HEADER DNA 12-JUN-24 8ZW3 TITLE SOLUTION STRUCTURE OF TMPRSS2 PROMOTER G-QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*TP*CP*TP*GP*GP*GP*CP*GP*GP*GP*CP*GP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP* COMPND 4 C)-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 TMPRSS2 PROMOTER, G-QUADRUPLEX, NMR SOLUTION STRUCTURE, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.B.WANG REVDAT 1 18-JUN-25 8ZW3 0 JRNL AUTH Z.Y.TANG,S.R.LI,Y.T.BIAN,Z.Y.CHEN,Y.Y.WANG,Y.Q.ZHANG,Y.P.LI, JRNL AUTH 2 Y.S.LIU,M.H.YANG,L.Y.KONG,K.B.WANG JRNL TITL NMR SOLUTION STRUCTURE OF THE MAJOR TMPRSS2 PROMOTER JRNL TITL 2 G-QUADRUPLEX AND ITS COMPLEX WITH BERBERINE 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 8ZW3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 15-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1300048597. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 298; 308 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 : 1.93 MM NONE BER-TMPRSS2_PU23M3, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC; REMARK 210 2D DQF-COSY 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 : 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 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 DT X 1 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT X 1 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC X 2 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC X 2 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DT X 3 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT X 3 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT X 3 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG X 5 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG X 6 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC X 7 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DC X 7 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG X 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG X 10 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC X 11 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC X 11 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA X 13 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DA X 13 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA X 13 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA X 13 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DG X 14 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG X 15 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG X 16 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC X 17 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC X 17 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG X 18 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DG X 19 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG X 20 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA X 21 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 21 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA X 21 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA X 21 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DC X 23 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DT X 1 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DT X 1 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DC X 2 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DC X 2 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DT X 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT X 3 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DG X 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG X 6 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC X 7 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC X 7 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG X 8 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG X 10 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DC X 11 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DA X 13 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DA X 13 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA X 13 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA X 13 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DG X 14 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 306 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 4 0.07 SIDE CHAIN REMARK 500 1 DG X 5 0.06 SIDE CHAIN REMARK 500 1 DG X 10 0.06 SIDE CHAIN REMARK 500 1 DG X 12 0.07 SIDE CHAIN REMARK 500 2 DG X 10 0.07 SIDE CHAIN REMARK 500 2 DG X 12 0.07 SIDE CHAIN REMARK 500 3 DG X 10 0.06 SIDE CHAIN REMARK 500 3 DG X 12 0.07 SIDE CHAIN REMARK 500 4 DG X 10 0.06 SIDE CHAIN REMARK 500 4 DG X 12 0.06 SIDE CHAIN REMARK 500 5 DG X 10 0.07 SIDE CHAIN REMARK 500 5 DG X 12 0.07 SIDE CHAIN REMARK 500 6 DG X 10 0.05 SIDE CHAIN REMARK 500 7 DG X 10 0.08 SIDE CHAIN REMARK 500 7 DG X 12 0.06 SIDE CHAIN REMARK 500 8 DT X 3 0.06 SIDE CHAIN REMARK 500 8 DG X 10 0.08 SIDE CHAIN REMARK 500 8 DG X 12 0.06 SIDE CHAIN REMARK 500 9 DG X 10 0.07 SIDE CHAIN REMARK 500 9 DG X 12 0.06 SIDE CHAIN REMARK 500 9 DG X 18 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36674 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF TMPRSS2 PROMOTER G-QUADRUPLEX DBREF 8ZW3 X 1 23 PDB 8ZW3 8ZW3 1 23 SEQRES 1 X 23 DT DC DT DG DG DG DC DG DG DG DC DG DA SEQRES 2 X 23 DG DG DG DC DG DG DG DA DG DC 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 CONECT 740 741 742 743 CONECT 741 740 744 745 CONECT 742 740 746 747 CONECT 743 740 748 765 CONECT 744 741 749 750 CONECT 745 741 751 766 CONECT 746 742 752 767 CONECT 747 742 750 768 769 CONECT 748 743 752 753 CONECT 749 744 754 770 CONECT 750 744 747 771 772 CONECT 751 745 754 755 CONECT 752 746 748 756 CONECT 753 748 757 773 CONECT 754 749 751 758 CONECT 755 751 759 CONECT 756 752 760 761 CONECT 757 753 760 774 CONECT 758 754 759 CONECT 759 755 758 775 776 CONECT 760 756 757 762 CONECT 761 756 763 CONECT 762 760 764 CONECT 763 761 777 778 779 CONECT 764 762 780 781 782 CONECT 765 743 CONECT 766 745 CONECT 767 746 CONECT 768 747 CONECT 769 747 CONECT 770 749 CONECT 771 750 CONECT 772 750 CONECT 773 753 CONECT 774 757 CONECT 775 759 CONECT 776 759 CONECT 777 763 CONECT 778 763 CONECT 779 763 CONECT 780 764 CONECT 781 764 CONECT 782 764 CONECT 783 784 785 786 CONECT 784 783 787 788 CONECT 785 783 789 790 CONECT 786 783 791 808 CONECT 787 784 792 793 CONECT 788 784 794 809 CONECT 789 785 795 810 CONECT 790 785 793 811 812 CONECT 791 786 795 796 CONECT 792 787 797 813 CONECT 793 787 790 814 815 CONECT 794 788 797 798 CONECT 795 789 791 799 CONECT 796 791 800 816 CONECT 797 792 794 801 CONECT 798 794 802 CONECT 799 795 803 804 CONECT 800 796 803 817 CONECT 801 797 802 CONECT 802 798 801 818 819 CONECT 803 799 800 805 CONECT 804 799 806 CONECT 805 803 807 CONECT 806 804 820 821 822 CONECT 807 805 823 824 825 CONECT 808 786 CONECT 809 788 CONECT 810 789 CONECT 811 790 CONECT 812 790 CONECT 813 792 CONECT 814 793 CONECT 815 793 CONECT 816 796 CONECT 817 800 CONECT 818 802 CONECT 819 802 CONECT 820 806 CONECT 821 806 CONECT 822 806 CONECT 823 807 CONECT 824 807 CONECT 825 807 MASTER 180 0 2 0 0 0 0 6 532 1 86 2 END