HEADER DNA 27-JUL-22 8DUT TITLE DUPLEX-G-QUADRUPLEX-DUPLEX (DGD) CLASS_1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUPLEX-G-QUADRUPLEX-DUPLEX (46-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DUPLEX-G-QUADRUPLEX-DUPLEX (46-MER); COMPND 7 CHAIN: B; 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 G-QUADRUPLEX, PROMOTER, DUPLEX, DNA EXPDTA ELECTRON MICROSCOPY AUTHOR R.C.MONSEN,E.Y.D.CHUA,J.B.HOPKINS,J.B.CHAIRES,J.O.TRENT REVDAT 2 15-MAR-23 8DUT 1 JRNL REVDAT 1 08-FEB-23 8DUT 0 JRNL AUTH R.C.MONSEN,E.Y.D.CHUA,J.B.HOPKINS,J.B.CHAIRES,J.O.TRENT JRNL TITL STRUCTURE OF A 28.5 KDA DUPLEX-EMBEDDED G-QUADRUPLEX SYSTEM JRNL TITL 2 RESOLVED TO 7.4 ANGSTROM RESOLUTION WITH CRYO-EM. JRNL REF NUCLEIC ACIDS RES. V. 51 1943 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 36715343 JRNL DOI 10.1093/NAR/GKAD014 REMARK 2 REMARK 2 RESOLUTION. 7.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, LEGINON, 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 : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : MAP CORRELATION REMARK 3 OVERALL ANISOTROPIC B VALUE : 557.200 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) : 7.400 REMARK 3 NUMBER OF PARTICLES : 110105 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 8DUT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000267408. 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 : 2D ARRAY REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : SYNTHETIC DUPLEX-G-QUADRUPLEX REMARK 245 -DUPLEX CONSTRUCT MIMICKING A REMARK 245 PROMOTER G4 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.50 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.20 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 12175 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) : 2700.00 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) : 6854.00 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DG A 1 C5 DG A 1 N7 -0.047 REMARK 500 DG A 1 O3' DC A 2 P 0.129 REMARK 500 DC A 2 P DC A 2 O5' 0.135 REMARK 500 DC A 2 C2 DC A 2 N3 0.059 REMARK 500 DC A 2 N3 DC A 2 C4 -0.051 REMARK 500 DC A 2 O3' DG A 3 P 0.126 REMARK 500 DG A 3 P DG A 3 O5' 0.134 REMARK 500 DG A 3 C5 DG A 3 N7 -0.046 REMARK 500 DG A 3 O3' DT A 4 P 0.126 REMARK 500 DT A 4 P DT A 4 O5' 0.132 REMARK 500 DT A 4 O3' DG A 5 P 0.123 REMARK 500 DG A 5 P DG A 5 O5' 0.133 REMARK 500 DG A 5 C5 DG A 5 N7 -0.045 REMARK 500 DG A 5 O3' DC A 6 P 0.126 REMARK 500 DC A 6 P DC A 6 O5' 0.135 REMARK 500 DC A 6 C2 DC A 6 N3 0.058 REMARK 500 DC A 6 N3 DC A 6 C4 -0.051 REMARK 500 DC A 6 O3' DC A 7 P 0.126 REMARK 500 DC A 7 P DC A 7 O5' 0.129 REMARK 500 DC A 7 C2 DC A 7 N3 0.056 REMARK 500 DC A 7 N3 DC A 7 C4 -0.050 REMARK 500 DC A 7 O3' DG A 8 P 0.125 REMARK 500 DG A 8 P DG A 8 O5' 0.133 REMARK 500 DG A 8 C5 DG A 8 N7 -0.045 REMARK 500 DG A 8 O3' DC A 9 P 0.116 REMARK 500 DC A 9 P DC A 9 O5' 0.133 REMARK 500 DC A 9 C2 DC A 9 N3 0.057 REMARK 500 DC A 9 N3 DC A 9 C4 -0.051 REMARK 500 DC A 9 O3' DA A 10 P 0.124 REMARK 500 DA A 10 P DA A 10 O5' 0.132 REMARK 500 DA A 10 C5 DA A 10 N7 -0.047 REMARK 500 DA A 10 C6 DA A 10 N6 0.056 REMARK 500 DA A 10 O3' DT A 11 P 0.128 REMARK 500 DT A 11 P DT A 11 O5' 0.135 REMARK 500 DT A 11 O3' DT A 12 P 0.127 REMARK 500 DT A 12 P DT A 12 O5' 0.131 REMARK 500 DT A 12 O3' DA A 13 P 0.122 REMARK 500 DA A 13 P DA A 13 O5' 0.132 REMARK 500 DA A 13 C5 DA A 13 N7 -0.048 REMARK 500 DA A 13 C6 DA A 13 N6 0.057 REMARK 500 DA A 13 O3' DA A 14 P 0.130 REMARK 500 DA A 14 P DA A 14 O5' 0.136 REMARK 500 DA A 14 C5 DA A 14 N7 -0.046 REMARK 500 DA A 14 C6 DA A 14 N6 0.057 REMARK 500 DA A 14 O3' DT A 15 P 0.134 REMARK 500 DT A 15 P DT A 15 O5' 0.143 REMARK 500 DT A 15 O3' DT A 16 P 0.137 REMARK 500 DT A 16 P DT A 16 O5' 0.147 REMARK 500 DT A 16 C5' DT A 16 C4' 0.043 REMARK 500 DT A 16 O3' DT A 17 P 0.126 REMARK 500 REMARK 500 THIS ENTRY HAS 263 BOND DEVIATIONS. 