HEADER DNA 08-NOV-24 9KG8 TITLE SOLUTION STRUCTURE OF THE 2:1 BERBERINE- HTERT-G4 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*AP*AP*GP*GP*GP*TP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*CP*GP*GP*GP*GP* COMPND 4 TP*T)-3'); COMPND 5 CHAIN: X; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS HTERT PROMOTER, G-QUADRUPLEX, NMR SOLUTION STRUCTURE, DNA EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR K.B.WANG REVDAT 1 03-JUN-26 9KG8 0 JRNL AUTH Y.Q.ZHANG,W.GU,S.H.HE,R.S.CHENG,Z.Y.CHEN,T.D.YAN,L.Y.KONG, JRNL AUTH 2 K.B.WANG JRNL TITL G146A MUTATION IN HTERT PROMOTER INDUCES A DISTINCT JRNL TITL 2 G-QUADRUPLEX THAT ACTIVATES HTERT TRANSCRIPTION: STRUCTURE JRNL TITL 3 DETERMINATION AND ITS POTENTIAL AS A DRUG TARGET JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 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 9KG8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 12-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300053530. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 298; 298 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 10; 10; 10 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.434 MM BER-MUT-HTERT-G4, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, X-PLOR NIH, NMRFAM REMARK 210 -SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 5 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA X 5 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 5 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DA X 6 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA X 6 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA X 6 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA X 6 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DA X 7 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA X 7 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA X 7 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DT X 11 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT X 11 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC X 12 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG X 13 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG X 15 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA X 16 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA X 16 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA X 16 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA X 16 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC X 17 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC X 17 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT X 18 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG X 19 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG X 20 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG X 21 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC X 22 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG X 23 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG X 25 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG X 26 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT X 27 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT X 28 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT X 28 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DA X 5 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA X 5 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA X 5 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DA X 5 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 2 DA X 6 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DA X 6 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA X 6 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA X 6 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DA X 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DA X 7 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA X 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA X 7 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 2 DG X 9 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG X 10 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DT X 11 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT X 11 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DC X 12 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC X 12 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 478 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 2 DG X 26 0.06 SIDE CHAIN REMARK 500 3 DG X 26 0.06 SIDE CHAIN REMARK 500 5 DG X 20 0.05 SIDE CHAIN REMARK 500 5 DG X 26 0.07 SIDE CHAIN REMARK 500 6 DG X 13 0.07 SIDE CHAIN REMARK 500 6 DT X 18 0.06 SIDE CHAIN REMARK 500 7 DG X 13 0.06 SIDE CHAIN REMARK 500 9 DG X 8 0.06 SIDE CHAIN REMARK 500 9 DG X 13 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36710 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE 2:1 BERBERINE- HTERT-G4 COMPLEX DBREF 9KG8 X 5 28 PDB 9KG8 9KG8 5 28 SEQRES 1 X 24 DA DA DA DG DG DG DT DC DG DG DG DA DC SEQRES 2 X 24 DT DG DG DG DC DG DG DG DG DT DT HET BER X 101 43 HET BER X 102 43 HETNAM BER BERBERINE FORMUL 2 BER 2(C20 H18 N O4 1+) 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL CONECT 776 777 778 779 CONECT 777 776 780 781 CONECT 778 776 782 783 CONECT 779 776 784 801 CONECT 780 777 785 786 CONECT 781 777 787 802 CONECT 782 778 788 803 CONECT 783 778 786 804 805 CONECT 784 779 788 789 CONECT 785 780 790 806 CONECT 786 780 783 807 808 CONECT 787 781 790 791 CONECT 788 782 784 792 CONECT 789 784 793 809 CONECT 790 785 787 794 CONECT 791 787 795 CONECT 792 788 796 797 CONECT 793 789 796 810 CONECT 794 790 795 CONECT 795 791 794 811 812 CONECT 796 792 793 798 CONECT 797 792 799 CONECT 798 796 800 CONECT 799 797 813 814 815 CONECT 800 798 816 817 818 CONECT 801 779 CONECT 802 781 CONECT 803 782 CONECT 804 783 CONECT 805 783 CONECT 806 785 CONECT 807 786 CONECT 808 786 CONECT 809 789 CONECT 810 793 CONECT 811 795 CONECT 812 795 CONECT 813 799 CONECT 814 799 CONECT 815 799 CONECT 816 800 CONECT 817 800 CONECT 818 800 CONECT 819 820 821 822 CONECT 820 819 823 824 CONECT 821 819 825 826 CONECT 822 819 827 844 CONECT 823 820 828 829 CONECT 824 820 830 845 CONECT 825 821 831 846 CONECT 826 821 829 847 848 CONECT 827 822 831 832 CONECT 828 823 833 849 CONECT 829 823 826 850 851 CONECT 830 824 833 834 CONECT 831 825 827 835 CONECT 832 827 836 852 CONECT 833 828 830 837 CONECT 834 830 838 CONECT 835 831 839 840 CONECT 836 832 839 853 CONECT 837 833 838 CONECT 838 834 837 854 855 CONECT 839 835 836 841 CONECT 840 835 842 CONECT 841 839 843 CONECT 842 840 856 857 858 CONECT 843 841 859 860 861 CONECT 844 822 CONECT 845 824 CONECT 846 825 CONECT 847 826 CONECT 848 826 CONECT 849 828 CONECT 850 829 CONECT 851 829 CONECT 852 832 CONECT 853 836 CONECT 854 838 CONECT 855 838 CONECT 856 842 CONECT 857 842 CONECT 858 842 CONECT 859 843 CONECT 860 843 CONECT 861 843 MASTER 168 0 2 0 0 0 0 6 554 1 86 2 END