HEADER RNA 11-SEP-24 9DLN TITLE NMR STRUCTURES OF SMALL MOLECULES BOUND TO A MODEL OF AN RNA CAG TITLE 2 REPEAT EXPANSION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAG_13MER RNA (5'- COMPND 3 R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: SELF COMPLEMENTARY DUPLEX WITH AA MISMATCH SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS CAG REPEATS, HUNTINGTONS DISEASE, MUSCLE BLIND-LIKE 1, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.L.CHEN,A.TAGHAVI,M.D.DISNEY,M.A.FOUNTAIN,J.L.CHILDS-DISNEY REVDAT 1 06-MAY-26 9DLN 0 JRNL AUTH J.L.CHEN,A.TAGHAVI,M.D.DISNEY,M.A.FOUNTAIN JRNL TITL NMR STRUCTURES OF SMALL MOLECULES BOUND TO A MODEL OF AN RNA JRNL TITL 2 CAG REPEAT EXPANSION. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 20 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 9DLN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000287965. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 282 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : 5; 5 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.4 MM RNA (5' REMARK 210 -R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3'), 0.6 MM 4-[(3- REMARK 210 METHOXYPHENYL)AMINO]-2-METHYLQUINOLINE-6-CARBOXIMIDAMIDE, 5 MM REMARK 210 POTASSIUM, 0.5 MM EDTA, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRFAM-SPARKY 1.470 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 A A 2 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 A A 2 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 2 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 3 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 A A 4 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 A A 4 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 4 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 C A 6 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 C A 6 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 A A 7 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 7 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 C A 13 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 A B 15 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A B 15 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C B 16 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 C B 16 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A B 17 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 A B 17 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 C B 19 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 A B 20 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A B 20 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 C B 22 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C B 22 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 C B 22 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 U B 23 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 U B 25 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C B 26 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 A A 2 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 A A 2 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 A A 2 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 C A 3 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 C A 3 N3 - C2 - O2 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 A A 4 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 4 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 4 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 C A 6 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 A A 7 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 A A 7 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 C A 9 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 C A 9 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 C A 13 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 A B 15 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 A B 15 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 C B 16 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 C B 16 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 A B 17 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 526 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 G A 5 0.07 SIDE CHAIN REMARK 500 1 G A 8 0.08 SIDE CHAIN REMARK 500 1 C A 9 0.06 SIDE CHAIN REMARK 500 1 G B 18 0.06 SIDE CHAIN REMARK 500 1 C B 19 0.06 SIDE CHAIN REMARK 500 2 G A 5 0.07 SIDE CHAIN REMARK 500 2 G B 18 0.05 SIDE CHAIN REMARK 500 2 G B 21 0.10 SIDE CHAIN REMARK 500 3 G A 8 0.06 SIDE CHAIN REMARK 500 3 A B 15 0.06 SIDE CHAIN REMARK 500 3 G B 21 0.10 SIDE CHAIN REMARK 500 4 C A 9 0.09 SIDE CHAIN REMARK 500 4 G B 18 0.07 SIDE CHAIN REMARK 500 4 G B 21 0.05 SIDE CHAIN REMARK 500 5 G A 5 0.07 SIDE CHAIN REMARK 500 5 G B 18 0.07 SIDE CHAIN REMARK 500 5 G B 21 0.06 SIDE CHAIN REMARK 500 5 U B 25 0.06 SIDE CHAIN REMARK 500 6 G A 5 0.06 SIDE CHAIN REMARK 500 6 A A 7 0.05 SIDE CHAIN REMARK 500 6 G A 8 0.09 SIDE CHAIN REMARK 500 6 G A 11 0.07 SIDE CHAIN REMARK 500 6 G B 18 0.06 SIDE CHAIN REMARK 500 7 G A 5 0.07 SIDE CHAIN REMARK 500 7 G A 8 0.05 SIDE CHAIN REMARK 500 7 G B 18 0.06 SIDE CHAIN REMARK 500 8 G B 18 0.06 SIDE CHAIN REMARK 500 9 G A 5 0.07 SIDE CHAIN REMARK 500 9 G A 8 0.06 SIDE CHAIN REMARK 500 9 G B 21 0.07 SIDE CHAIN REMARK 500 10 C A 6 0.07 SIDE CHAIN REMARK 500 10 G A 8 0.05 SIDE CHAIN REMARK 500 10 C A 9 0.08 SIDE CHAIN REMARK 500 10 U A 12 0.09 SIDE CHAIN REMARK 500 10 A B 15 0.06 SIDE CHAIN REMARK 500 10 G B 18 0.08 SIDE CHAIN REMARK 500 11 G A 5 0.08 SIDE CHAIN REMARK 500 11 A A 7 0.06 SIDE CHAIN REMARK 500 11 G B 21 0.06 SIDE CHAIN REMARK 500 11 G B 24 0.06 SIDE CHAIN REMARK 500 12 C A 6 0.08 SIDE CHAIN REMARK 500 12 G A 8 0.09 SIDE CHAIN REMARK 500 13 G A 5 0.06 SIDE CHAIN REMARK 500 13 G A 8 0.06 SIDE CHAIN REMARK 500 13 G B 18 0.07 SIDE CHAIN REMARK 500 13 G B 21 0.06 SIDE CHAIN REMARK 500 14 G A 5 0.06 SIDE CHAIN REMARK 500 14 G B 21 0.07 SIDE CHAIN REMARK 500 15 G A 5 0.06 SIDE CHAIN REMARK 500 15 G A 8 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 66 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31204 RELATED DB: BMRB REMARK 900 NMR STRUCTURES OF SMALL MOLECULES BOUND TO A MODEL OF AN RNA CAG REMARK 900 REPEAT EXPANSION. DBREF 9DLN A 1 13 PDB 9DLN 9DLN 1 13 DBREF 9DLN B 14 26 PDB 9DLN 9DLN 14 26 SEQRES 1 A 13 G A C A G C A G C U G U C SEQRES 1 B 13 G A C A G C A G C U G U C HET MQC A 101 43 HETNAM MQC 4-[(3-METHOXYPHENYL)AMINO]-2-METHYLQUINOLINE-6- HETNAM 2 MQC CARBOXIMIDAMIDE FORMUL 3 MQC C18 H18 N4 O 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 MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 839 840 862 CONECT 840 839 841 842 CONECT 841 840 863 864 CONECT 842 840 843 845 CONECT 843 842 844 865 CONECT 844 843 847 852 CONECT 845 842 846 866 CONECT 846 845 847 867 CONECT 847 844 846 848 CONECT 848 847 849 CONECT 849 848 850 851 CONECT 850 849 868 869 870 CONECT 851 849 852 871 CONECT 852 844 851 853 CONECT 853 852 854 872 CONECT 854 853 855 856 CONECT 855 854 859 873 CONECT 856 854 857 874 CONECT 857 856 858 875 CONECT 858 857 859 876 CONECT 859 855 858 860 CONECT 860 859 861 CONECT 861 860 877 878 879 CONECT 862 839 CONECT 863 841 CONECT 864 841 CONECT 865 843 CONECT 866 845 CONECT 867 846 CONECT 868 850 CONECT 869 850 CONECT 870 850 CONECT 871 851 CONECT 872 853 CONECT 873 855 CONECT 874 856 CONECT 875 857 CONECT 876 858 CONECT 877 861 CONECT 878 861 CONECT 879 861 MASTER 212 0 1 0 0 0 0 6 573 2 41 2 END