HEADER RNA 12-SEP-18 6HMO TITLE SOLUTION STRUCTURE OF THE RNA DUPLEX FORMED BY THE 5'-END OF U1SNRNA TITLE 2 AND THE 5'-SPLICE SITE OF SMN2 EXON7 IN COMPLEX WITH THE SMN-C5 TITLE 3 SPLICING MODIFIER COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*AP*UP*AP*CP*(PSU)P*(PSU)P*AP*CP*CP*UP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (5'-R(*GP*GP*AP*GP*UP*AP*AP*GP*UP*CP*U)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS 5'-SPLICE SITE BULGE REPAIR, U1 SNRNA, SPINAL MUSCULAR ATROPHY, BULGE KEYWDS 2 NUCLEOTIDE, SPLICING MODIFIER, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.CAMPAGNE,F.H.ALLAIN REVDAT 3 15-MAY-24 6HMO 1 REMARK REVDAT 2 26-FEB-20 6HMO 1 JRNL REVDAT 1 14-AUG-19 6HMO 0 JRNL AUTH S.CAMPAGNE,S.BOIGNER,S.RUDISSER,A.MOURSY,L.GILLIOZ, JRNL AUTH 2 A.KNORLEIN,J.HALL,H.RATNI,A.CLERY,F.H.ALLAIN JRNL TITL STRUCTURAL BASIS OF A SMALL MOLECULE TARGETING RNA FOR A JRNL TITL 2 SPECIFIC SPLICING CORRECTION. JRNL REF NAT.CHEM.BIOL. V. 15 1191 2019 JRNL REFN ESSN 1552-4469 JRNL PMID 31636429 JRNL DOI 10.1038/S41589-019-0384-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 12 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 6HMO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1200011913. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : ATM PA REMARK 210 SAMPLE CONTENTS : 10 MM DEUTERATED MES, 50 MM REMARK 210 UNLABELLED SODIUM CHLORIDE, 6 % REMARK 210 DEUTERATED GLYCEROL, 100% D2O; REMARK 210 10 MM DEUTERATED MES, 50 MM REMARK 210 UNLABLED SODIUM CHLORIDE, 6 % REMARK 210 DEUTERATED GLYCEROL, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC; 3D 1H-13C REMARK 210 NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : 900 AVANCE; 600 AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.2, CARA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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 1 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 A A 1 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 A A 1 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 A A 1 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 6 G A 11 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 A A 1 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 18 A A 1 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES 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 5 G A 11 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDZ A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues PSU A 5 and PSU A 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34312 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE RNA DUPLEX FORMED BY THE 5'-END OF REMARK 900 U1SNRNA AND THE 5'-SPLICE SITE OF SMN2 EXON7 IN COMPLEX WITH THE REMARK 900 SMN-C5 SPLICING MODIFIER DBREF 6HMO A 1 11 PDB 6HMO 6HMO 1 11 DBREF 6HMO B 12 22 PDB 6HMO 6HMO 12 22 SEQRES 1 A 11 A U A C PSU PSU A C C U G SEQRES 1 B 11 G G A G U A A G U C U HET PSU A 5 30 HET PSU A 6 30 HET GDZ A 101 50 HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETNAM GDZ 2-(8-FLUORANYL-2-METHYL-IMIDAZO[1,2-A]PYRIDIN-6-YL)-7- HETNAM 2 GDZ (4-METHYLPIPERAZIN-1-YL)PYRIDO[1,2-A]PYRIMIDIN-4-ONE HETSYN GDZ SMN-C5 FORMUL 1 PSU 2(C9 H13 N2 O9 P) FORMUL 3 GDZ C21 H21 F N6 O LINK O3' C A 4 P PSU A 5 1555 1555 1.62 LINK O3' PSU A 5 P PSU A 6 1555 1555 1.61 LINK O3' PSU A 6 P A A 7 1555 1555 1.60 SITE 1 AC1 4 C A 8 C A 9 A B 14 G B 15 SITE 1 AC2 5 C A 4 A A 7 A B 17 A B 18 SITE 2 AC2 5 G B 19 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 103 143 CONECT 126 127 131 146 CONECT 127 126 128 132 CONECT 128 127 129 147 CONECT 129 128 130 133 CONECT 130 129 131 134 CONECT 131 126 130 148 CONECT 132 127 CONECT 133 129 CONECT 134 130 135 140 149 CONECT 135 134 136 137 150 CONECT 136 135 151 CONECT 137 135 138 139 152 CONECT 138 137 140 141 153 CONECT 139 137 173 CONECT 140 134 138 CONECT 141 138 142 154 155 CONECT 142 141 143 CONECT 143 103 142 144 145 CONECT 144 143 CONECT 145 143 CONECT 146 126 CONECT 147 128 CONECT 148 131 CONECT 149 134 CONECT 150 135 CONECT 151 136 CONECT 152 137 CONECT 153 138 CONECT 154 141 CONECT 155 141 CONECT 156 157 161 176 CONECT 157 156 158 162 CONECT 158 157 159 177 CONECT 159 158 160 163 CONECT 160 159 161 164 CONECT 161 156 160 178 CONECT 162 157 CONECT 163 159 CONECT 164 160 165 170 179 CONECT 165 164 166 167 180 CONECT 166 165 181 CONECT 167 165 168 169 182 CONECT 168 167 170 171 183 CONECT 169 167 186 CONECT 170 164 168 CONECT 171 168 172 184 185 CONECT 172 171 173 CONECT 173 139 172 174 175 CONECT 174 173 CONECT 175 173 CONECT 176 156 CONECT 177 158 CONECT 178 161 CONECT 179 164 CONECT 180 165 CONECT 181 166 CONECT 182 167 CONECT 183 168 CONECT 184 171 CONECT 185 171 CONECT 186 169 CONECT 703 704 709 732 733 CONECT 704 703 705 734 735 CONECT 705 704 706 707 CONECT 706 705 736 737 738 CONECT 707 705 708 739 740 CONECT 708 707 709 741 742 CONECT 709 703 708 710 CONECT 710 709 711 712 CONECT 711 710 716 743 CONECT 712 710 713 744 CONECT 713 712 714 745 CONECT 714 713 715 716 CONECT 715 714 720 CONECT 716 711 714 717 CONECT 717 716 718 719 CONECT 718 717 CONECT 719 717 720 746 CONECT 720 715 719 721 CONECT 721 720 722 723 CONECT 722 721 728 747 CONECT 723 721 724 748 CONECT 724 723 725 726 CONECT 725 724 CONECT 726 724 727 728 CONECT 727 726 730 CONECT 728 722 726 729 CONECT 729 728 730 749 CONECT 730 727 729 731 CONECT 731 730 750 751 752 CONECT 732 703 CONECT 733 703 CONECT 734 704 CONECT 735 704 CONECT 736 706 CONECT 737 706 CONECT 738 706 CONECT 739 707 CONECT 740 707 CONECT 741 708 CONECT 742 708 CONECT 743 711 CONECT 744 712 CONECT 745 713 CONECT 746 719 CONECT 747 722 CONECT 748 723 CONECT 749 729 CONECT 750 731 CONECT 751 731 CONECT 752 731 MASTER 134 0 3 0 0 0 3 6 490 2 112 2 END