HEADER DNA 18-NOV-19 6V0L TITLE PDGFR-B PROMOTER FORMS A G-VACANCY QUADRUPLEX THAT CAN BE COMPLEMENTED TITLE 2 BY DGMP: MOLECULAR STRUCTURE AND RECOGNITION OF GUANINE DERIVATIVES TITLE 3 AND METABOLITES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*(3D1) COMPND 3 P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP*A)-3'); COMPND 4 CHAIN: X; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEX, PDGFR-B, PROMOTER, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.B.WANG,J.DICKERHOFF,G.WU,D.YANG REVDAT 3 01-MAY-24 6V0L 1 REMARK REVDAT 2 01-APR-20 6V0L 1 JRNL REVDAT 1 11-MAR-20 6V0L 0 JRNL AUTH K.B.WANG,J.DICKERHOFF,G.WU,D.YANG JRNL TITL PDGFR-BETA PROMOTER FORMS A VACANCY G-QUADRUPLEX THAT CAN BE JRNL TITL 2 FILLED IN BY DGMP: SOLUTION STRUCTURE AND MOLECULAR JRNL TITL 3 RECOGNITION OF GUANINE METABOLITES AND DRUGS. JRNL REF J.AM.CHEM.SOC. V. 142 5204 2020 JRNL REFN ESSN 1520-5126 JRNL PMID 32101424 JRNL DOI 10.1021/JACS.9B12770 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, X-PLOR NIH REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN (AMBER), SCHWIETERS, REMARK 3 KUSZEWSKI, TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MOLECULAR DYNAMICS REMARK 4 REMARK 4 6V0L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1000245534. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 298; 278 REMARK 210 PH : 7.0; 7; 7 REMARK 210 IONIC STRENGTH : 50; 50; 50 REMARK 210 PRESSURE : 760 MMHG; 760 MMHG; 760 MMHG REMARK 210 SAMPLE CONTENTS : 3600 UM 1H DNA (5' REMARK 210 -D(*(DA5)P*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*AP*CP* REMARK 210 (DA3)P*-3')(DGP), 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-1H COSY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, TOPSPIN, AMBER, X-PLOR REMARK 210 NIH REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: X 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 DA X 2 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA X 2 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 2 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG X 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG X 5 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA X 6 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA X 6 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 6 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG X 7 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG X 8 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG X 9 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DC X 10 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DC X 10 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DG X 11 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC X 13 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC X 13 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG X 14 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG X 15 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG X 16 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA X 17 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA X 17 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA X 17 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA X 17 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DC X 18 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC X 18 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DA X 19 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA X 19 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA X 19 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 2 DA X 2 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DA X 2 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA X 2 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DG X 3 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DG X 5 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DA X 6 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA X 6 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA