HEADER DNA 07-OCT-20 7ALU TITLE NMR STRUCTURE OF A DNA G-QUADRUPLEX CONTAINING TWO SP1 BINDING SITES TITLE 2 FROM HIV-1 PROMOTER COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*GP*GP*GP*AP*GP*GP*TP*GP*TP*GP*GP*CP*CP*TP*GP*GP*GP*CP*GP*GP*G)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 4 ORGANISM_TAXID: 11676 KEYWDS VIRUS, HIV-1, G-QUADRUPLEX, SP1, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.DE RACHE,J.MARQUEVIELLE,S.AMRANE REVDAT 3 13-DEC-23 7ALU 1 JRNL REVDAT 2 14-JUN-23 7ALU 1 REMARK REVDAT 1 01-JUN-22 7ALU 0 JRNL AUTH A.DE RACHE,J.MARQUEVIELLE,S.BOUAZIZ,B.VIALET,M.L.ANDREOLA, JRNL AUTH 2 J.L.MERGNY,S.AMRANE JRNL TITL STRUCTURE OF A DNA G-QUADRUPLEX THAT MODULATES SP1 BINDING JRNL TITL 2 SITES ARCHITECTURE IN HIV-1 PROMOTER. JRNL REF J.MOL.BIOL. 68359 2023 JRNL REFN ESSN 1089-8638 JRNL PMID 37952768 JRNL DOI 10.1016/J.JMB.2023.168359 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 7ALU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1292111419. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 70 KCL; 20 KPI REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2.4 MM NONE HIVPRO3, 100% D2O; REMARK 210 857 UM NONE HIVPRO3, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, ARIA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 750 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 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 1 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 2 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DG A 2 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 3 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.5 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. = 4.4 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -8.0 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 6 N1 - C6 - O6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 7 N1 - C6 - O6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 9 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 9 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG A 9 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 10 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DC A 13 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC A 13 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DC A 14 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 15 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 18 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES REMARK 500 1 DC A 19 O4' - C1' - C2' ANGL. DEV. = -7.4 DEGREES REMARK 500 1 DC A 19 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 20 N3 - C4 - C5 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 20 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 20 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG A 20 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 1 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DG A 2 N3 - C4 - C5 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DG A 2 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 2 DG A 4 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 2 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 5 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DG A 6 N1 - C6 - O6 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 DG A 7 N1 - C6 - O6 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 8.