HEADER RNA 09-JUN-22 7Y2B TITLE CRYSTAL STRUCTURE OF CUG REPEAT RNA DUPLEX CONTAINING U-U MISMATCHES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(P*UP*UP*CP*UP*GP*CP*UP*GP*CP*UP*GP*AP*A)-3'); COMPND 3 CHAIN: S; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS CUG REPEATS, U-U MISMATCH, MYOTONIC DYSTROPHY TYPE 1 (DM1), WATER KEYWDS 2 MEDIATED U-U MISMATCH, RNA EXPDTA X-RAY DIFFRACTION AUTHOR S.C.WANG,R.B.SATANGE,M.H.HOU REVDAT 4 29-NOV-23 7Y2B 1 REMARK REVDAT 3 12-JUL-23 7Y2B 1 JRNL REVDAT 2 07-JUN-23 7Y2B 1 JRNL REVDAT 1 31-MAY-23 7Y2B 0 JRNL AUTH S.C.WANG,Y.T.CHEN,R.SATANGE,J.W.CHU,M.H.HOU JRNL TITL STRUCTURAL BASIS FOR WATER MODULATING RNA DUPLEX FORMATION JRNL TITL 2 IN THE CUG REPEATS OF MYOTONIC DYSTROPHY TYPE 1. JRNL REF J.BIOL.CHEM. V. 299 04864 2023 JRNL REFN ESSN 1083-351X JRNL PMID 37245780 JRNL DOI 10.1016/J.JBC.2023.104864 REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 4326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 424 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.6300 - 2.7100 0.97 1322 141 0.1900 0.1904 REMARK 3 2 2.7000 - 1.9400 1.00 1293 138 0.2428 0.2898 REMARK 3 3 1.9400 - 1.8800 1.00 1287 145 0.2589 0.2781 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7Y2B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030127. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4355 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 0.38300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.18.2_3874 REMARK 200 STARTING MODEL: 1ZEV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 MM OLIGONUCLEOTIDE, 3.5 MM REMARK 280 SPERMINE TETRAHYDROCHLORIDE, 50 MM HEPES PH 6.5, 10% MPD, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.09333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 12.04667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 12.04667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.09333 REMARK 290 REMARK 290 REMARK: NULL 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: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: S 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 12.04667 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH S 140 LIES ON A SPECIAL POSITION. REMARK 375 HOH S 145 LIES ON A SPECIAL POSITION. REMARK 375 HOH S 151 LIES ON A SPECIAL POSITION. DBREF 7Y2B S 1 13 PDB 7Y2B 7Y2B 1 13 SEQRES 1 S 13 U U C U G C U G C U G A A FORMUL 2 HOH *58(H2 O) CRYST1 49.262 49.262 36.140 90.00 90.00 120.00 P 32 2 1 6 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 0.020300 0.011720 0.000000 0.00000 SCALE2 0.000000 0.023440 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027670 0.00000 TER 275 A S 13 HETATM 276 O HOH S 101 13.228 -0.790 15.616 1.00 35.36 O HETATM 277 O HOH S 102 22.377 -10.262 21.206 1.00 43.70 O HETATM 278 O HOH S 103 14.532 4.438 9.888 1.00 40.09 O HETATM 279 O HOH S 104 16.649 10.666 7.139 1.00 53.65 O HETATM 280 O HOH S 105 16.052 -7.050 -16.159 1.00 26.73 O HETATM 281 O HOH S 106 32.695 -2.355 5.741 1.00 