HEADER RNA BINDING PROTEIN/RNA 20-FEB-25 9NEP TITLE CRYO-EM STRUCTURE OF RO60/MINIMAL MISFOLDED PRE-5S RRNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN RO60; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MINIMAL MISFOLDED PRE-5S RRNA; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 11 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 12 ORGANISM_TAXID: 8355 KEYWDS RO60 AUTOANTIGEN, RNA CHAPERONE, RNA FOLDING, RNA BINDING PROTEIN, KEYWDS 2 RNA BINDING PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR H.NAM,J.C.DEME,S.M.LEA,S.L.WOLIN REVDAT 1 04-FEB-26 9NEP 0 JRNL AUTH H.NAM,J.C.DEME,S.SIM,M.BOCCITTO,S.M.LEA,S.L.WOLIN JRNL TITL MECHANISTIC INSIGHTS INTO RNA CHAPERONING BY RO60 AND LA JRNL TITL 2 AUTOANTIGENS JRNL REF CELL(CAMBRIDGE,MASS.) 2026 JRNL REFN ISSN 0092-8674 JRNL DOI 10.1016/J.CELL.2025.12.030 REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.700 REMARK 3 NUMBER OF PARTICLES : 190106 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 9NEP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000293223. 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 : RO60/MINIMAL MISFOLDED PRE-5S REMARK 245 RRNA COMPLEX 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 : NULL 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) : 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) : 4980.00 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 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 REMARK 465 SER A 4 REMARK 465 GLU A 215 REMARK 465 LYS A 216 REMARK 465 MET A 537 REMARK 465 ILE A 538 REMARK 465 A B 11 REMARK 465 C B 12 REMARK 465 A B 13 REMARK 465 C B 14 REMARK 465 U B 15 REMARK 465 U B 22 REMARK 465 U B 23 REMARK 465 C B 24 REMARK 465 G B 25 REMARK 465 U B 38 REMARK 465 G B 39 REMARK 465 U B 41 REMARK 465 U B 42 REMARK 465 U B 43 REMARK 465 U B 44 REMARK 465 U B 45 REMARK 465 C B 46 REMARK 465 A B 47 REMARK 465 U B 63 REMARK 465 U B 64 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 OG1 THR A 502 OD1 ASN A 504 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 6 140.93 71.83 REMARK 500 ASN A 175 27.48 47.50 REMARK 500 TYR A 213 35.64 -99.08 REMARK 500 GLU A 300 -8.98 72.47 REMARK 500 ILE A 349 -55.62 66.04 REMARK 500 ASP A 409 59.43 -90.83 REMARK 500 MET A 437 51.85 -92.80 REMARK 500 LYS A 489 -8.43 72.07 REMARK 500 LEU A 535 50.80 -92.