HEADER DNA 31-MAR-22 7ZEK TITLE STRUCTURE OF A HYBRID-TYPE G-QUADRUPLEX WITH A SNAPBACK LOOP (HYBRID TITLE 2 1R') COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*(DG5)P*GP*CP*TP*AP*(BG) COMPND 3 P*GP*GP*TP*CP*AP*GP*GP*GP*TP*GP*GP*GP*TP*CP*AP*(DG3))-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS HYBRID G-QUADRUPLEX, SNAPBACK LOOP, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.JANA,Y.M.VIANNEY,N.SCHROEDER,K.WEISZ REVDAT 3 30-NOV-22 7ZEK 1 JRNL REVDAT 2 06-JUL-22 7ZEK 1 JRNL REVDAT 1 22-JUN-22 7ZEK 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 7ZEK 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_1292121766. 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 (5' REMARK 210 -D(*(DG5)P*GP*CP*TP*AP*(BG)P*GP*GP*TP*CP*AP*GP*GP*GP*TP*GP*GP*GP* REMARK 210 TP*CP*AP*(DG3))-3'), 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 1H-1H COSY; 2D DQF- REMARK 210 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 : TOPSPIN 4.0.7, CCPNMR ANALYSIS REMARK 210 2.4.2, X-PLOR NIH 3.2 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 DC A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 3 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC A 10 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DA A 11 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 11 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 11 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT A 19 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DC A 20 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DC A 20 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DA A 21 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 21 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DC A 3 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 5 N1 - C6 - N6 ANGL. DEV. = -6.5 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DC A 10 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DA A 11 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DA A 11 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA A 11 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 11 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 13 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DG A 14 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT A 15 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DG A 16 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DG A 17 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DG A 17 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 DG A 18 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DT A 19 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT A 19 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 286 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 14 0.07 SIDE CHAIN REMARK 500 1 DT A 15 0.09 SIDE CHAIN REMARK 500 1 DT A 19 0.06 SIDE CHAIN REMARK 500 2 DG A 14 0.09 SIDE CHAIN REMARK 500 3 DG A 14 0.09 SIDE CHAIN REMARK 500 3 DT A 15 0.09 SIDE CHAIN REMARK 500 3 DT A 19 0.06 SIDE CHAIN REMARK 500 3 DA A 21 0.06 SIDE CHAIN REMARK 500 3 DG A 22 0.07 SIDE CHAIN REMARK 500 4 DG A 14 0.08 SIDE CHAIN REMARK 500 4 DG A 22 0.08 SIDE CHAIN REMARK 500 5 DG A 14 0.08 SIDE CHAIN REMARK 500 5 DT A 15 0.09 SIDE CHAIN REMARK 500 5 DT A 19 0.09 SIDE CHAIN