42.45 O HETATM 282 O HOH S 107 35.956 -1.937 -4.453 1.00 51.17 O HETATM 283 O HOH S 108 23.933 0.356 19.167 1.00 31.81 O HETATM 284 O HOH S 109 22.981 -4.762 18.369 1.00 59.45 O HETATM 285 O HOH S 110 27.769 -9.875 -11.765 1.00 41.68 O HETATM 286 O HOH S 111 24.812 -9.511 -1.983 1.00 27.42 O HETATM 287 O HOH S 112 24.127 -8.967 -11.910 1.00 28.53 O HETATM 288 O HOH S 113 22.311 13.858 4.624 1.00 43.56 O HETATM 289 O HOH S 114 15.892 -10.794 -9.261 1.00 24.14 O HETATM 290 O HOH S 115 32.189 8.637 6.562 1.00 24.54 O HETATM 291 O HOH S 116 17.134 -7.702 -6.027 1.00 29.33 O HETATM 292 O HOH S 117 27.540 -0.731 -0.333 1.00 33.53 O HETATM 293 O HOH S 118 27.910 -6.536 -8.996 1.00 38.76 O HETATM 294 O HOH S 119 31.584 -3.145 -4.111 1.00 29.47 O HETATM 295 O HOH S 120 15.722 -0.292 22.416 1.00 35.19 O HETATM 296 O HOH S 121 30.062 -11.529 -10.139 1.00 38.11 O HETATM 297 O HOH S 122 31.705 -11.842 -4.314 1.00 27.15 O HETATM 298 O HOH S 123 35.819 -3.406 3.725 1.00 33.62 O HETATM 299 O HOH S 124 25.041 -14.559 -6.469 1.00 31.04 O HETATM 300 O HOH S 125 14.772 -2.749 21.788 1.00 37.26 O HETATM 301 O HOH S 126 17.893 7.578 4.431 1.00 45.77 O HETATM 302 O HOH S 127 24.373 7.743 3.248 1.00 33.84 O HETATM 303 O HOH S 128 13.034 -6.091 -13.675 1.00 38.70 O HETATM 304 O HOH S 129 30.795 11.923 3.804 1.00 26.23 O HETATM 305 O HOH S 130 15.159 -3.976 -10.295 1.00 40.39 O HETATM 306 O HOH S 131 22.482 -10.929 -4.001 1.00 25.99 O HETATM 307 O HOH S 132 22.227 6.759 6.031 1.00 31.75 O HETATM 308 O HOH S 133 27.357 -4.488 -7.070 1.00 31.71 O HETATM 309 O HOH S 134 23.061 -0.475 15.465 1.00 44.03 O HETATM 310 O HOH S 135 26.122 11.317 12.201 1.00 25.28 O HETATM 311 O HOH S 136 31.544 -5.354 -8.299 1.00 37.41 O HETATM 312 O HOH S 137 22.646 12.771 12.928 1.00 42.84 O HETATM 313 O HOH S 138 25.571 -7.383 -8.578 1.00 31.32 O HETATM 314 O HOH S 139 25.140 -3.895 -7.998 1.00 36.92 O HETATM 315 O HOH S 140 27.584 0.000 6.023 0.50 31.52 O HETATM 316 O HOH S 141 24.828 12.190 1.406 1.00 36.25 O HETATM 317 O HOH S 142 24.601 -4.376 -10.953 1.00 30.59 O HETATM 318 O HOH S 143 22.045 4.326 9.911 1.00 32.59 O HETATM 319 O HOH S 144 33.727 6.435 5.627 1.00 27.44 O HETATM 320 O HOH S 145 31.522 0.000 6.023 0.50 32.97 O HETATM 321 O HOH S 146 34.826 -7.899 2.431 1.00 22.00 O HETATM 322 O HOH S 147 26.427 5.803 0.627 1.00 35.26 O HETATM 323 O HOH S 148 20.808 2.846 13.171 1.00 33.78 O HETATM 324 O HOH S 149 23.887 -2.939 -0.605 1.00 36.21 O HETATM 325 O HOH S 150 34.170 -5.619 3.857 1.00 28.41 O HETATM 326 O HOH S 151 25.256 0.000 24.093 0.50 35.21 O HETATM 327 O HOH S 152 20.411 0.156 12.700 1.00 39.38 O HETATM 328 O HOH S 153 24.167 1.959 10.637 1.00 42.47 O HETATM 329 O HOH S 154 24.164 10.098 0.427 1.00 40.12 O HETATM 330 O HOH S 155 14.281 -6.252 -8.502 1.00 39.30 O HETATM 331 O HOH S 156 23.853 -12.717 -13.995 1.00 39.60 O HETATM 332 O HOH S 157 36.240 2.739 5.741 1.00 39.16 O HETATM 333 O HOH S 158 38.015 -4.490 2.576 1.00 36.54 O MASTER 216 0 0 0 0 0 0 6 332 1 0 1 END