X 6 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DG X 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG X 9 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC X 10 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DC X 10 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DG X 11 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC X 13 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DC X 13 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DG X 15 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG X 16 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA X 17 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA X 17 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA X 17 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA X 17 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DC X 18 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 260 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 X 8 0.06 SIDE CHAIN REMARK 500 1 DG X 16 0.05 SIDE CHAIN REMARK 500 1 DA X 17 0.11 SIDE CHAIN REMARK 500 2 DG X 12 0.07 SIDE CHAIN REMARK 500 2 DA X 17 0.07 SIDE CHAIN REMARK 500 3 DG X 3 0.07 SIDE CHAIN REMARK 500 3 DG X 5 0.08 SIDE CHAIN REMARK 500 3 DG X 8 0.07 SIDE CHAIN REMARK 500 3 DG X 14 0.06 SIDE CHAIN REMARK 500 3 DA X 17 0.06 SIDE CHAIN REMARK 500 4 DG X 3 0.07 SIDE CHAIN REMARK 500 4 DG X 8 0.07 SIDE CHAIN REMARK 500 4 DA X 17 0.08 SIDE CHAIN REMARK 500 6 DG X 8 0.06 SIDE CHAIN REMARK 500 9 DG X 8 0.07 SIDE CHAIN REMARK 500 9 DA X 17 0.07 SIDE CHAIN REMARK 500 10 DG X 12 0.06 SIDE CHAIN REMARK 500 10 DA X 17 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DGP X 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30688 RELATED DB: BMRB REMARK 900 DGMP FILL-IN G-QUADRUPLEX IN THE PDGFR-B PROMOTER DBREF 6V0L X 1 19 PDB 6V0L 6V0L 1 19 SEQRES 1 X 19 3D1 DA DG DG DG DA DG DG DG DC DG DG DC SEQRES 2 X 19 DG DG DG DA DC DA HET 3D1 X 1 30 HET DGP X 101 36 HETNAM 3D1 (2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2- HETNAM 2 3D1 (HYDROXYMETHYL)FURAN-3-OL HETNAM DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE HETSYN 3D1 2'-DEOXYADENOSINE FORMUL 1 3D1 C10 H13 N5 O3 FORMUL 2 DGP C10 H14 N5 O7 P LINK O3' 3D1 X 1 P DA X 2 1555 1555 1.61 SITE 1 AC1 5 3D1 X 1 DG X 7 DG X 8 DG X 11 SITE 2 AC1 5 DG X 14 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' 3D1 X 1 20.410 30.336 21.898 1.00 0.00 O HETATM 2 C5' 3D1 X 1 20.333 30.552 23.305 1.00 0.00 C HETATM 3 C4' 3D1 X 1 21.356 31.578 23.829 1.00 0.00 C HETATM 4 O4' 3D1 X 1 22.674 31.087 23.612 1.00 0.00 O HETATM 5 C1' 3D1 X 1 23.433 32.062 22.919 1.00 0.00 C HETATM 6 N9 3D1 X 1 24.443 31.458 22.017 1.00 0.00 N HETATM 7 C4 3D1 X 1 24.235 30.446 21.100 1.00 0.00 C HETATM 8 N3 3D1 X 1 23.069 29.776 20.847 1.00 0.00 N HETATM 9 C2 3D1 X 1 23.206 28.868 19.887 1.00 0.00 C HETATM 10 N1 3D1 X 1 24.295 28.581 19.190 1.00 0.00 N HETATM 11 C6 3D1 X 1 25.410 29.257 19.467 1.00 0.00 C HETATM 12 N6 3D1 X 1 26.433 28.897 18.716 1.00 0.00 N HETATM 13 C5 3D1 X 1 25.439 30.258 20.472 1.00 0.00 C HETATM 14 N7 3D1 X 1 26.427 31.107 20.998 1.00 0.00 N HETATM 15 C8 3D1 X 1 25.785 31.753 21.940 1.00 0.00 C HETATM 16 C2' 3D1 X 1 22.427 32.925 22.159 1.00 0.00 C HETATM 17 C3' 3D1 X 1 21.251 32.943 23.128 1.00 0.00 C HETATM 18 O3' 3D1 X 1 21.415 34.006 24.056 1.00 0.00 O HETATM 19 H5'1 3D1 X 1 20.495 29.606 23.823 1.00 0.00 H HETATM 20 H5'2 3D1 X 1 19.330 30.902 23.557 1.00 0.00 H HETATM 21 H4' 3D1 X 1 21.190 31.715 24.899 1.00 0.00 H HETATM 22 H1' 3D1 X 1 23.941 32.689 23.656 1.00 0.00 H HETATM 23 H2 3D1 X 1 22.318 28.300 19.639 1.00 0.00 H HETATM 24 HN61 3D1 X 1 27.333 29.324 18.861 1.00 0.00 H HETATM 25 HN62 3D1 X 1 26.300 28.123 18.076 1.00 0.00 H HETATM 26 H8 3D1 X 1 26.255 32.489 22.583 1.00 0.00 H HETATM 27 H2'1 3D1 X 1 22.131 32.450 21.224 1.00 0.00 H HETATM 28 H2'2 3D1 X 1 22.818 33.925 21.969 1.00 0.00 H HETATM 29 H3' 3D1 X 1 20.305 33.029 22.589 1.00 0.00 H HETATM 30 HO5' 3D1 X 1 21.344 30.143 21.658 1.00 0.00 H