HEADER RNA 14-NOV-25 9Z6I TITLE CRYO-EM STRUCTURE OF THE OPEN STATE OF CIL RNA AT 4.3 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (155-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: RNA WAS PRODUCED IN VITRO BY TRANSCRIBING A SYNTHETIC SOURCE 6 DNA CONSTRUCT USING T7 RNA POLYMERASE FROM A LINEARIZED PUC307HP SOURCE 7 PLASMID KEYWDS RNA, RIBOZYME, U1A, RIBONUCLEOPROTEIN (SNRNP) COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR E.V.FILIPPOVA,A.A.KOSSIAKOFF REVDAT 1 27-MAY-26 9Z6I 0 JRNL AUTH E.V.FILIPPOVA,D.KROCHMAL,S.MUKHERJEE,J.A.PICCIRILLI, JRNL AUTH 2 A.A.KOSSIAKOFF JRNL TITL A UNIVERSAL FAB TARGETING A CONSERVED U1A-RNA EPITOPE FOR JRNL TITL 2 RNA STRUCTURE DETERMINATION BY CRYO-EM JRNL REF NUCLEIC ACIDS RES. V. 54 2026 JRNL REFN ESSN 1362-4962 JRNL DOI 10.1093/NAR/GKAG502 REMARK 2 REMARK 2 RESOLUTION. 4.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 3HHN REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 4.320 REMARK 3 NUMBER OF PARTICLES : 59244 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: THE FINAL MAP RESOLUTION WAS ESTIMATED BASED ON THE REMARK 3 GOLD-STANDARD FOURIER SHELL CORRELATION (FSC) USING THE 0.143 REMARK 3 CUT-OFF CRITERION AS IMPLEMENTED IN CRYOSPARC REMARK 4 REMARK 4 9Z6I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-25. REMARK 100 THE DEPOSITION ID IS D_1000302109. 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 : CIL-U1A-FAB1R-PGA1-SFFAB18 REMARK 245 QUATERNARY COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 10696 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 900.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 6000.00 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 U A -7 REMARK 465 U A 20 REMARK 465 A A 21 REMARK 465 A A 22 REMARK 465 U A 23 REMARK 465 C A 24 REMARK 465 A A 25 REMARK 465 A A 26 REMARK 465 A A 27 REMARK 465 G A 28 REMARK 465 A A 57A REMARK 465 A A 57B REMARK 465 C A 57C REMARK 465 C A 57D REMARK 465 C A 57E REMARK 465 A A 57F REMARK 465 U A 57G REMARK 465 U A 57H REMARK 465 G A 57I REMARK 465 C A 57J REMARK 465 A A 57K REMARK 465 C A 57L REMARK 465 U A 57M REMARK 465 C A 57N REMARK 465 C A 57O REMARK 465 G A 57P REMARK 465 G A 57Q REMARK 465 G A 57R REMARK 465 U A 57S REMARK 465 U A 999 REMARK 465 G A 1000 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 O3' U A 57 P A A 1001 1.60 REMARK 500 P A A 67 O3' U A 1018 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-73655 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-73618 RELATED DB: EMDB REMARK 900 RELATED ID: 9YXV RELATED DB: PDB REMARK 900 STRUCTURE OF THE CORE REGION REMARK 900 RELATED ID: EMD-73840 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE OPEN STATE OF CIL RNA REGION AT 4.3 A REMARK 900 RESOLUTION DBREF 9Z6I A -7 1018 PDB 9Z6I 9Z6I -7 1018 SEQRES 1 A 155 U C C A G U A G G A A C A SEQRES 2 A 155 C U A U A C U A C U G G A SEQRES 3 A 155 U A A U C A A A G A C A A SEQRES 4 A 155 A U C U G C C C G A A G G SEQRES 5 A 155 G C U U G A G A A C A U A SEQRES 6 A 155 A C C C A U U G C A C U C SEQRES 7 A 155 C G G G U A U G C A G A G SEQRES 8 A 155 G U G G C A G C C U C C G SEQRES 9 A 155 G U G G G U U A A A A C C SEQRES 10 A 155 C A A C G U U C U C A A C SEQRES 11 A 155 A A U A G U G A C C C A U SEQRES 12 A 155 U G C A C U C C G G G 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 155 0 0 0 0 0 0 6 2644 1 0 12 END