HEADER RNA 28-FEB-24 8S6W TITLE SMALL CIRCULAR RNA DIMER - CLASS 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (36-MER); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (36-MER); COMPND 7 CHAIN: C, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS SMALL RNA CIRCLES, DIMER, RNA CROSSOVER, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR E.K.MCRAE,E.L.KRISTOFFERSEN,P.HOLLIGER,E.S.ANDERSEN REVDAT 1 29-JAN-25 8S6W 0 JRNL AUTH E.L.KRISTOFFERSEN,E.K.MCRAE,N.R.SORENSEN,P.HOLLIGER, JRNL AUTH 2 E.S.ANDERSEN JRNL TITL SMALL CIRCULAR RNA DIMER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 5.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC 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) : 5.300 REMARK 3 NUMBER OF PARTICLES : 116769 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 8S6W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292136925. 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 : DIMER COMPOSED OF TWO SMALL REMARK 245 CIRCULAR RNAS AND TWO REMARK 245 COMPLIMENTARY RNAS 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 : DIMER PREPARED BY ANNEALING REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 6820 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) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 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 : 130000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 P A D 1 O3' C D 36 1.60 REMARK 500 P A C 1 O3' C C 36 1.60 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 A 1 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 A A 4 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 A A 4 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 5 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 A A 7 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 7 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 A A 8 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 8 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 A A 9 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 9 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 C A 11 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 C A 11 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 G A 12 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 A A 13 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 13 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 A A 14 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 14 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 A A 16 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 A A 16 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 A A 16 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 A A 17 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 A A 17 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 A A 19 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 A A 19 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 19 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 A A 22 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 A A 22 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 A A 22 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 22 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 A A 23 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 23 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 A A 25 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 A A 25 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 25 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 A A 26 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 A A 26 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 C A 27 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 C A 27 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 C A 29 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 C A 29 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 A A 31 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 31 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES REMARK 500 A A 32 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 32 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 A A 34 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 A A 34 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 A A 35 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 159 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 G A 21 0.06 SIDE CHAIN REMARK 500 C A 27 0.07 SIDE CHAIN REMARK 500 A B 19 0.05 SIDE CHAIN REMARK 500 A B 22 0.09 SIDE CHAIN REMARK 500 C B 27 0.07 SIDE CHAIN REMARK 500 A C 1 0.10 SIDE CHAIN REMARK 500 C C 6 0.07 SIDE CHAIN REMARK 500 A C 11 0.06 SIDE CHAIN REMARK 500 A C 20 0.07 SIDE CHAIN REMARK 500 U C 22 0.09 SIDE CHAIN REMARK 500 U C 25 0.11 SIDE CHAIN REMARK 500 G C 28 0.07 SIDE CHAIN REMARK 500 U C 35 0.09 SIDE CHAIN REMARK 500 A D 1 0.09 SIDE CHAIN REMARK 500 A D 11 0.06 SIDE CHAIN REMARK 500 A D 20 0.07 SIDE CHAIN REMARK 500 U D 23 0.08 SIDE CHAIN REMARK 500 U D 25 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-19759 RELATED DB: EMDB REMARK 900 SMALL CIRCULAR RNA DIMER DBREF 8S6W A 1 36 PDB 8S6W 8S6W 1 36 DBREF 8S6W B 1 36 PDB 8S6W 8S6W 1 36 DBREF 8S6W C 1 36 PDB 8S6W 8S6W 1 36 DBREF 8S6W D 1 36 PDB 8S6W 8S6W 1 36 SEQRES 1 A 36 U G G A A G A A A U C G A SEQRES 2 A 36 A G A A G A U G A A G A A SEQRES 3 A 36 C G C G A A G A A C SEQRES 1 B 36 U G G A A G A A A U C G A SEQRES 2 B 36 A G A A G A U G A A G A A SEQRES 3 B 36 C G C G A A G A A C SEQRES 1 C 36 A U C U U C U U C G A U U SEQRES 2 C 36 U C U U C C A G U U C U U SEQRES 3 C 36 C G C G U U C U U C SEQRES 1 D 36 A U C U U C U U C G A U U SEQRES 2 D 36 U C U U C C A G U U C U U SEQRES 3 D 36 C G C G U U C U U C 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