PDB Short entry for 2MS5 HEADER RNA 23-JUL-14 2MS5 TITLE STRUCTURAL DYNAMICS OF DOUBLE-HELICAL RNA HAVING CAG MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA_(5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3'); COMPND 3 CHAIN: S, A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS CAG REPEAT EXPANSION, TRINUCLEOTIDE REPEATS, HUNTINGTON'S DISEASE, KEYWDS 2 RNA EXPDTA SOLUTION NMR AUTHOR A.KUMAR,A.TAWANI REVDAT 3 14-JUN-23 2MS5 1 REMARK REVDAT 2 15-JUL-15 2MS5 1 JRNL REVDAT 1 28-JAN-15 2MS5 0 JRNL AUTH A.TAWANI,A.KUMAR JRNL TITL STRUCTURAL INSIGHTS REVEAL THE DYNAMICS OF THE REPEATING JRNL TITL 2 R(CAG) TRANSCRIPT FOUND IN HUNTINGTON'S DISEASE (HD) AND JRNL TITL 3 SPINOCEREBELLAR ATAXIAS (SCAS) JRNL REF PLOS ONE V. 10 31788 2015 JRNL REFN ESSN 1932-6203 JRNL PMID 26148061 JRNL DOI 10.1371/JOURNAL.PONE.0131788 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER, DISCOVER REMARK 3 AUTHORS : ACCELRYS SOFTWARE INC. (DISCOVER), MOLECULAR REMARK 3 SIMULATIONS INC. (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MS5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000103986. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.018 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.35 MM RNA (5' REMARK 210 -R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3')-1, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D DQF-COSY; 2D 1H-1H NOESY; 2D REMARK 210 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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 APPLY THE FOLLOWING TO CHAINS: S, 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 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 C S 1 P C S 1 OP1 0.116 REMARK 500 C S 1 C2' C S 1 C1' 0.067 REMARK 500 C S 1 C5 C S 1 C6 0.066 REMARK 500 C S 1 O3' C S 2 P -0.080 REMARK 500 C S 2 C4 C S 2 C5 -0.050 REMARK 500 G S 3 N7 G S 3 C8 0.055 REMARK 500 C S 4 O4' C S 4 C4' -0.101 REMARK 500 C S 4 C4 C S 4 C5 -0.062 REMARK 500 C S 4 C5 C S 4 C6 0.070 REMARK 500 A S 5 P A S 5 O5' -0.074 REMARK 500 A S 5 N3 A S 5 C4 -0.041 REMARK 500 A S 5 C6 A S 5 N6 0.084 REMARK 500 A S 5 O3' G S 6 P -0.079 REMARK 500 C S 7 P C S 7 O5' -0.095 REMARK 500 C S 7 C2 C S 7 N3 0.084 REMARK 500 C S 7 C5 C S 7 C6 0.054 REMARK 500 G S 8 C6 G S 8 N1 -0.045 REMARK 500 G S 9 N1 G S 9 C2 -0.055 REMARK 500 C A 1 P C A 1 OP2 0.104 REMARK 500 C A 2 P C A 2 O5' -0.093 REMARK 500 C A 2 C5 C A 2 C6 0.060 REMARK 500 G A 3 P G A 3 O5' -0.090 REMARK 500 G A 3 C6 G A 3 N1 -0.047 REMARK 500 G A 3 N7 G A 3 C8 0.059 REMARK 500 C A 4 P C A 4 OP1 0.116 REMARK 500 C A 4 P C A 4 O5' -0.079 REMARK 500 C A 4 N1 C A 4 C6 -0.056 REMARK 500 A A 5 N9 A A 5 C4 -0.047 REMARK 500 A A 5 O3' G A 6 P -0.093 REMARK 500 G A 6 C2 G A 6 N3 0.060 REMARK 500 G A 6 C5 G A 6 N7 -0.061 REMARK 500 G A 6 N7 G A 6 C8 0.083 REMARK 500 G A 6 C8 G A 6 N9 -0.075 REMARK 500 G A 6 N9 G A 6 C4 0.054 REMARK 500 C A 7 N1 C A 7 C6 -0.038 REMARK 500 C A 7 C4 C A 7 C5 -0.068 REMARK 500 G A 8 C4 G A 8 C5 0.083 REMARK 500 G A 9 C6 G A 9 N1 -0.046 REMARK 500 G A 9 C5 G A 9 N7 -0.044 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 C S 1 OP1 - P - OP2 ANGL. DEV. = -13.5 DEGREES REMARK 500 C S 1 O5' - P - OP1 ANGL. DEV. = -6.8 DEGREES REMARK 500 C S 1 C2 - N3 - C4 ANGL. DEV. = 3.9 DEGREES REMARK 500 C S 2 OP1 - P - OP2 ANGL. DEV. = -12.2 DEGREES REMARK 500 C S 2 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 C S 