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49329 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF RO60/MINIMAL MISFOLDED PRE-5S RRNA COMPLEX DBREF 9NEP A 1 538 PDB 9NEP 9NEP 1 538 DBREF 9NEP B 1 64 PDB 9NEP 9NEP 1 64 SEQRES 1 A 538 MET GLU GLU SER VAL ASN GLN MET GLN PRO LEU ASN GLU SEQRES 2 A 538 LYS GLN ILE ALA ASN SER GLN ASP GLY TYR VAL TRP GLN SEQRES 3 A 538 VAL THR ASP MET ASN ARG LEU HIS ARG PHE LEU CYS PHE SEQRES 4 A 538 GLY SER GLU GLY GLY THR TYR TYR ILE LYS GLU GLN LYS SEQRES 5 A 538 LEU GLY LEU GLU ASN ALA GLU ALA LEU ILE ARG LEU ILE SEQRES 6 A 538 GLU ASP GLY ARG GLY CYS GLU VAL ILE GLN GLU ILE LYS SEQRES 7 A 538 SER PHE SER GLN GLU GLY ARG THR THR LYS GLN GLU PRO SEQRES 8 A 538 MET LEU PHE ALA LEU ALA ILE CYS SER GLN CYS SER ASP SEQRES 9 A 538 ILE SER THR LYS GLN ALA ALA PHE LYS ALA VAL SER GLU SEQRES 10 A 538 VAL CYS ARG ILE PRO THR HIS LEU PHE THR PHE ILE GLN SEQRES 11 A 538 PHE LYS LYS ASP LEU LYS GLU SER MET LYS CYS GLY MET SEQRES 12 A 538 TRP GLY ARG ALA LEU ARG LYS ALA ILE ALA ASP TRP TYR SEQRES 13 A 538 ASN GLU LYS GLY GLY MET ALA LEU ALA LEU ALA VAL THR SEQRES 14 A 538 LYS TYR LYS GLN ARG ASN GLY TRP SER HIS LYS ASP LEU SEQRES 15 A 538 LEU ARG LEU SER HIS LEU LYS PRO SER SER GLU GLY LEU SEQRES 16 A 538 ALA ILE VAL THR LYS TYR ILE THR LYS GLY TRP LYS GLU SEQRES 17 A 538 VAL HIS GLU LEU TYR LYS GLU LYS ALA LEU SER VAL GLU SEQRES 18 A 538 THR GLU LYS LEU LEU LYS TYR LEU GLU ALA VAL GLU LYS SEQRES 19 A 538 VAL LYS ARG THR LYS ASP GLU LEU GLU VAL ILE HIS LEU SEQRES 20 A 538 ILE GLU GLU HIS ARG LEU VAL ARG GLU HIS LEU LEU THR SEQRES 21 A 538 ASN HIS LEU LYS SER LYS GLU VAL TRP LYS ALA LEU LEU SEQRES 22 A 538 GLN GLU MET PRO LEU THR ALA LEU LEU ARG ASN LEU GLY SEQRES 23 A 538 LYS MET THR ALA ASN SER VAL LEU GLU PRO GLY ASN SER SEQRES 24 A 538 GLU VAL SER LEU VAL CYS GLU LYS LEU CYS ASN GLU LYS SEQRES 25 A 538 LEU LEU LYS LYS ALA ARG ILE HIS PRO PHE HIS ILE LEU SEQRES 26 A 538 ILE ALA LEU GLU THR TYR LYS THR GLY HIS GLY LEU ARG SEQRES 27 A 538 GLY LYS LEU LYS TRP ARG PRO ASP GLU GLU ILE LEU LYS SEQRES 28 A 538 ALA LEU ASP ALA ALA PHE TYR LYS THR PHE LYS THR VAL SEQRES 29 A 538 GLU PRO THR GLY LYS ARG PHE LEU LEU ALA VAL ASP VAL SEQRES 30 A 538 SER ALA SER MET ASN GLN ARG VAL LEU GLY SER ILE LEU SEQRES 31 A 538 ASN ALA SER THR VAL ALA ALA ALA MET CYS MET VAL VAL SEQRES 32 A 538 THR ARG THR GLU LYS ASP SER TYR VAL VAL ALA PHE SER SEQRES 33 A 538 ASP GLU MET VAL PRO CYS PRO VAL THR THR ASP MET THR SEQRES 34 A 538 LEU GLN GLN VAL LEU MET ALA MET SER GLN ILE PRO ALA SEQRES 35 A 538 GLY GLY THR ASP CYS SER LEU PRO MET ILE TRP ALA GLN SEQRES 36 A 538 LYS THR