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 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA A 13 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA A 14 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT A 15 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT A 16 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT A 17 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT A 18 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT A 19 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT A 20 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 DT A 21 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT A 22 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 DT A 24 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 25 O4' - C4' - C3' ANGL. DEV. = -5.9 DEGREES REMARK 500 DT A 25 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 26 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT A 27 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT A 28 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT A 29 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT A 31 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT A 33 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG A 37 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 39 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA A 41 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC A 42 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA A 43 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA A 45 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG A 46 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 47 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA B 49 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT B 50 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG B 51 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 52 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 53 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DA B 53 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT B 54 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 55 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 56 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 57 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA B 58 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 59 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 60 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA B 61 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 62 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 63 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 64 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG B 67 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 69 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 DG A 1 0.05 SIDE CHAIN REMARK 500 DC A 7 0.08 SIDE CHAIN REMARK 500 DA A 14 0.09 SIDE CHAIN REMARK 500 DT A 16 0.09 SIDE CHAIN REMARK 500 DT A 20 0.10 SIDE CHAIN REMARK 500 DT A 21 0.09 SIDE CHAIN REMARK 500 DT A 26 0.06 SIDE CHAIN REMARK 500 DT A 33 0.06 SIDE CHAIN REMARK 500 DT A 36 0.07 SIDE CHAIN REMARK 500 DG B 64 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-27726 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-27725 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-27727 RELATED DB: EMDB DBREF 8DUT A 1 46 PDB 8DUT 8DUT 1 46 DBREF 8DUT B 47 92 PDB 8DUT 8DUT 47 92 SEQRES 1 A 46 DG DC DG DT DG DC DC DG DC DA DT DT DA SEQRES 2 A 46 DA DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 3 A 46 DT DT DT DT DT DT DT DT DT DT DG DT DA SEQRES 4 A 46 DT DA DC DA DT DA DG SEQRES 1 B 46 DC DT DA DT DG DT DA DT DA DC DA DA DA SEQRES 2 B 46 DG DA DG DG DG DT DG DG DG DT DA DG DG SEQRES 3 B 46 DG DT DG DG DG DT DT DT DA DA DT DG DC SEQRES 4 B 46 DG DG DC DA DC DG DC 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