HEADER RNA BINDING PROTEIN 19-DEC-21 7QL7 TITLE CRYSTAL STRUCTURE OF YTHDF1 YTH DOMAIN IN COMPLEX WITH THE EBSULFUR TITLE 2 DERIVATIVE COMPOUND 9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTH DOMAIN-CONTAINING FAMILY PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: YTH DOMAIN (RESIDUES 361-559); COMPND 5 SYNONYM: DF1,DERMATOMYOSITIS ASSOCIATED WITH CANCER PUTATIVE COMPND 6 AUTOANTIGEN 1,DACA-1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: YTHDF1, C20ORF21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MRNA BINDING AND STABILITY, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.DALLE VEDOVE,G.CAZZANELLI,A.QUATTRONE,A.PROVENZANI,G.LOLLI REVDAT 2 31-JAN-24 7QL7 1 REMARK REVDAT 1 23-NOV-22 7QL7 0 JRNL AUTH M.MICAELLI,A.DALLE VEDOVE,L.CEROFOLINI,J.VIGNA,D.SIGHEL, JRNL AUTH 2 S.ZACCARA,I.BONOMO,G.POULENTZAS,E.F.ROSATTI,G.CAZZANELLI, JRNL AUTH 3 L.ALUNNO,R.BELLI,D.PERONI,E.DASSI,S.MURAKAMI,S.R.JAFFREY, JRNL AUTH 4 M.FRAGAI,I.MANCINI,G.LOLLI,A.QUATTRONE,A.PROVENZANI JRNL TITL SMALL-MOLECULE EBSELEN BINDS TO YTHDF PROTEINS INTERFERING JRNL TITL 2 WITH THE RECOGNITION OF N 6 -METHYLADENOSINE-MODIFIED RNAS. JRNL REF ACS PHARMACOL TRANSL SCI V. 5 872 2022 JRNL REFN ESSN 2575-910 JRNL PMID 36268123 JRNL DOI 10.1021/ACSPTSCI.2C00008 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 25895 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1275 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 44.2310 - 4.7825 1.00 2916 155 0.1643 0.1969 REMARK 3 2 4.7825 - 3.7967 1.00 2796 131 0.1610 0.2098 REMARK 3 3 3.7967 - 3.3170 1.00 2737 146 0.2053 0.2588 REMARK 3 4 3.3170 - 3.0138 1.00 2719 140 0.2279 0.2785 REMARK 3 5 3.0138 - 2.7978 1.00 2713 142 0.2425 0.2517 REMARK 3 6 2.7978 - 2.6329 1.00 2690 144 0.2378 0.2908 REMARK 3 7 2.6329 - 2.5010 1.00 2724 112 0.2373 0.3066 REMARK 3 8 2.5010 - 2.3921 1.00 2669 149 0.2491 0.2958 REMARK 3 9 2.3921 - 2.3001 1.00 2656 156 0.2618 0.2990 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.36 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 : 0.008 3132 REMARK 3 ANGLE : 1.019 4200 REMARK 3 CHIRALITY : 0.066 435 REMARK 3 PLANARITY : 0.006 536 REMARK 3 DIHEDRAL : 21.666 1895 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 15 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 363 THROUGH 374 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.2308 -55.2731 1.7495 REMARK 3 T TENSOR REMARK 3 T11: 0.6282 T22: 0.5692 REMARK 3 T33: 0.5798 T12: -0.0537 REMARK 3 T13: -0.0526 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 2.9779 L22: 6.0028 REMARK 3 L33: 6.7098 L12: 3.4536 REMARK 3 L13: -0.5477 L23: 2.9533 REMARK 3 S TENSOR REMARK 3 S11: 0.4214 S12: -0.2576 S13: -0.8640 REMARK 3 S21: -0.3702 S22: -0.6719 S23: 0.1677 REMARK 3 S31: 1.7359 S32: -0.4635 S33: 0.4296 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 375 THROUGH 398 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.7317 -41.2737 -0.2962 REMARK 3 T TENSOR REMARK 3 T11: 0.4848 T22: 0.5163 REMARK 3 T33: 0.4614 T12: -0.0016 REMARK 3 T13: -0.0283 T23: 0.0926 REMARK 3 L TENSOR REMARK 3 L11: 5.9042 L22: 6.2745 REMARK 3 L33: 3.1812 L12: 2.0833 REMARK 3 L13: -0.6935 L23: -0.0503 REMARK 3 S TENSOR REMARK 3 S11: -0.0922 S12: 0.5142 S13: 0.3024 REMARK 3 S21: -0.5484 S22: 0.1106 S23: 0.0585 REMARK 3 S31: -0.1553 S32: 0.7267 S33: -0.0407 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 399 THROUGH 414 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.5178 -41.5368 10.0474 REMARK 3 T TENSOR REMARK 3 T11: 0.5409 T22: 0.4555 REMARK 3 T33: 0.4935 T12: -0.0046 REMARK 3 T13: -0.0298 T23: -0.0195 REMARK 3 L TENSOR REMARK 3 L11: 4.3462 L22: 5.2221 REMARK 3 L33: 3.7736 L12: 0.9766 REMARK 3 L13: -0.2477 L23: -1.6856 REMARK 3 S TENSOR REMARK 3 S11: 0.2100 S12: 0.0108 S13: -0.0493 REMARK 3 S21: 0.7965 S22: 0.0736 S23: 0.0575 REMARK 3 S31: -0.5923 S32: -0.1330 S33: -0.1857 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 415 THROUGH 475 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3973 -32.9458 5.1190 REMARK 3 T TENSOR REMARK 3 T11: 0.5217 T22: 0.4487 REMARK 3 T33: 0.5072 T12: -0.0914 REMARK 3 T13: -0.0834 T23: 0.0208 REMARK 3 L TENSOR REMARK 3 L11: 7.2212 L22: 5.1178 REMARK 3 L33: 3.9637 L12: -0.7979 REMARK 3 L13: 0.5309 L23: -0.5388 REMARK 3 S TENSOR REMARK 3 S11: -0.2788 S12: 0.0030 S13: 0.7855 REMARK 3 S21: -0.1118 S22: 0.1498 S23: 0.2246 REMARK 3 S31: -0.7992 S32: 0.2398 S33: 0.1102 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 476 THROUGH 531 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.3637 -42.1701 6.3424 REMARK 3 T TENSOR REMARK 3 T11: 0.4245 T22: 0.5486 REMARK 3 T33: 0.4694 T12: -0.0544 REMARK 3 T13: -0.0002 T23: 0.0628 REMARK 3 L TENSOR REMARK 3 L11: 4.1135 L22: 6.3783 REMARK 3 L33: 2.4941 L12: 0.0440 REMARK 3 L13: 0.6395 L23: 0.1453 REMARK 3 S TENSOR REMARK 3 S11: -0.0597 S12: 0.0547 S13: 0.0076 REMARK 3 S21: 0.0286 S22: -0.1298 S23: -0.8060 REMARK 3 S31: -0.1864 S32: 0.5319 S33: 0.1566 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 532 THROUGH 558 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.5022 -48.1011 18.7718 REMARK 3 T TENSOR REMARK 3 T11: 0.5364 T22: 0.5986 REMARK 3 T33: 0.5774 T12: -0.0479 REMARK 3 T13: -0.0427 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 8.7094 L22: 2.2732 REMARK 3 L33: 6.2919 L12: -1.8401 REMARK 3 L13: -5.7008 L23: 3.3976 REMARK 3 S TENSOR REMARK 3 S11: 0.1414 S12: -0.4196 S13: -0.0267 REMARK 3 S21: -0.1409 S22: -0.2444 S23: 0.3687 REMARK 3 S31: -0.2941 S32: 0.0567 S33: 0.0007 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 364 THROUGH 374 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.9630 -51.4907 41.8421 REMARK 3 T TENSOR REMARK 3 T11: 0.6851 T22: 0.6208 REMARK 3 T33: 0.5026 T12: -0.0393 REMARK 3 T13: 0.1291 T23: 0.0835 REMARK 3 L TENSOR REMARK 3 L11: 6.1023 L22: 7.6363 REMARK 3 L33: 1.9634 