEADER RNA 07-JAN-25 9LEC TITLE FOCUSED ASYMMETRIC UNIT OF SAG-18RS21 GOLLD RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAG-18RS21 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 EXPDTA ELECTRON MICROSCOPY AUTHOR K.ZHANG,S.LI REVDAT 2 29-OCT-25 9LEC 1 JRNL REVDAT 1 10-SEP-25 9LEC 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. 2.51 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) : 2.510 REMARK 3 NUMBER OF PARTICLES : 357191 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 9LEC 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_1300055485. 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 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: 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 O4 U J 141 O2' U J 245 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 109 C5 A J 109 N7 -0.039 REMARK 500 A J 131 C5 A J 131 N7 -0.040 REMARK 500 A J 131 N9 A J 131 C4 -0.049 REMARK 500 A J 215 C4 A J 215 C5 -0.043 REMARK 500 G J 218 C5 G J 218 N7 -0.041 REMARK 500 A J 329 C5 A J 329 N7 -0.044 REMARK 500 G J 347 N3 G J 347 C4 -0.044 REMARK 500 G J 347 N9 G J 347 C4 -0.049 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 U J 16 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 U J 17 O5' - P - OP2 ANGL. DEV. = -5.9 DEGREES REMARK 500 U J 17 C2 - N1 - C1' ANGL. DEV. = 8.4 DEGREES REMARK 500 U J 19 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 A J 29 O3' - P - OP1 ANGL. DEV. = 9.9 DEGREES REMARK 500 C J 41 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 A J 49 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 A J 49 C5 - N7 - C8 ANGL. DEV. = -3.5 DEGREES REMARK 500 A J 49 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 G J 56 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 A J 109 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 A J 109 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 A J 109 N7 - C8 - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 A J 109 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 C J 113 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES REMARK 500 C J 113 N1 - C2 - O2 ANGL. DEV. = 5.0 DEGREES REMARK 500 C J 113 N3 - C2 - O2 ANGL. DEV. = -6.0 DEGREES REMARK 500 C J 113 C2 - N1 - C1' ANGL. DEV. = 7.5 DEGREES REMARK 500 C J 120 N1 - C2 - O2 ANGL. DEV. = 4.7 DEGREES REMARK 500 C J 120 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 C J 125 C2 - N1 - C1' ANGL. DEV. = 6.6 DEGREES REMARK 500 A J 131 C4 - C5 - N7 ANGL. DEV. = 3.1 DEGREES REMARK 500 A J 131 C5 - N7 - C8 ANGL. DEV. = -4.2 DEGREES REMARK 500 A J 131 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 A J 131 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 U J 141 N1 - C2 - O2 ANGL. DEV. = 5.3 DEGREES REMARK 500 C J 142 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 G J 151 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 C J 171 C6 - N1 - C2 ANGL. DEV. = -2.4 DEGREES REMARK 500 A J 185 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 C J 211 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 G J 218 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 G J 218 C6 - C5 - N7 ANGL. DEV. = -5.0 DEGREES REMARK 500 G J 218 N1 - C6 - O6 ANGL. DEV. = 3.9 DEGREES REMARK 500 A J 237 C2 - N3 - C4 ANGL. DEV. = 5.3 DEGREES REMARK 500 A J 237 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 U J 248 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 C J 258 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 A J 261 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 A J 262 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 A J 262 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 C J 263 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 C J 263 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 C J 263 C6 - N1 - C1' ANGL. DEV. = -8.5 DEGREES REMARK 500 C J 263 C2 - N1 - C1' ANGL. DEV. = 9.8 DEGREES REMARK 500 G J 268 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 G J 268 C4 - C5 - N7 ANGL. DEV. = 3.3 DEGREES REMARK 500 G J 268 C5 - N7 - C8 ANGL. DEV. = -4.5 DEGREES REMARK 500 G J 268 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 G J 268 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 96 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-63022 RELATED DB: EMDB REMARK 900 FOCUSED ASYMMETRIC UNIT OF SAG-18RS21 GOLLD RNA DBREF 9LEC J -1 376 PDB 9LEC 9LEC -1 376 SEQRES 1 J 378 G G A G U A G G C G U U G SEQRES 2 J 378 C G C A U U U U G U U G C SEQRES 3 J 378 U C A A A A G G C G A C G SEQRES 4 J 378 A A A C G C A A G G C A A SEQRES 5 J 378 U G C A C G U C U G C G A SEQRES 6 J 378 U A C A C G A A A A C A A SEQRES 7 J 378 U G C U A U U U G U U G A SEQRES 8 J 378 A A A U A U U G G A A U A SEQRES 9 J 378 A A G C A A A A G U C A U SEQRES 10 J 378 U G C C C G U C G C A A A SEQRES 11 J 378 C G A A A G U G U G C U U SEQRES 12 J 378 C G G U A G C U A G G C U SEQRES 13 J 378 A C C U G C U A G A G U C SEQRES 14 J 378 U C G C A A G G A U A A U SEQRES 15 J 378 A G C A A A G U C A A A G SEQRES 16 J 378 A G U A A A G C A G C U U SEQRES 17 J 378 A G A C C U U U A G C G G SEQRES 18 J 378 G G U U U U C G U U A A U SEQRES 19 J 378 U G A A A A A U G G C U U SEQRES 20 J 378 A G U A G U U U G C G G C SEQRES 21 J 378 G U A A C G A G U G G U U SEQRES 22 J 378 A G C G A U A C U A A C C SEQRES 23 J 378 G C G C A U G G U U G U U SEQRES 24 J 378 A C U U G A A G G G A U U SEQRES 25 J 378 U G A G U G G A U A A A A SEQRES 26 J 378 A A C U A A A A C A U A A SEQRES 27 J 378 G G U U U U G A A A G A C SEQRES 28 J 378 A A C U G A C U A A A C G SEQRES 29 J 378 U G U A A U C U C A G C G SEQRES 30 J 378 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 TER 7195 U J 376 MASTER 252 0 0 0 0 0 0 6 7194 1 0 30 END