2 N1 - C2 - O2 ANGL. DEV. = 4.8 DEGREES REMARK 500 G S 3 C3' - C2' - C1' ANGL. DEV. = -4.5 DEGREES REMARK 500 G S 3 N3 - C4 - C5 ANGL. DEV. = -5.2 DEGREES REMARK 500 G S 3 C5 - C6 - O6 ANGL. DEV. = -5.6 DEGREES REMARK 500 C S 4 C2 - N3 - C4 ANGL. DEV. = 4.9 DEGREES REMARK 500 C S 4 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 C S 4 N3 - C4 - N4 ANGL. DEV. = 5.6 DEGREES REMARK 500 C S 4 C5 - C4 - N4 ANGL. DEV. = -4.5 DEGREES REMARK 500 A S 5 OP1 - P - OP2 ANGL. DEV. = -13.6 DEGREES REMARK 500 A S 5 N9 - C1' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 A S 5 N1 - C2 - N3 ANGL. DEV. = -5.0 DEGREES REMARK 500 A S 5 C2 - N3 - C4 ANGL. DEV. = 5.7 DEGREES REMARK 500 A S 5 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 A S 5 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 A S 5 N9 - C4 - C5 ANGL. DEV. = -4.0 DEGREES REMARK 500 A S 5 N3 - C4 - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 G S 6 C2 - N3 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 G S 6 N3 - C4 - C5 ANGL. DEV. = -5.0 DEGREES REMARK 500 G S 6 C4 - C5 - N7 ANGL. DEV. = -2.9 DEGREES REMARK 500 G S 6 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 G S 6 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 G S 6 N1 - C6 - O6 ANGL. DEV. = 6.0 DEGREES REMARK 500 G S 6 C5 - C6 - O6 ANGL. DEV. = -4.5 DEGREES REMARK 500 C S 7 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 C S 7 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 G S 8 C6 - N1 - C2 ANGL. DEV. = 4.1 DEGREES REMARK 500 G S 9 N3 - C4 - C5 ANGL. DEV. = -3.9 DEGREES REMARK 500 G S 9 C4 - C5 - N7 ANGL. DEV. = -3.5 DEGREES REMARK 500 C A 1 OP1 - P - OP2 ANGL. DEV. = -13.6 DEGREES REMARK 500 C A 1 C6 - N1 - C2 ANGL. DEV. = 3.3 DEGREES REMARK 500 C A 1 N1 - C2 - N3 ANGL. DEV. = -4.3 DEGREES REMARK 500 C A 1 C2 - N3 - C4 ANGL. DEV. = 7.2 DEGREES REMARK 500 C A 1 N3 - C4 - C5 ANGL. DEV. = -5.9 DEGREES REMARK 500 C A 1 N3 - C4 - N4 ANGL. DEV. = 5.4 DEGREES REMARK 500 G A 3 OP1 - P - OP2 ANGL. DEV. = -9.2 DEGREES REMARK 500 G A 3 N3 - C4 - C5 ANGL. DEV. = -6.9 DEGREES REMARK 500 G A 3 C4 - C5 - C6 ANGL. DEV. = 4.3 DEGREES REMARK 500 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 G A 3 C8 - N9 - C4 ANGL. DEV. = -4.8 DEGREES REMARK 500 G A 3 N9 - C4 - C5 ANGL. DEV. = 4.4 DEGREES REMARK 500 C A 4 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 C A 4 N1 - C2 - N3 ANGL. DEV. = -5.6 DEGREES REMARK 500 C A 4 C2 - N3 - C4 ANGL. DEV. = 7.6 DEGREES REMARK 500 C A 4 N3 - C4 - C5 ANGL. DEV. = -5.4 DEGREES REMARK 500 C A 4 N3 - C2 - O2 ANGL. DEV. = 4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 91 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 A S 5 0.06 SIDE CHAIN REMARK 500 G S 8 0.06 SIDE CHAIN REMARK 500 G S 9 0.06 SIDE CHAIN REMARK 500 G A 6 0.07 SIDE CHAIN REMARK 500 G A 8 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NJ6 RELATED DB: PDB REMARK 900 0.95 A RESOLUTION X-RAY STRUCTURE OF (GGCAGCAGCC)2 REMARK 900 RELATED ID: 3NJ7 RELATED DB: PDB REMARK 900 1.9 A RESOLUTION X-RAY STRUCTURE OF (GGCAGCAGCC)2 REMARK 900 RELATED ID: 4J50 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN EXPANDED RNA CAG REPEAT REMARK 900 RELATED ID: 25106 RELATED DB: BMRB DBREF 2MS5 S 1 9 PDB 2MS5 2MS5 1 9 DBREF 2MS5 A 1 9 PDB 2MS5 2MS5 1 9 SEQRES 1 S 9 C C G C A G C G G SEQRES 1 A 9 C C G C A G C G G 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