HEADER DNA 31-MAR-22 7ZEO TITLE STRUCTURE OF A HYBRID-TYPE G-QUADRUPLEX WITH A SNAPBACK LOOP AND AN TITLE 2 ALL-SYN G-COLUMN (HYBRID-1R) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*(DG5)P*(BGM) COMPND 3 P*CP*TP*AP*GP*GP*GP*TP*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 7ZEO 1 JRNL REVDAT 2 06-JUL-22 7ZEO 1 JRNL REVDAT 1 15-JUN-22 7ZEO 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 7ZEO 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_1292122142. 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, CCPNMR REMARK 210 ANALYSIS 2.4.2, TOPSPIN 4.0.7 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. = 2.7 DEGREES REMARK 500 1 DC A 3 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 13 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DT A 17 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DC A 18 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 18 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA A 19 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 19 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC A 3 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA A 5 N1 - C6 - N6 ANGL. DEV. = -7.4 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT A 13 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT A 13 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG A 14 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 15 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT A 17 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DT A 17 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DC A 18 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DC A 18 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DA A 19 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DA A 19 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 3 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DC A 3 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 3 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 DA A 5 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 3 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 212 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 DT A 17 0.09 SIDE CHAIN REMARK 500 1 DG A 20 0.07 SIDE CHAIN REMARK 500 2 DT A 17 0.10 SIDE CHAIN REMARK 500 2 DG A 20 0.08 SIDE CHAIN REMARK 500 3 DG A 12 0.07 SIDE CHAIN REMARK 500 3 DT A 17 0.07 SIDE CHAIN REMARK 500 3 DG A 20 0.07 SIDE CHAIN REMARK 500 4 DG A 7 0.05 SIDE CHAIN REMARK 500 4 DT A 17 0.09 SIDE CHAIN REMARK 500 4 DG A 20 0.07 SIDE CHAIN REMARK 500 5 DT A 17 0.09 SIDE CHAIN REMARK 500 5 DG A 20 0.06 SIDE CHAIN REMARK 500 7 DT A 13 0.08 SIDE CHAIN REMARK 500 8 DT A 17 0.08 SIDE CHAIN REMARK 500 8 DG A 20 0.10 SIDE CHAIN REMARK 500 9 DG A 14 0.06 SIDE CHAIN REMARK 500 9 DT A 17 0.08 SIDE CHAIN REMARK 500 9 DG A 20 0.08 SIDE CHAIN REMARK 500 10 DT A 17 0.12 SIDE CHAIN REMARK 500 10 DG A 20 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34723 RELATED DB: BMRB REMARK 900 STRUCTURE OF A HYBRID-TYPE G-QUADRUPLEX WITH A SNAPBACK LOOP AND AN REMARK 900 ALL-SYN G-COLUMN (HYBRID-1R) DBREF 7ZEO A 1 20 PDB 7ZEO 7ZEO 1 20 SEQRES 1 A 20 L1J BGM DC DT DA DG DG DG DT DG DG DG DT SEQRES 2 A 20 DG DG DG DT DC DA DG HET L1J A 1 31 HET BGM A 2 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 BGM A 2 1555 1555 1.62 LINK O3' BGM A 2 P DC A 3 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 20.893 26.853 20.311 1.00 0.00 O HETATM 