HEADER SPLICING 29-NOV-23 8R8P TITLE SOLUTION STRUCTURE OF SMN-CX BOUND TO THE RNA HELIX FORMED UPON SMN2 TITLE 2 EXON7 5'-SPLICE SITE RECOGNITION 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(P*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 SPECIFIC SPLICING CORRECTION, MOLECULAR GLUE, SMALL MOLECULE SPLICING KEYWDS 2 MODIFIER, U1 SNRNP, 5'-SPLICE SITE RECOGNITION, SPLICING EXPDTA SOLID-STATE NMR NUMMDL 15 AUTHOR F.MALARD,S.CAMPAGNE REVDAT 3 22-MAY-24 8R8P 1 JRNL REVDAT 2 10-APR-24 8R8P 1 JRNL REVDAT 1 06-MAR-24 8R8P 0 JRNL AUTH F.MALARD,A.C.WOLTER,J.MARQUEVIELLE,E.MORVAN,A.ECOUTIN, JRNL AUTH 2 S.H.RUDISSER,F.H.T.ALLAIN,S.CAMPAGNE JRNL TITL THE DIVERSITY OF SPLICING MODIFIERS ACTING ON A-1 BULGED JRNL TITL 2 5'-SPLICE SITES REVEALS RULES FOR RATIONAL DRUG DESIGN. JRNL REF NUCLEIC ACIDS RES. V. 52 4124 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38554107 JRNL DOI 10.1093/NAR/GKAE201 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 8R8P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1292134921. 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 ATM REMARK 210 SAMPLE CONTENTS : 10 MM MES, 50 MM SODIUM REMARK 210 CHLORIDE, 1 MM RNA (5'-R(*AP*UP*AP*CP*(PSU)P*(PSU)P*AP*CP*CP*UP* REMARK 210 G)-3'), 1 MM RNA (5'-R(P*GP*GP*AP*GP*UP*AP*AP*GP*UP*CP*U)-3'), REMARK 210 1.5 MM SCX, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC ALIPHATIC; 2D 1H REMARK 210 -13C HSQC AROMATIC; 2D 1H-1H REMARK 210 NOESY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.98, CARA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 A A 7 C6 A A 7 N1 -0.043 REMARK 500 1 A B 14 C6 A B 14 N1 -0.043 REMARK 500 1 A B 17 C6 A B 17 N1 -0.044 REMARK 500 1 A B 18 C6 A B 18 N1 -0.043 REMARK 500 2 A A 3 C6 A A 3 N1 -0.043 REMARK 500 2 A A 7 C6 A A 7 N1 -0.042 REMARK 500 2 A B 14 C6 A B 14 N1 -0.044 REMARK 500 2 A B 17 C6 A B 17 N1 -0.043 REMARK 500 2 A B 18 C6 A B 18 N1 -0.042 REMARK 500 3 A A 1 C6 A A 1 N1 -0.044 REMARK 500 3 A A 3 C6 A A 3 N1 -0.043 REMARK 500 3 A A 7 C6 A A 7 N1 -0.043 REMARK 500 3 A B 14 C6 A B 14 N1 -0.042 REMARK 500 3 A B 17 C6 A B 17 N1 -0.043 REMARK 500 3 A B 18 C6 A B 18 N1 -0.042 REMARK 500 4 A A 1 C6 A A 1 N1 -0.045 REMARK 500 4 A A 7 C6 A A 7 N1 -0.045 REMARK 500 5 A A 1 C6 A A 1 N1 -0.042 REMARK 500 5 A B 14 C6 A B 14 N1 -0.042 REMARK 500 5 A B 17 C6 A B 17 N1 -0.043 REMARK 500 5 A B 18 C6 A B 18 N1 -0.045 REMARK 500 6 A A 1 C6 A A 1 N1 -0.044 REMARK 500 6 A A 3 C6 A A 3 N1 -0.044 REMARK 500 6 A B 17 C6 A B 17 N1 -0.046 REMARK 500 7 A A 3 C6 A A 3 N1 -0.044 REMARK 500 7 A B 14 C6 A B 14 N1 -0.043 REMARK 500 7 A B 17 C6 A B 17 N1 -0.044 REMARK 500 8 A A 3 C6 A A 3 N1 -0.044 REMARK 500 8 A A 7 C6 A A 7 N1 -0.044 REMARK 500 8 A B 14 C6 A B 14 N1 -0.043 REMARK 500 8 A B 17 C6 A B 17 N1 -0.044 REMARK 500 9 A A 3 C6 A A 3 N1 -0.043 REMARK 500 9 A B 18 C6 A B 18 N1 -0.042 REMARK 500 10 A A 1 C6 A A 1 N1 -0.043 REMARK 500 10 A A 3 C6 A A 3 N1 -0.044 REMARK 500 10 A A 7 C6 A A 7 N1 -0.042 REMARK 500 10 A B 14 C6 A B 14 N1 -0.047 REMARK 500 10 A B 17 C6 A B 17 N1 -0.045 REMARK 500 10 A B 18 C6 A B 18 N1 -0.043 REMARK 500 11 A A 3 C6 A A 3 N1 -0.043 REMARK 500 11 A B 14 C6 A B 14 N1 -0.044 REMARK 500 11 A B 18 C6 A B 18 N1 -0.044 REMARK 500 12 A A 1 C6 A A 1 N1 -0.043 REMARK 500 12 A A 3 C6 A A 3 N1 -0.043 REMARK 500 12 A B 14 C6 A B 14 N1 -0.043 REMARK 500 12 A B 17 C6 A B 17 N1 -0.043 REMARK 500 12 A B 18 C6 A B 18 N1 -0.044 REMARK 500 13 A A 3 C6 A A 3 N1 -0.043 REMARK 500 13 A A 7 C6 A A 7 N1 -0.045 REMARK 500 13 A B 17 C6 A B 17 N1 -0.043 REMARK 500 REMARK 500 THIS ENTRY HAS 61 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 U A 2 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 1 A A 3 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 