HEADER DNA 05-MAY-26 13GQ TITLE 95-BP DOUBLE-STRANDED DNA MINICIRCLE: POLY(A:T) MODEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (95-MER); COMPND 3 CHAIN: i; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE DEPOSITED COORDINATES REPRESENT A SURROGATE COMPND 6 POLY(DA) SEQUENCE INSTEAD OF THE ACTUAL DNA SEQUENCE; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (95-MER); COMPND 9 CHAIN: j; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: THE DEPOSITED COORDINATES REPRESENT A SURROGATE COMPND 12 POLY(DT) SEQUENCE INSTEAD OF THE ACTUAL DNA SEQUENCE. 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 DNA MINICIRCLE, DNA EXPDTA ELECTRON MICROSCOPY AUTHOR Y.LIU,P.Z.QIN REVDAT 1 30-SEP-26 13GQ 0 JRNL AUTH Y.LIU,K.Y.LEE,Y.HE,D.KIM,H.CHANG,V.CHEREZOV,J.FEIGON,P.Z.QIN JRNL TITL CRYO-EM STRUCTURE OF A 95-BASE-PAIR DOUBLE-STRANDED DNA JRNL TITL 2 MINICIRCLE AT 5.3 ANGSTROM RESOLUTION. JRNL REF NUCLEIC ACIDS RES. V. 54 2026 JRNL REFN ESSN 1362-4962 JRNL PMID 42755369 JRNL DOI 10.1093/NAR/GKAG885 REMARK 2 REMARK 2 RESOLUTION. 5.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, 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) : 5.270 REMARK 3 NUMBER OF PARTICLES : 344629 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 13GQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-26. REMARK 100 THE DEPOSITION ID IS D_1000307226. 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 : SYNTHETIC 95-BP DOUBLE-STRANDED REMARK 245 DNA MINICIRCLE; DNA (95-MER); REMARK 245 DNA (95-MER) REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.70 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 : 30028 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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: i, j 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 DA i 1 O3' DA i 95 1.61 REMARK 500 P DT j 1 O3' DT j 95 1.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-77061 RELATED DB: EMDB REMARK 900 95-BP DOUBLE-STRANDED DNA MINICIRCLE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE COORDINATES CONTAIN AN A-T ONLY DNA MODEL BECAUSE THE REMARK 999 MAP DOES NOT SUPPORT SEQUENCE-SPECIFIC ASSIGNMENT. THE ACTUAL DNA REMARK 999 SEQUENCES ARE: REMARK 999 CGATCAAGCCAGTGATAAGTGGAATGCCATGTGGTAAGATCGGTAGTCGTAGGCTCTCAA REMARK 999 CTCGTATTCATCAACTGCATTCTGCCTACGACTAC REMARK 999 AND REMARK 999 GTAGTCGTAGGCAGAATGCAGTTGATGAATACGAGTTGAGAGCCTACGACTACCGATCTT REMARK 999 ACCACATGGCATTCCACTTATCACTGGCTTGATCG. DBREF 13GQ i 1 95 PDB 13GQ 13GQ 1 95 DBREF 13GQ j 1 95 PDB 13GQ 13GQ 1 95 SEQRES 1 i 95 DA DA DA DA DA DA DA DA DA DA DA DA DA SEQRES 2 i 95 DA DA DA DA DA DA DA DA DA DA DA DA DA SEQRES 3 i 95 DA DA DA DA DA DA DA DA DA DA DA DA DA SEQRES 4 i 95 DA DA DA DA DA DA DA DA DA DA DA DA DA SEQRES 5 i 95 DA DA DA DA DA DA DA DA DA DA DA DA DA SEQRES 6 i 95 DA DA DA DA DA DA DA DA DA DA DA DA DA SEQRES 7 i 95 DA DA DA DA DA DA DA DA DA DA DA DA DA SEQRES 8 i 95 DA DA DA DA SEQRES 1 j 95 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 2 j 95 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 3 j 95 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 4 j 95 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 5 j 95 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 6 j 95 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 7 j 95 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 8 j 95 DT DT DT DT 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 121 0 0 0 0 0 0 6 3895 2 0 16 END