L12: -0.5707 REMARK 3 L13: 1.9301 L23: 1.9931 REMARK 3 S TENSOR REMARK 3 S11: 0.3982 S12: -1.1875 S13: -0.5760 REMARK 3 S21: 0.7188 S22: -0.4981 S23: 0.3739 REMARK 3 S31: -0.3156 S32: -0.5563 S33: 0.1281 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 375 THROUGH 389 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.3432 -30.2515 47.2114 REMARK 3 T TENSOR REMARK 3 T11: 1.1377 T22: 0.8415 REMARK 3 T33: 0.7446 T12: -0.1613 REMARK 3 T13: 0.2029 T23: -0.1652 REMARK 3 L TENSOR REMARK 3 L11: 3.3703 L22: 8.8850 REMARK 3 L33: 2.1000 L12: 0.6693 REMARK 3 L13: 1.1312 L23: 1.1657 REMARK 3 S TENSOR REMARK 3 S11: 0.3530 S12: -0.8944 S13: 0.1881 REMARK 3 S21: 1.5870 S22: -0.4216 S23: 0.3497 REMARK 3 S31: -0.5133 S32: -0.0127 S33: -0.0655 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 390 THROUGH 398 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1099 -29.6245 30.3656 REMARK 3 T TENSOR REMARK 3 T11: 1.0036 T22: 0.5370 REMARK 3 T33: 0.7271 T12: -0.2245 REMARK 3 T13: 0.2173 T23: -0.0775 REMARK 3 L TENSOR REMARK 3 L11: 4.5917 L22: 6.4247 REMARK 3 L33: 7.1894 L12: 4.7365 REMARK 3 L13: 5.6006 L23: 6.5272 REMARK 3 S TENSOR REMARK 3 S11: 0.6241 S12: -0.2532 S13: 0.4110 REMARK 3 S21: -1.5687 S22: 0.1114 S23: -1.1328 REMARK 3 S31: -1.7444 S32: 0.8438 S33: -0.3422 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 399 THROUGH 414 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.2757 -41.5320 31.7417 REMARK 3 T TENSOR REMARK 3 T11: 0.5741 T22: 0.5394 REMARK 3 T33: 0.4386 T12: -0.1777 REMARK 3 T13: 0.0150 T23: 0.0131 REMARK 3 L TENSOR REMARK 3 L11: 2.1742 L22: 8.4649 REMARK 3 L33: 7.2425 L12: 0.5275 REMARK 3 L13: -1.7583 L23: -2.3527 REMARK 3 S TENSOR REMARK 3 S11: -0.2167 S12: -0.0242 S13: -0.4871 REMARK 3 S21: -0.7433 S22: 0.0239 S23: 0.1845 REMARK 3 S31: -0.6126 S32: 0.9106 S33: 0.1823 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 415 THROUGH 428 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.1510 -26.3586 34.0663 REMARK 3 T TENSOR REMARK 3 T11: 1.1317 T22: 0.9635 REMARK 3 T33: 0.9320 T12: -0.4939 REMARK 3 T13: 0.1475 T23: -0.0395 REMARK 3 L TENSOR REMARK 3 L11: 7.9666 L22: 2.0927 REMARK 3 L33: 8.2971 L12: 1.4362 REMARK 3 L13: 1.2983 L23: 2.4196 REMARK 3 S TENSOR REMARK 3 S11: 0.7816 S12: -1.1583 S13: 0.5324 REMARK 3 S21: -0.3793 S22: -0.2164 S23: -0.6966 REMARK 3 S31: -1.0897 S32: 1.2410 S33: -0.5735 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 429 THROUGH 440 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3259 -28.3317 39.1695 REMARK 3 T TENSOR REMARK 3 T11: 1.0446 T22: 0.7996 REMARK 3 T33: 0.6988 T12: -0.1895 REMARK 3 T13: 0.0995 T23: -0.0741 REMARK 3 L TENSOR REMARK 3 L11: 5.6205 L22: 2.6168 REMARK 3 L33: 6.6195 L12: -0.9727 REMARK 3 L13: -4.2333 L23: 2.2999 REMARK 3 S TENSOR REMARK 3 S11: 0.4011 S12: -1.0614 S13: 0.3528 REMARK 3 S21: 0.7825 S22: -0.4692 S23: -0.1204 REMARK 3 S31: -0.5442 S32: 0.6241 S33: -0.0754 