HEADER RNA 22-NOV-24 9KPH TITLE FUSOBACTERIUM NUCLEATUM ARRPOF RNA DIMER CONFORMATION 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (255-MER); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: FUSOBACTERIUM NUCLEATUM; SOURCE 4 ORGANISM_TAXID: 851 KEYWDS CRYOEM, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR Y.F.TU,S.T.SHANG,Z.M.SU REVDAT 3 14-MAY-25 9KPH 1 JRNL REVDAT 2 26-MAR-25 9KPH 1 JRNL REVDAT 1 19-MAR-25 9KPH 0 JRNL AUTH L.WANG,J.XIE,T.GONG,H.WU,Y.TU,X.PENG,S.SHANG,X.JIA,H.MA, JRNL AUTH 2 J.ZOU,S.XU,X.ZHENG,D.ZHANG,Y.LIU,C.ZHANG,Y.LUO,Z.HUANG, JRNL AUTH 3 B.SHAO,B.YING,Y.CHENG,Y.GUO,Y.LAI,D.HUANG,J.LIU,Y.WEI,S.SUN, JRNL AUTH 4 X.ZHOU,Z.SU JRNL TITL CRYO-EM REVEALS MECHANISMS OF NATURAL RNA MULTIVALENCY. JRNL REF SCIENCE V. 388 545 2025 JRNL REFN ESSN 1095-9203 JRNL PMID 40080543 JRNL DOI 10.1126/SCIENCE.ADV3451 REMARK 2 REMARK 2 RESOLUTION. 3.93 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) : 3.930 REMARK 3 NUMBER OF PARTICLES : 230137 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 9KPH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 25-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300054020. 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 : FUSOBACTERIUM NUCLEATUM ARRPOF REMARK 245 RNA DIMER CONFORMATION 2 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 K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 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) : 5700.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 A A 1 REMARK 465 A A 2 REMARK 465 A A 3 REMARK 465 A A 4 REMARK 465 A A 5 REMARK 465 A A 6 REMARK 465 A B 1 REMARK 465 A B 2 REMARK 465 A B 3 REMARK 465 A B 4 REMARK 465 A B 5 REMARK 465 A B 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62487 RELATED DB: EMDB REMARK 900 FUSOBACTERIUM NUCLEATUM ARRPOF RNA DIMER CONFORMATION 2 DBREF 9KPH A 1 255 GB 15419626 AF295336.1 1435 1689 DBREF 9KPH B 1 255 GB 15419626 AF295336.1 1435 1689 SEQRES 1 A 255 A A A A A A C U U A C U A SEQRES 2 A 255 U U A U A U U U G U A A C SEQRES 3 A 255 A A A U U U U A U A C A U SEQRES 4 A 255 A A G A U A A A U U C G U SEQRES 5 A 255 A U G U A U A G C C G U U SEQRES 6 A 255 C U G C U C G A A A C G G SEQRES 7 A 255 U A U A G C A C C G U A A SEQRES 8 A 255 U G G U G G U A U U A U G SEQRES 9 A 255 A A U U G U A G C A A G G SEQRES 10 A 255 U G C G A G G C U A C C U SEQRES 11 A 255 U U A A A A G U C U U G G SEQRES 12 A 255 A G G U G C U C U G A G U SEQRES 13 A 255 G G G U A C U U U A U U A SEQRES 14 A 255 G G G U U A U A A U U U A SEQRES 15 A 255 G A A A G U A A G C U A A SEQRES 16 A 255 A A C U C U A G G U G U U SEQRES 17 A 255 G G G C A G G G C U A A C SEQRES 18 A 255 A C U G G C A U A U A A U SEQRES 19 A 255 U A A A U A U G C G A U A SEQRES 20 A 255 A A G U A A G U SEQRES 1 B 255 A A A A A A C U U A C U A SEQRES 2 B 255 U U A U A U U U G U A A C SEQRES 3 B 255 A A A U U U U A U A C A U SEQRES 4 B 255 A A G A U A A A U U C G U SEQRES 5 B 255 A U G U A U A G C C G U U SEQRES 6 B 255 C U G C U C G A A A C G G SEQRES 7 B 255 U A U A G C A C C G U A A SEQRES 8 B 255 U G G U G G U A U U A U G SEQRES 9 B 255 A A U U G U A G C A A G G SEQRES 10 B 255 U G C G A G G C U A C C U SEQRES 11 B 255 U U A A A A G U C U U G G SEQRES 12 B 255 A G G U G C U C U G A G U SEQRES 13 B 255 G G G U A C U U U A U U A SEQRES 14 B 255 G G G U U A U A A U U U A SEQRES 15 B 255 G A A A G U A A G C U A A SEQRES 16 B 255 A A C U C U A G G U G U U SEQRES 17 B 255 G G G C A G G G C U A A C SEQRES 18 B 255 A C U G G C A U A U A A U SEQRES 19 B 255 U A A A U A U G C G A U A SEQRES 20 B 255 A A G U A A G U CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 5310 U A 255 TER 10620 U B 255 MASTER 118 0 0 0 0 0 0 610618 2 0 40 END