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 421 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 DA A 1 0.07 SIDE CHAIN REMARK 500 1 DG A 2 0.05 SIDE CHAIN REMARK 500 1 DG A 4 0.07 SIDE CHAIN REMARK 500 1 DG A 7 0.06 SIDE CHAIN REMARK 500 1 DG A 11 0.06 SIDE CHAIN REMARK 500 1 DC A 13 0.06 SIDE CHAIN REMARK 500 1 DC A 14 0.23 SIDE CHAIN REMARK 500 1 DG A 17 0.06 SIDE CHAIN REMARK 500 1 DG A 18 0.14 SIDE CHAIN REMARK 500 1 DC A 19 0.21 SIDE CHAIN REMARK 500 2 DG A 4 0.06 SIDE CHAIN REMARK 500 2 DG A 7 0.05 SIDE CHAIN REMARK 500 2 DC A 14 0.20 SIDE CHAIN REMARK 500 2 DG A 17 0.13 SIDE CHAIN REMARK 500 2 DG A 18 0.13 SIDE CHAIN REMARK 500 3 DG A 4 0.08 SIDE CHAIN REMARK 500 3 DA A 5 0.06 SIDE CHAIN REMARK 500 3 DG A 7 0.08 SIDE CHAIN REMARK 500 3 DG A 11 0.07 SIDE CHAIN REMARK 500 3 DC A 14 0.21 SIDE CHAIN REMARK 500 3 DG A 17 0.07 SIDE CHAIN REMARK 500 3 DG A 18 0.14 SIDE CHAIN REMARK 500 4 DG A 4 0.07 SIDE CHAIN REMARK 500 4 DT A 8 0.07 SIDE CHAIN REMARK 500 4 DG A 9 0.08 SIDE CHAIN REMARK 500 4 DG A 11 0.06 SIDE CHAIN REMARK 500 4 DC A 14 0.21 SIDE CHAIN REMARK 500 4 DG A 17 0.15 SIDE CHAIN REMARK 500 4 DG A 18 0.13 SIDE CHAIN REMARK 500 4 DG A 20 0.06 SIDE CHAIN REMARK 500 5 DG A 4 0.10 SIDE CHAIN REMARK 500 5 DA A 5 0.06 SIDE CHAIN REMARK 500 5 DG A 6 0.05 SIDE CHAIN REMARK 500 5 DT A 8 0.07 SIDE CHAIN REMARK 500 5 DG A 9 0.10 SIDE CHAIN REMARK 500 5 DT A 10 0.07 SIDE CHAIN REMARK 500 5 DC A 14 0.17 SIDE CHAIN REMARK 500 5 DG A 17 0.07 SIDE CHAIN REMARK 500 5 DG A 18 0.12 SIDE CHAIN REMARK 500 5 DC A 19 0.12 SIDE CHAIN REMARK 500 6 DA A 5 0.09 SIDE CHAIN REMARK 500 6 DG A 7 0.07 SIDE CHAIN REMARK 500 6 DT A 8 0.09 SIDE CHAIN REMARK 500 6 DG A 9 0.07 SIDE CHAIN REMARK 500 6 DC A 14 0.22 SIDE CHAIN REMARK 500 6 DG A 17 0.10 SIDE CHAIN REMARK 500 6 DG A 18 0.16 SIDE CHAIN REMARK 500 6 DC A 19 0.16 SIDE CHAIN REMARK 500 6 DG A 20 0.08 SIDE CHAIN REMARK 500 7 DA A 1 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 87 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 2 O6 REMARK 620 2 DG A 3 O6 76.8 REMARK 620 3 DG A 11 O6 103.5 70.6 REMARK 620 4 DG A 12 O6 74.4 122.6 69.4 REMARK 620 5 DG A 16 O6 123.0 156.0 112.6 78.9 REMARK 620 6 DG A 17 O6 164.1 87.3 70.3 115.0 72.5 REMARK 620 7 DG A 20 O6 86.9 91.7 156.3 134.3 77.3 93.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 O6 REMARK 620 2 DG A 4 O6 71.7 REMARK 620 3 DG A 9 O6 123.7 77.0 REMARK 620 4 DG A 11 O6 68.0 89.1 65.9 REMARK 620 5 DG A 17 O6 88.5 153.0 100.6 66.1 REMARK 620 6 DG A 18 O6 160.3 120.5 75.7 124.1 83.9 REMARK 620 7 DG A 21 O6 58.6 114.1 167.6 107.3 67.0 101.7 REMARK 620 8 DG A 22 O6 92.5 75.1 122.9 158.3 125.2 77.3 67.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34565 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF A DNA G-QUADRUPLEX CONTAINING TWO SP1 BINDING REMARK 900 SITES FROM HIV-1 PROMOTER DBREF 7ALU A 1 22 PDB 7ALU 7ALU 1 22 SEQRES 1 A 22 DA DG DG DG DA DG DG DT DG DT DG DG DC SEQRES 2 A 22 DC DT DG DG DG DC DG DG DG HET K A 101 1 HET K A 102 1 HETNAM K POTASSIUM ION FORMUL 2 K 2(K 1+) LINK O6 DG A 2 K K A 101 1555 1555 2.61 LINK O6 DG A 3 K K A 101 1555 1555 2.85 LINK O6 DG A 3 K K A 102 1555 1555 2.77 LINK O6 DG A 4 K K A 102 1555 1555 2.74 LINK O6 DG A 9 K K A 102 1555 1555 2.66 LINK O6 DG A 11 K K A 101 1555 1555 2.71 LINK O6 DG A 11 K K A 102 1555 1555 2.97 LINK O6 DG A 12 K K A 101 1555 1555 2.98 LINK O6 DG A 16 K K A 101 1555 1555 2.65 LINK O6 DG A 17 K K A 101 1555 1555 2.67 LINK O6 DG A 17 K K A 102 1555 1555 2.69 LINK O6 DG A 18 K K A 102 1555 1555 2.78 LINK O6 DG A 20 K K A 101 1555 1555 2.62 LINK O6 DG A 21 K K A 102 1555 1555 2.98 LINK O6 DG A 22 K K A 102 1555 1555 2.71 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