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 441 THROUGH 475 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.8988 -34.4919 34.0658 REMARK 3 T TENSOR REMARK 3 T11: 0.7812 T22: 0.5299 REMARK 3 T33: 0.5910 T12: -0.1187 REMARK 3 T13: 0.0084 T23: 0.0103 REMARK 3 L TENSOR REMARK 3 L11: 6.4196 L22: 4.7687 REMARK 3 L33: 5.6224 L12: 0.1485 REMARK 3 L13: -1.2066 L23: 1.1396 REMARK 3 S TENSOR REMARK 3 S11: 0.3974 S12: -0.2056 S13: 0.7081 REMARK 3 S21: 0.0149 S22: -0.3346 S23: -0.4151 REMARK 3 S31: -0.9351 S32: 0.7333 S33: -0.1156 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 476 THROUGH 531 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.9898 -26.0371 34.1285 REMARK 3 T TENSOR REMARK 3 T11: 0.9688 T22: 0.4933 REMARK 3 T33: 0.8500 T12: 0.0204 REMARK 3 T13: 0.1517 T23: -0.0757 REMARK 3 L TENSOR REMARK 3 L11: 6.4505 L22: 4.4451 REMARK 3 L33: 3.6744 L12: 1.4289 REMARK 3 L13: -0.7381 L23: 0.4659 REMARK 3 S TENSOR REMARK 3 S11: 0.4683 S12: 0.1721 S13: 1.0661 REMARK 3 S21: -0.3722 S22: -0.3094 S23: 0.6824 REMARK 3 S31: -1.2774 S32: -0.1435 S33: -0.0899 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 532 THROUGH 558 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.9410 -53.2372 24.1312 REMARK 3 T TENSOR REMARK 3 T11: 0.5197 T22: 0.4970 REMARK 3 T33: 0.5233 T12: 0.0182 REMARK 3 T13: -0.0114 T23: 0.0329 REMARK 3 L TENSOR REMARK 3 L11: 4.9213 L22: 5.3411 REMARK 3 L33: 5.1936 L12: -2.6200 REMARK 3 L13: -2.6703 L23: 2.4136 REMARK 3 S TENSOR REMARK 3 S11: -0.2872 S12: 0.0226 S13: 0.0934 REMARK 3 S21: 0.3124 S22: 0.0294 S23: -0.0836 REMARK 3 S31: 0.3379 S32: 0.1971 S33: 0.2564 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND RESID 364 THROUGH 558) REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 1774 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7QL7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1292119918. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25950 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 65.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 24.30 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 21.80 REMARK 200 R MERGE FOR SHELL (I) : 1.85700 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: PHASER REMARK 200 STARTING MODEL: 4RCI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% PEG3350, 0.2 M KSCN, PH 9.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.15300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 59.92700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 59.92700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.72950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 59.92700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 59.92700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.57650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 59.92700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.92700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 