HEADER DNA 31-MAR-22 7ZEM TITLE STRUCTURE OF A PARALLEL G-QUADRUPLEX WITH A SNAPBACK LOOP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*(DT5) COMPND 3 P*GP*GP*CP*TP*AP*GP*GP*GP*TP*CP*AP*GP*GP*GP*TP*GP*GP*GP*TP*CP*AP*(DG3 COMPND 4 ))-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS G-QUADRUPLEX, PARALLEL, SNAPBACK LOOP, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.JANA,Y.M.VIANNEY,N.SCHROEDER,K.WEISZ REVDAT 4 19-JUN-24 7ZEM 1 REMARK REVDAT 3 30-NOV-22 7ZEM 1 JRNL REVDAT 2 06-JUL-22 7ZEM 1 JRNL REVDAT 1 15-JUN-22 7ZEM 0 JRNL AUTH J.JANA,Y.M.VIANNEY,N.SCHRODER,K.WEISZ JRNL TITL GUIDING THE FOLDING OF G-QUADRUPLEXES THROUGH LOOP RESIDUE JRNL TITL 2 INTERACTIONS. JRNL REF NUCLEIC ACIDS RES. V. 50 7161 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 35758626 JRNL DOI 10.1093/NAR/GKAC549 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 16 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7ZEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-APR-22. REMARK 100 THE DEPOSITION ID IS D_1292122135. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.3 MM DNA, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC AROMATIC; 2D 1H REMARK 210 -1H NOESY; 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH 3.0.3, TOPSPIN 4.0.7, REMARK 210 CCPNMR ANALYSIS 2.4.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC A 4 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 6 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA A 6 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 6 N1 - C6 - N6 ANGL. DEV. = -6.7 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 12 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 12 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 12 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 16 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 16 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 20 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DT A 20 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC A 21 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DC A 21 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DA A 22 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 22 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DC A 4 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA A 6 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DA A 6 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA A 6 N1 - C6 - N6 ANGL. DEV. = -6.5 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DA A 12 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DA A 12 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA A 12 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 DG A 14 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG A 15 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 16 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 273 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 1 DG A 9 0.07 SIDE CHAIN REMARK 500 1 DT A 20 0.09 SIDE CHAIN REMARK 500 2 DT A 20 0.10 SIDE CHAIN REMARK 500 3 DG A 8 0.05 SIDE CHAIN REMARK 500 3 DT A 20 0.06 SIDE CHAIN REMARK 500 3 DG A 23 0.06 SIDE CHAIN REMARK 500 4 DT A 5 0.06 SIDE CHAIN REMARK 500 4 DT A 20 0.07 SIDE CHAIN REMARK 500 5 DT A 20 0.10 SIDE CHAIN REMARK 500 6 DC A 4 0.09 SIDE CHAIN REMARK 500 6 DG A 17 0.07 SIDE CHAIN REMARK 500 6 DT A 20 0.09 SIDE CHAIN REMARK 500 7 DT A 20 0.09 SIDE CHAIN REMARK 500 8 DG A 15 0.06 SIDE CHAIN REMARK 500 8 DT A 20 0.08 SIDE CHAIN REMARK 500 9 DT A 20 0.09 SIDE CHAIN REMARK 500 10 DG A 3 0.06 SIDE CHAIN REMARK 500 10 DG A 8 0.05 SIDE CHAIN REMARK 500 10 DG A 9 0.05 SIDE CHAIN REMARK 500 10 DG A 14 0.05 SIDE CHAIN REMARK 500 10 DT A 20 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34722 RELATED DB: BMRB REMARK 900 STRUCTURE OF A PARALLEL G-QUADRUPLEX WITH A SNAPBACK LOOP DBREF 7ZEM A 1 23 PDB 7ZEM 7ZEM 1 23 SEQRES 1 A 23 THM DG DG DC DT DA DG DG DG DT DC DA DG SEQRES 2 A 23 DG DG DT DG DG DG DT DC DA DG HET THM A 1 30 HETNAM THM THYMIDINE HETSYN THM DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE FORMUL 1 THM C10 H14 N2 O5 LINK O3' THM A 1 P DG A 2 1555 1555 1.62 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 MODEL 1 HETATM 1 O5' THM A 1 23.820 39.686 31.886 1.00 0.00 O HETATM 2 C5' THM A 1 22.413 39.812 31.677 1.00 0.00 C HETATM 3 C4' THM A 1 21.728 38.474 31.349 1.00 0.00 C HETATM 4 O4' THM A 1 22.265 37.920 30.152 1.00 0.00 O HETATM 5 C3' THM A 1 21.874 37.428 32.472 1.00 0.00 C HETATM 6 O3' THM A 1 20.574 37.073 32.941 1.00 0.00 O HETATM 7 C2' THM A 1 22.635 36.292 31.781 1.00 0.00 C HETATM 8 C1' THM A 1 22.334 36.513 30.300 1.00 0.00 C HETATM 9 N1 THM A 1 23.370 35.963 29.377 1.00 0.00 N HETATM 10 C2 THM A 1 22.968 35.074 28.367 1.00 0.00 C HETATM 11 O2 THM A 1 21.812 34.678 28.217 1.00 0.00 O HETATM 12 N3 THM A 1 23.942 34.641 27.495 1.00 0.00 N HETATM 13 C4 THM A 1 25.268 35.007 27.528 1.00 0.00 C HETATM 14 O4 THM A 1 26.026 34.558 26.670 1.00 0.00 O HETATM 15 C5 THM A 1 25.628 35.933 28.600 1.00 0.00 C HETATM 16 C5M THM A 1 27.052 36.452 28.718 1.00 0.00 C HETATM 17 C6 THM A 1 24.687 36.367 29.480 1.00 0.00 C HETATM 18 HO5' THM A 1 24.247 39.447 31.038 1.00 0.00 H HETATM 19 H5'1 THM A 1 22.225 40.510 30.859 1.00 0.00 H HETATM 20 H5'2 THM A 1 21.952 40.222 32.578 1.00 0.00 H HETATM 21 H4' THM A 1 20.663 38.666 31.196 1.00 0.00 H HETATM 22 H3' THM A 1 22.469 37.823 33.298 1.00 0.00 H HETATM 23 H2'1 THM A 1 23.698 36.398 31.992 1.00 0.00 H HETATM 24 H2'2 THM A 1 22.298 35.311 32.098 1.00 0.00 H HETATM 25 H1' THM A 1 21.353 36.077 30.082 1.00 0.00 H HETATM 26 HN3 THM A 1 23.650 34.043 26.736 1.00 0.00 H HETATM 27 HM51 THM A 1 27.741 35.616 28.813 1.00 0.00 H HETATM 28 HM52 THM A 1 27.164 37.111 29.579 1.00 0.00 H HETATM 29 HM53 THM A 1 27.309 37.001 27.811 1.00 0.00 H HETATM 30 H6 THM A 1 24.963 37.075 30.252 1.00 0.00 H