REMARK 500 5 DG A 22 0.06 SIDE CHAIN REMARK 500 6 DG A 2 0.07 SIDE CHAIN REMARK 500 6 DG A 14 0.10 SIDE CHAIN REMARK 500 6 DT A 15 0.06 SIDE CHAIN REMARK 500 6 DT A 19 0.08 SIDE CHAIN REMARK 500 6 DG A 22 0.06 SIDE CHAIN REMARK 500 7 DG A 7 0.05 SIDE CHAIN REMARK 500 7 DT A 9 0.07 SIDE CHAIN REMARK 500 7 DG A 14 0.07 SIDE CHAIN REMARK 500 7 DT A 15 0.07 SIDE CHAIN REMARK 500 7 DA A 21 0.06 SIDE CHAIN REMARK 500 7 DG A 22 0.07 SIDE CHAIN REMARK 500 8 DG A 14 0.08 SIDE CHAIN REMARK 500 8 DT A 15 0.07 SIDE CHAIN REMARK 500 8 DT A 19 0.08 SIDE CHAIN REMARK 500 8 DG A 22 0.06 SIDE CHAIN REMARK 500 9 DG A 13 0.05 SIDE CHAIN REMARK 500 9 DG A 16 0.05 SIDE CHAIN REMARK 500 9 DT A 19 0.09 SIDE CHAIN REMARK 500 9 DG A 22 0.09 SIDE CHAIN REMARK 500 10 DG A 14 0.10 SIDE CHAIN REMARK 500 10 DT A 15 0.07 SIDE CHAIN REMARK 500 10 DG A 22 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34721 RELATED DB: BMRB REMARK 900 STRUCTURE OF A HYBRID-TYPE G-QUADRUPLEX WITH A SNAPBACK LOOP REMARK 900 (HYBRID 1R') DBREF 7ZEK A 1 22 PDB 7ZEK 7ZEK 1 22 SEQRES 1 A 22 L1J DG DC DT DA BGM DG DG DT DC DA DG DG SEQRES 2 A 22 DG DT DG DG DG DT DC DA DG HET L1J A 1 31 HET BGM A 6 33 HETNAM L1J 2-AZANYL-9-[(2~{R},4~{S},5~{R})-5-(HYDROXYMETHYL)-4- HETNAM 2 L1J OXIDANYL-OXOLAN-2-YL]-1~{H}-PURIN-6-ONE HETNAM BGM 8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE FORMUL 1 L1J C10 H13 N5 O4 FORMUL 1 BGM C10 H13 BR N5 O7 P LINK O3' L1J A 1 P DG A 2 1555 1555 1.61 LINK O3' DA A 5 P BGM A 6 1555 1555 1.61 LINK O3' BGM A 6 P DG A 7 1555 1555 1.61 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' L1J A 1 32.148 30.920 22.673 1.00 0.00 O HETATM 2 C5' L1J A 1 32.336 32.309 22.425 1.00 0.00 C HETATM 3 C4' L1J A 1 32.340 33.173 23.700 1.00 0.00 C HETATM 4 O4' L1J A 1 31.094 33.018 24.375 1.00 0.00 O HETATM 5 C1' L1J A 1 31.361 32.622 25.711 1.00 0.00 C HETATM 6 N9 L1J A 1 30.261 31.807 26.273 1.00 0.00 N HETATM 7 C8 L1J A 1 29.472 32.133 27.348 1.00 0.00 C HETATM 8 N7 L1J A 1 28.494 31.297 27.568 1.00 0.00 N HETATM 9 C5 L1J A 1 28.644 30.343 26.557 1.00 0.00 C HETATM 10 C4 L1J A 1 29.730 30.634 25.764 1.00 0.00 C HETATM 11 N3 L1J A 1 30.168 29.907 24.689 1.00 0.00 N HETATM 12 C2 L1J A 1 29.445 28.810 24.475 1.00 0.00 C HETATM 13 N1 L1J A 1 28.356 28.439 25.197 1.00 0.00 N HETATM 14 C6 L1J A 1 27.861 29.179 26.252 1.00 0.00 C HETATM 15 O6 L1J A 1 26.838 28.791 26.813 1.00 0.00 O HETATM 16 N2 L1J A 1 29.801 28.061 23.468 1.00 0.00 N HETATM 17 C2' L1J A 1 32.709 31.912 25.685 1.00 0.00 C HETATM 18 C3' L1J A 1 33.456 32.807 24.699 1.00 0.00 C HETATM 19 O3' L1J A 1 33.931 34.009 25.310 1.00 0.00 O HETATM 20 HO5' L1J A 1 31.436 30.808 23.337 1.00 0.00 H HETATM 21 H5'2 L1J A 1 33.283 32.455 21.902 1.00 0.00 H HETATM 22 H5'1 L1J A 1 31.539 32.670 21.773 1.00 0.00 H HETATM 23 H4' L1J A 1 32.463 34.217 23.403 1.00 0.00 H HETATM 24 H1' L1J A 1 31.477 33.521 26.321 1.00 0.00 H HETATM 25 H8 L1J A 1 29.652 33.012 27.956 1.00 0.00 H HETATM 26 HN1 L1J A 1 27.871 27.581 24.983 1.00 0.00 H HETATM 27 HN22 L1J A 1 30.623 28.340 22.961 1.00 0.00 H HETATM 28 HN21 L1J A 1 29.321 27.198 23.245 1.00 0.00 H HETATM 29 H2'2 L1J A 1 33.169 31.885 26.669 1.00 0.00 H HETATM 30 H2'1 L1J A 1 32.619 30.901 25.289 1.00 0.00 H HETATM 31 H3' L1J A 1 34.265 32.267 24.203 1.00 0.00 H