2 C5' L1J A 1 20.520 27.924 19.449 1.00 0.00 C HETATM 3 C4' L1J A 1 21.710 28.570 18.715 1.00 0.00 C HETATM 4 O4' L1J A 1 22.580 29.145 19.684 1.00 0.00 O HETATM 5 C1' L1J A 1 23.887 28.648 19.460 1.00 0.00 C HETATM 6 N9 L1J A 1 24.665 28.583 20.714 1.00 0.00 N HETATM 7 C8 L1J A 1 25.820 29.260 21.017 1.00 0.00 C HETATM 8 N7 L1J A 1 26.328 28.962 22.183 1.00 0.00 N HETATM 9 C5 L1J A 1 25.415 28.039 22.706 1.00 0.00 C HETATM 10 C4 L1J A 1 24.370 27.832 21.834 1.00 0.00 C HETATM 11 N3 L1J A 1 23.289 27.017 22.033 1.00 0.00 N HETATM 12 C2 L1J A 1 23.336 26.361 23.187 1.00 0.00 C HETATM 13 N1 L1J A 1 24.338 26.462 24.097 1.00 0.00 N HETATM 14 C6 L1J A 1 25.417 27.309 23.942 1.00 0.00 C HETATM 15 O6 L1J A 1 26.259 27.342 24.836 1.00 0.00 O HETATM 16 N2 L1J A 1 22.312 25.604 23.462 1.00 0.00 N HETATM 17 C2' L1J A 1 23.711 27.289 18.788 1.00 0.00 C HETATM 18 C3' L1J A 1 22.535 27.586 17.860 1.00 0.00 C HETATM 19 O3' L1J A 1 22.928 28.222 16.644 1.00 0.00 O HETATM 20 HO5' L1J A 1 21.690 27.118 20.818 1.00 0.00 H HETATM 21 H5'2 L1J A 1 19.808 27.556 18.706 1.00 0.00 H HETATM 22 H5'1 L1J A 1 20.021 28.699 20.033 1.00 0.00 H HETATM 23 H4' L1J A 1 21.323 29.361 18.067 1.00 0.00 H HETATM 24 H1' L1J A 1 24.401 29.305 18.756 1.00 0.00 H HETATM 25 H8 L1J A 1 26.282 29.955 20.325 1.00 0.00 H HETATM 26 HN1 L1J A 1 24.308 25.919 24.947 1.00 0.00 H HETATM 27 HN22 L1J A 1 21.580 25.558 22.776 1.00 0.00 H HETATM 28 HN21 L1J A 1 22.266 25.052 24.310 1.00 0.00 H HETATM 29 H2'2 L1J A 1 24.614 26.974 18.271 1.00 0.00 H HETATM 30 H2'1 L1J A 1 23.425 26.519 19.500 1.00 0.00 H HETATM 31 H3' L1J A 1 21.967 26.676 17.650 1.00 0.00 H HETATM 32 P BGM A 2 23.888 27.524 15.547 1.00 0.00 P HETATM 33 OP1 BGM A 2 23.695 28.244 14.262 1.00 0.00 O HETATM 34 OP2 BGM A 2 23.654 26.058 15.579 1.00 0.00 O HETATM 35 O5' BGM A 2 25.384 27.824 16.078 1.00 0.00 O HETATM 36 C5' BGM A 2 25.900 29.147 16.112 1.00 0.00 C HETATM 37 C4' BGM A 2 27.307 29.232 16.725 1.00 0.00 C HETATM 38 O4' BGM A 2 27.314 28.974 18.132 1.00 0.00 O HETATM 39 C1' BGM A 2 28.567 28.355 18.373 1.00 0.00 C HETATM 40 N9 BGM A 2 28.810 27.785 19.727 1.00 0.00 N HETATM 41 C8 BGM A 2 29.821 28.131 20.601 1.00 0.00 C HETATM 42 N7 BGM A 2 29.850 27.438 21.702 1.00 0.00 N HETATM 43 C5 BGM A 2 28.747 26.595 21.583 1.00 0.00 C HETATM 44 C4 BGM A 2 28.094 26.797 20.384 1.00 0.00 C HETATM 45 N3 BGM A 2 26.962 26.145 19.967 1.00 0.00 N HETATM 46 C2 BGM A 2 26.491 25.270 20.862 1.00 0.00 C HETATM 47 N2 BGM A 2 25.388 24.625 20.580 1.00 0.00 N HETATM 48 N1 BGM A 2 27.065 25.017 22.070 1.00 0.00 N HETATM 49 C6 BGM A 2 28.233 25.620 22.503 1.00 0.00 C HETATM 50 O6 BGM A 2 28.703 25.287 23.590 1.00 0.00 O HETATM 51 C2' BGM A 2 28.693 27.352 17.238 1.00 0.00 C HETATM 52 C3' BGM A 2 28.323 28.265 16.070 1.00 0.00 C HETATM 53 O3' BGM A 2 29.505 28.953 15.665 1.00 0.00 O HETATM 54 BR BGM A 2 31.136 29.461 20.291 1.00 0.00 BR HETATM 55 H5' BGM A 2 25.230 29.786 16.686 1.00 0.00 H HETATM 56 H5'' BGM A 2 25.944 29.537 15.093 1.00 0.00 H HETATM 57 H4' BGM A 2 27.666 30.251 16.570 1.00 0.00 H HETATM 58 H1' BGM A 2 29.333 29.113 18.205 1.00 0.00 H HETATM 59 H21 BGM A 2 24.950 23.997 21.246 1.00 0.00 H HETATM 60 H22 BGM A 2 24.969 24.792 19.680 1.00 0.00 H HETATM 61 H1 BGM A 2 26.632 24.359 22.701 1.00 0.00 H HETATM 62 H2' BGM A 2 29.708 26.962 17.154 1.00 0.00 H HETATM 63 H2'' BGM A 2 27.963 26.549 17.347 1.00 0.00 H HETATM 64 H3' BGM A 2 27.884 27.689 15.252 1.00 0.00 H