HEADER RNA 20-DEC-24 9MMG TITLE ROOLEFA-MONOMER-ALONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (410-MER); COMPND 3 CHAIN: c SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS JH1; SOURCE 3 ORGANISM_TAXID: 565648 KEYWDS NATURAL RNA NANOCAGE, CRYO-EM, DRUG DELIVERY, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR X.B.LING,W.W.FANG,J.B.MA,A.A.KOROSTELEV REVDAT 3 10-SEP-25 9MMG 1 JRNL REVDAT 2 25-JUN-25 9MMG 1 JRNL REVDAT 1 04-JUN-25 9MMG 0 JRNL AUTH X.LING,D.GOLOVENKO,J.GAN,J.MA,A.A.KOROSTELEV,W.FANG JRNL TITL CRYO-EM STRUCTURE OF A NATURAL RNA NANOCAGE. JRNL REF NATURE V. 644 1107 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 40523399 JRNL DOI 10.1038/S41586-025-09262-X REMARK 2 REMARK 2 RESOLUTION. 3.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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) : 3.250 REMARK 3 NUMBER OF PARTICLES : 364347 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 9MMG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000291317. 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 : LNCRNA-ROOLEFA-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 : 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 BIOCONTINUUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 5200.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: c 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 U c 220 REMARK 465 A c 221 REMARK 465 G c 222 REMARK 465 A c 223 REMARK 465 C c 224 REMARK 465 G c 225 REMARK 465 C c 226 REMARK 465 U c 227 REMARK 465 C c 228 REMARK 465 C c 229 REMARK 465 A c 230 REMARK 465 G c 231 REMARK 465 U c 232 REMARK 465 G c 233 REMARK 465 G c 234 REMARK 465 A c 235 REMARK 465 G c 236 REMARK 465 A c 237 REMARK 465 A c 238 REMARK 465 U c 239 REMARK 465 A c 240 REMARK 465 A c 241 REMARK 465 U c 242 REMARK 465 C c 243 REMARK 465 U c 244 REMARK 465 A c 245 REMARK 465 A c 246 REMARK 465 G c 247 REMARK 465 U c 248 REMARK 465 U c 249 REMARK 465 A c 250 REMARK 465 G c 251 REMARK 465 G c 252 REMARK 465 U c 253 REMARK 465 G c 254 REMARK 465 G c 255 REMARK 465 A c 256 REMARK 465 A c 257 REMARK 465 G c 258 REMARK 465 U c 259 REMARK 465 G c 260 REMARK 465 U c 261 REMARK 465 G c 262 REMARK 465 A c 263 REMARK 465 G c 264 REMARK 465 A c 265 REMARK 465 A c 266 REMARK 465 G c 267 REMARK 465 C c 268 REMARK 465 U c 269 REMARK 465 U c 270 REMARK 465 G c 271 REMARK 465 G c 272 REMARK 465 C c 273 REMARK 465 A c 274 REMARK 465 G c 275 REMARK 465 A c 276 REMARK 465 C c 277 REMARK 465 C c 278 REMARK 465 U c 279 REMARK 465 U c 280 REMARK 465 A c 281 REMARK 465 G c 282 REMARK 465 A c 283 REMARK 465 A c 284 REMARK 465 A c 285 REMARK 465 A c 286 REMARK 465 C c 287 REMARK 465 U c 288 REMARK 465 C c 289 REMARK 465 U c 303 REMARK 465 G c 304 REMARK 465 C c 305 REMARK 465 A c 306 REMARK 465 G c 307 REMARK 465 A c 308 REMARK 465 G c 309 REMARK 465 A c 310 REMARK 465 A c 311 REMARK 465 A c 312 REMARK 465 C c 313 REMARK 465 U c 314 REMARK 465 G c 315 REMARK 465 A c 316 REMARK 465 G c 317 REMARK 465 A c 318 REMARK 465 A c 319 REMARK 465 A c 320 REMARK 465 U c 321 REMARK 465 C c 322 REMARK 465 A c 323 REMARK 465 G c 324 REMARK 465 U c 325 REMARK 465 G c 326 REMARK 465 U c 327 REMARK 465 U c 328 REMARK 465 U c 329 REMARK 465 A c 330 REMARK 465 C c 382 REMARK 465 A c 383 REMARK 465 A c 384 REMARK 465 A c 385 REMARK 465 U c 386 REMARK 465 A c 387 REMARK 465 A c 388 REMARK 465 U c 389 REMARK 465 A c 390 REMARK 465 A c 391 REMARK 465 A c 392 REMARK 465 A c 393 REMARK 465 A c 394 REMARK 465 U c 395 REMARK 465 G c 396 REMARK 465 