1 C A 4 OP1 - P - OP2 ANGL. DEV. = -10.4 DEGREES REMARK 500 1 A A 7 OP1 - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 1 C A 8 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 1 C A 9 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 1 U A 10 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 1 G A 11 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 1 G B 12 OP1 - P - OP2 ANGL. DEV. = -13.3 DEGREES REMARK 500 1 G B 13 OP1 - P - OP2 ANGL. DEV. = -11.2 DEGREES REMARK 500 1 A B 14 OP1 - P - OP2 ANGL. DEV. = -10.4 DEGREES REMARK 500 1 G B 15 OP1 - P - OP2 ANGL. DEV. = -10.9 DEGREES REMARK 500 1 U B 16 OP1 - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 1 A B 17 OP1 - P - OP2 ANGL. DEV. = -11.2 DEGREES REMARK 500 1 A B 18 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 1 G B 19 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 1 U B 20 OP1 - P - OP2 ANGL. DEV. = -10.9 DEGREES REMARK 500 1 C B 21 OP1 - P - OP2 ANGL. DEV. = -10.9 DEGREES REMARK 500 1 U B 22 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 2 U A 2 OP1 - P - OP2 ANGL. DEV. = -11.0 DEGREES REMARK 500 2 A A 3 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 2 C A 4 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 2 A A 7 OP1 - P - OP2 ANGL. DEV. = -10.8 DEGREES REMARK 500 2 C A 8 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 2 C A 9 OP1 - P - OP2 ANGL. DEV. = -11.0 DEGREES REMARK 500 2 U A 10 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 2 G A 11 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 2 G B 12 OP1 - P - OP2 ANGL. DEV. = -13.4 DEGREES REMARK 500 2 G B 13 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 2 A B 14 OP1 - P - OP2 ANGL. DEV. = -11.2 DEGREES REMARK 500 2 G B 15 OP1 - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 2 U B 16 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 2 A B 17 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 2 A B 18 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 2 G B 19 OP1 - P - OP2 ANGL. DEV. = -10.8 DEGREES REMARK 500 2 U B 20 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 2 C B 21 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 2 U B 22 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 3 U A 2 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 3 A A 3 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 3 C A 4 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 3 A A 7 OP1 - P - OP2 ANGL. DEV. = -11.3 DEGREES REMARK 500 3 C A 8 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 3 C A 9 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 3 U A 10 OP1 - P - OP2 ANGL. DEV. = -11.2 DEGREES REMARK 500 3 G A 11 OP1 - P - OP2 ANGL. DEV. = -10.8 DEGREES REMARK 500 3 G B 12 OP1 - P - OP2 ANGL. DEV. = -12.8 DEGREES REMARK 500 3 G B 13 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 3 A B 14 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 3 G B 15 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 285 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34885 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF SMN-CX BOUND TO THE RNA HELIX FORMED UPON REMARK 900 SMN2 EXON7 5'-SPLICE SITE RECOGNITION DBREF 8R8P A 1 11 PDB 8R8P 8R8P 1 11 DBREF 8R8P B 12 22 PDB 8R8P 8R8P 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 YB3 B 101 51 HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETNAM YB3 2-(8-FLUORANYL-2-METHYL-IMIDAZO[1,2-A]PYRIDIN-6-YL)-6- HETNAM 2 YB3 (4-METHYLPIPERAZIN-1-YL)QUINAZOLINE FORMUL 1 PSU 2(C9 H13 N2 O9 P) FORMUL 3 YB3 C21 H21 F N6 LINK O3' C A 4 P PSU A 5 1555 1555 1.60 LINK O3' PSU A 5 P PSU A 6 1555 1555 1.60 LINK O3' PSU A 6 P A A 7 1555 1555 1.60 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