HEADER DNA 14-MAR-22 7X8M TITLE NMR SOLUTION STRUCTURE OF THE 2:1 BERBERINE-KRAS-G4 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (24-MER); COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEX, KRAS, BERBERINE, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.B.WANG,Y.LIU,J.LI,C.XIAO,W.GU,Y.LI,Y.Z.XIA,T.YAN,M.H.YANG,L.Y.KONG REVDAT 2 22-MAR-23 7X8M 1 JRNL REVDAT 1 07-SEP-22 7X8M 0 JRNL AUTH K.B.WANG,Y.LIU,J.LI,C.XIAO,Y.WANG,W.GU,Y.LI,Y.Z.XIA,T.YAN, JRNL AUTH 2 M.H.YANG,L.Y.KONG JRNL TITL STRUCTURAL INSIGHT INTO THE BULGE-CONTAINING KRAS ONCOGENE JRNL TITL 2 PROMOTER G-QUADRUPLEX BOUND TO BERBERINE AND COPTISINE. JRNL REF NAT COMMUN V. 13 6016 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36224201 JRNL DOI 10.1038/S41467-022-33761-4 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 7X8M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028339. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 308 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 50; 50 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.5 MM NONE KRAS_PU24M1, 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; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRFAM-SPARKY, X-PLOR REMARK 210 NIH, AMBER 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 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 3 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA X 3 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA X 3 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG X 5 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC X 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC X 7 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG X 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT X 10 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT X 10 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG X 11 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT X 12 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT X 12 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG X 13 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG X 14 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG X 15 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA X 16 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA X 16 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 16 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA X 17 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DA X 17 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA X 17 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA X 17 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT X 18 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT X 18 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA X 19 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA X 19 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA X 19 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA X 19 N1 - C6 - N6 ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DG X 20 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG X 21 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG X 22 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA X 23 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA X 23 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA X 23 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 23 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA X 24 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA X 24 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 24 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 DG X 2 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA X 3 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DA X 3 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DA X 3 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA X 3 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DG X 5 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DG X 6 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC X 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DC X 7 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DG X 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT X 10 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DT X 10 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 394 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 20 0.07 SIDE CHAIN REMARK 500 3 DG X 5 0.07 SIDE CHAIN REMARK 500 3 DG X 9 0.07 SIDE CHAIN REMARK 500 3 DG X 15 0.06 SIDE CHAIN REMARK 500 3 DG X 20 0.08 SIDE CHAIN REMARK 500 5 DA X 19 0.05 SIDE CHAIN REMARK 500 5 DG X 20 0.08 SIDE CHAIN REMARK 500 6 DG X 6 0.06 SIDE CHAIN REMARK 500 7 DA X 3 0.07 SIDE CHAIN REMARK 500 7 DG X 20 0.09 SIDE CHAIN REMARK 500 8 DG X 20 0.07 SIDE CHAIN REMARK 500 9 DT X 12 0.06 SIDE CHAIN REMARK 500 10 DA X 3 0.08 SIDE CHAIN REMARK 500 10 DA X 19 0.05 SIDE CHAIN REMARK 500 10 DG X 20 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36475 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF THE 2:1 BERBERINE-KRAS-G4 COMPLEX DBREF 7X8M X 1 24 PDB 7X8M 7X8M 1 24 SEQRES 1 X 24 THM DG DA DG DG DG DC DG DG DT DG DT DG SEQRES 2 X 24 DG DG DA DA DT DA DG DG DG DA DA HET THM X 1 30 HET BER X 101 43 HET BER X 102 43 HETNAM THM THYMIDINE HETNAM BER BERBERINE HETSYN THM DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE FORMUL 1 THM C10 H14 N2 O5 FORMUL 2 BER 2(C20 H18 N O4 1+) LINK O3' THM X 1 P DG X 2 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' THM X 1 20.628 43.421 33.383 1.00 0.00 O HETATM 2 C5' THM X 1 20.564 44.636 32.637 1.00 0.00 C HETATM 3 C4' THM X 1 21.430 44.622 31.363 1.00 0.00 C HETATM 4 O4' THM X 1 22.805 44.432 31.690 1.00 0.00 O HETATM 5 C3' THM X 1 21.030 43.512 30.375 1.00 0.00 C HETATM 6 O3' THM X 1 20.950 44.090 29.074 1.00 0.00 O HETATM 7 C2' THM X 1 22.183 42.515 30.515 1.00 0.00 C HETATM 8 C1' THM X 1 23.344 43.464 30.804 1.00 0.00 C HETATM 9 N1 THM X 1 24.553 42.842 31.416 1.00 0.00 N HETATM 10 C2 THM X 1 25.802 43.106 30.831 1.00 0.00 C HETATM 11 O2 THM X 1 25.956 43.748 29.791 1.00 0.00 O HETATM 12 N3 THM X 1 26.912 42.627 31.491 1.00 0.00 N HETATM 13 C4 THM X 1 26.907 41.937 32.683 1.00 0.00 C HETATM 14 O4 THM X 1 27.987 41.603 33.170 1.00 0.00 O HETATM 15 C5 THM X 1 25.575 41.673 33.231 1.00 0.00 C HETATM 16 C5M THM X 1 25.395 40.929 34.544 1.00 0.00 C HETATM 17 C6 THM X 1 24.462 42.115 32.587 1.00 0.00 C HETATM 18 HO5' THM X 1 21.518 43.339 33.782 1.00 0.00 H HETATM 19 H5'1 THM X 1 20.884 45.469 33.266 1.00 0.00 H HETATM 20 H5'2 THM X 1 19.529 44.819 32.343 1.00 0.00 H HETATM 21 H4' THM X 1 21.314 45.588 30.867 1.00 0.00 H HETATM 22 H3' THM X 1 20.080 43.057 30.663 1.00 0.00 H HETATM 23 H2'1 THM X 1 21.992 41.848 31.355 1.00 0.00 H HETATM 24 H2'2 THM X 1 22.349 41.938 29.609 1.00 0.00 H HETATM 25 H1' THM X 1 23.610 43.954 29.862 1.00 0.00 H HETATM 26 HN3 THM X 1 27.805 42.820 31.076 1.00 0.00 H HETATM 27 HM51 THM X 1 24.904 41.578 35.270 1.00 0.00 H HETATM 28 HM52 THM X 1 26.362 40.629 34.950 1.00 0.00 H HETATM 29 HM53 THM X 1 24.795 40.033 34.383 1.00 0.00 H HETATM 30 H6 THM X 1 23.490 41.933 33.027 1.00 0.00 H