G c 397 REMARK 465 G c 398 REMARK 465 A c 399 REMARK 465 C c 400 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 c 52 C6 - N1 - C2 ANGL. DEV. = -2.4 DEGREES REMARK 500 U c 89 N1 - C2 - O2 ANGL. DEV. = 5.0 DEGREES REMARK 500 U c 89 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 U c 89 C2 - N1 - C1' ANGL. DEV. = 9.0 DEGREES REMARK 500 A c 172 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 U c 180 O3' - P - OP1 ANGL. DEV. = 6.9 DEGREES REMARK 500 A c 210 OP1 - P - OP2 ANGL. DEV. = -10.4 DEGREES REMARK 500 G c 353 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 A c 410 OP1 - P - OP2 ANGL. DEV. = -9.7 DEGREES REMARK 500 C c 414 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 G c 416 N3 - C4 - N9 ANGL. DEV. = -4.0 DEGREES REMARK 500 G c 416 C4 - N9 - C1' ANGL. DEV. = -8.0 DEGREES REMARK 500 A c 464 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 U c 496 O5' - P - OP1 ANGL. DEV. = 8.5 DEGREES REMARK 500 U c 496 O5' - P - OP2 ANGL. DEV. = -5.9 DEGREES REMARK 500 C c 529 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 C c 529 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 G c 550 N3 - C4 - C5 ANGL. DEV. = -3.6 DEGREES REMARK 500 G c 550 N3 - C4 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 G c 550 C8 - N9 - C1' ANGL. DEV. = -8.7 DEGREES REMARK 500 G c 550 C4 - N9 - C1' ANGL. DEV. = 10.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-48391 RELATED DB: EMDB REMARK 900 LNCRNA,ROOLEFA-MONOMER DBREF1 9MMG c 1 580 GB CP060804.1 DBREF2 9MMG c 1899451202 2479786 2479207 SEQRES 1 c 580 A A U U G A A A A A U C A SEQRES 2 c 580 A U A G A U U U A A A C C SEQRES 3 c 580 U A G U G A A G A G C A U SEQRES 4 c 580 U U G A A C A A U G U G C SEQRES 5 c 580 U A G G G U A G U A U G G SEQRES 6 c 580 G A U A A G U C G A U A A SEQRES 7 c 580 C U A A A A U G A A U U G SEQRES 8 c 580 G G A U A C U G A U U G A SEQRES 9 c 580 U U U U A G U G G U G G A SEQRES 10 c 580 U U U U A C A G C A A U G SEQRES 11 c 580 U A A A A A G G A C U A A SEQRES 12 c 580 U A G U A A A A G C U A U SEQRES 13 c 580 U A A U C G C A A A G U A SEQRES 14 c 580 C U A C G U G G A A U U U SEQRES 15 c 580 G U G C A G G U G U A A G SEQRES 16 c 580 G U A C G A A A C U U U C SEQRES 17 c 580 G A G U G U G A C A A U A SEQRES 18 c 580 G A C G C U C C A G U G G SEQRES 19 c 580 A G A A U A A U C U A A G SEQRES 20 c 580 U U A G G U G G A A G U G SEQRES 21 c 580 U G A G A A G C U U G G C SEQRES 22 c 580 A G A C C U U A G A A A A SEQRES 23 c 580 C U C A A A C C A A G C G SEQRES 24 c 580 C U U U G C A G A G A A A SEQRES 25 c 580 C U G A G A A A U C A G U SEQRES 26 c 580 G U U U A A C G A A A G A SEQRES 27 c 580 A G U C G G U A C G A G U SEQRES 28 c 580 A G C U U A A U G C A G C SEQRES 29 c 580 A A U U U A U U U A C A G SEQRES 30 c 580 A U G A C A A A U A A U A SEQRES 31 c 580 A A A A U G G G A C U C U SEQRES 32 c 580 U A U G U A A A U G C U G SEQRES 33 c 580 A A U G U U C A A G U G A SEQRES 34 c 580 A A G U U A U U A G C C A SEQRES 35 c 580 G U A G A G C U A G A U C SEQRES 36 c 580 A U A C A G A A A A A G C SEQRES 37 c 580 A A A G A G A A G C U A U SEQRES 38 c 580 U G G G U A G C G C C C G SEQRES 39 c 580 A U A G U U C A G C C U C SEQRES 40 c 580 U U U G G G U A U G U G A SEQRES 41 c 580 C U G A A U A A C A C U G SEQRES 42 c 580 U A A A C A A A G G A A G SEQRES 43 c 580 C A G G A A G A A A A G C SEQRES 44 c 580 C U A A A U C U G U U G A SEQRES 45 c 580 U U U U U G A 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 TER 9928 G c 580 MASTER 263 0 0 0 0 0 0 6 9927 1 0 45 END