ASN THR PRO ALA ASP VAL PHE ILE VAL PHE THR SEQRES 37 A 538 ASP ASN GLU THR PHE ALA GLY GLY VAL HIS PRO ALA ILE SEQRES 38 A 538 ALA LEU ARG GLU TYR ARG LYS LYS MET ASP ILE PRO ALA SEQRES 39 A 538 LYS LEU ILE VAL CYS GLY MET THR SER ASN GLY PHE THR SEQRES 40 A 538 ILE ALA ASP PRO ASP ASP ARG GLY MET LEU ASP MET CYS SEQRES 41 A 538 GLY PHE ASP THR GLY ALA LEU ASP VAL ILE ARG ASN PHE SEQRES 42 A 538 THR LEU ASP MET ILE SEQRES 1 B 64 G C C U A C C C G C A C A SEQRES 2 B 64 C U A C C C U G U U C G C SEQRES 3 B 64 A G G G U C G G C G G U G SEQRES 4 B 64 G U U U U U C A U A G G C SEQRES 5 B 64 U U U U C A A A G U U U HET MG A 601 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG MG 2+ HELIX 1 AA1 THR A 28 GLY A 40 1 13 HELIX 2 AA2 LYS A 49 GLY A 68 1 20 HELIX 3 AA3 ARG A 69 GLU A 83 1 15 HELIX 4 AA4 GLN A 89 GLN A 101 1 13 HELIX 5 AA5 ASP A 104 CYS A 119 1 16 HELIX 6 AA6 ILE A 121 LYS A 140 1 20 HELIX 7 AA7 GLY A 145 GLU A 158 1 14 HELIX 8 AA8 GLY A 160 TYR A 171 1 12 HELIX 9 AA9 HIS A 179 HIS A 187 1 9 HELIX 10 AB1 SER A 192 LYS A 204 1 13 HELIX 11 AB2 GLY A 205 TYR A 213 1 9 HELIX 12 AB3 SER A 219 VAL A 235 1 17 HELIX 13 AB4 GLU A 241 ARG A 252 1 12 HELIX 14 AB5 VAL A 254 LEU A 258 5 5 HELIX 15 AB6 ASN A 261 LYS A 264 5 4 HELIX 16 AB7 SER A 265 GLN A 274 1 10 HELIX 17 AB8 PRO A 277 ASN A 284 1 8 HELIX 18 AB9 ASN A 284 ASN A 291 1 8 HELIX 19 AC1 VAL A 301 CYS A 309 1 9 HELIX 20 AC2 ASN A 310 ALA A 317 1 8 HELIX 21 AC3 HIS A 320 LYS A 332 1 13 HELIX 22 AC4 ASP A 346 THR A 360 1 15 HELIX 23 AC5 SER A 378 GLN A 383 5 6 HELIX 24 AC6 ASN A 391 GLU A 407 1 17 HELIX 25 AC7 THR A 429 MET A 437 1 9 HELIX 26 AC8 SER A 448 ASN A 458 1 11 HELIX 27 AC9 HIS A 478 LYS A 488 1 11 HELIX 28 AD1 GLY A 525 LEU A 535 1 11 SHEET 1 AA1 3 ILE A 16 ALA A 17 0 SHEET 2 AA1 3 TYR A 23 GLN A 26 -1 O VAL A 24 N ILE A 16 SHEET 3 AA1 3 PHE A 506 THR A 507 -1 O THR A 507 N TRP A 25 SHEET 1 AA2 2 GLN A 173 ARG A 174 0 SHEET 2 AA2 2 TRP A 177 SER A 178 -1 O TRP A 177 N ARG A 174 SHEET 1 AA3 6 MET A 419 VAL A 420 0 SHEET 2 AA3 6 SER A 410 PHE A 415 -1 N ALA A 414 O VAL A 420 SHEET 3 AA3 6 PHE A 371 ASP A 376 1 N LEU A 373 O VAL A 413 SHEET 4 AA3 6 VAL A 463 THR A 468 1 O PHE A 467 N ALA A 374 SHEET 5 AA3 6 LYS A 495 GLY A 500 1 O ILE A 497 N PHE A 464 SHEET 6 AA3 6 MET A 516 CYS A 520 1 O MET A 519 N VAL A 498 LINK OH TYR A 47 MG MG A 601 1555 1555 2.74 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 CONECT 353 5114 CONECT 5114 353 MASTER 169 0 1 28 11 0 0 6 5112 2 2 47 END