58.72950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 59.92700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.92700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.57650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 39.15300 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 360 REMARK 465 SER A 361 REMARK 465 VAL A 362 REMARK 465 GLY A 459 REMARK 465 THR A 460 REMARK 465 SER A 461 REMARK 465 ALA A 462 REMARK 465 GLY A 463 REMARK 465 VAL A 464 REMARK 465 TRP A 465 REMARK 465 SER A 466 REMARK 465 GLN A 467 REMARK 465 ASP A 468 REMARK 465 LYS A 469 REMARK 465 TRP A 470 REMARK 465 GLN A 559 REMARK 465 GLY B 360 REMARK 465 SER B 361 REMARK 465 VAL B 362 REMARK 465 GLU B 363 REMARK 465 GLY B 459 REMARK 465 THR B 460 REMARK 465 SER B 461 REMARK 465 ALA B 462 REMARK 465 GLY B 463 REMARK 465 VAL B 464 REMARK 465 TRP B 465 REMARK 465 SER B 466 REMARK 465 GLN B 467 REMARK 465 ASP B 468 REMARK 465 LYS B 469 REMARK 465 TRP B 470 REMARK 465 GLN B 559 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 CYS B 412 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 482 147.23 -176.52 REMARK 500 ASN A 497 56.97 -148.48 REMARK 500 LYS B 482 148.22 -174.28 REMARK 500 ASN B 497 62.07 -154.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7PCU RELATED DB: PDB REMARK 900 7PCU CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR INHIBITOR REMARK 900 RELATED ID: 7QKN RELATED DB: PDB REMARK 900 7QKN CONTAINS THE SAME PROTEIN COMPLEXED WITH A SIMILAR INHIBITOR DBREF 7QL7 A 361 559 UNP Q9BYJ9 YTHD1_HUMAN 361 559 DBREF 7QL7 B 361 559 UNP Q9BYJ9 YTHD1_HUMAN 361 559 SEQADV 7QL7 GLY A 360 UNP Q9BYJ9 EXPRESSION TAG SEQADV 7QL7 ALA A 544 UNP Q9BYJ9 GLU 544 ENGINEERED MUTATION SEQADV 7QL7 VAL A 545 UNP Q9BYJ9 GLU 545 ENGINEERED MUTATION SEQADV 7QL7 VAL A 546 UNP Q9BYJ9 GLU 546 ENGINEERED MUTATION SEQADV 7QL7 GLY B 360 UNP Q9BYJ9 EXPRESSION TAG SEQADV 7QL7 ALA B 544 UNP Q9BYJ9 GLU 544 ENGINEERED MUTATION SEQADV 7QL7 VAL B 545 UNP Q9BYJ9 GLU 545 ENGINEERED MUTATION SEQADV 7QL7 VAL B 546 UNP Q9BYJ9 GLU 546 ENGINEERED MUTATION SEQRES 1 A 200 GLY SER VAL GLU SER HIS PRO VAL LEU GLU LYS LEU LYS SEQRES 2 A 200 ALA ALA HIS SER TYR ASN PRO LYS GLU PHE GLU TRP ASN SEQRES 3 A 200 LEU LYS SER GLY ARG VAL PHE ILE ILE LYS SER TYR SER SEQRES 4 A 200 GLU ASP ASP ILE HIS ARG SER ILE LYS TYR SER ILE TRP SEQRES 5 A 200 CYS SER THR GLU HIS GLY ASN LYS ARG LEU ASP SER ALA SEQRES 6 A 200 PHE ARG CYS MET SER SER LYS GLY PRO VAL TYR LEU LEU SEQRES 7 A 200 PHE SER VAL ASN GLY SER GLY HIS PHE CYS GLY VAL ALA SEQRES 8 A 200 GLU MET LYS SER PRO VAL ASP TYR GLY THR SER ALA GLY SEQRES 9 A 200 VAL TRP SER GLN ASP LYS TRP LYS GLY LYS PHE ASP VAL SEQRES 10 A 200 GLN TRP ILE PHE VAL LYS ASP VAL PRO ASN ASN GLN LEU SEQRES 11 A 200 ARG HIS ILE ARG LEU GLU ASN ASN ASP ASN LYS PRO VAL SEQRES 12 A 200 THR ASN SER ARG ASP THR GLN GLU VAL PRO LEU GLU LYS SEQRES 13 A 200 ALA LYS GLN VAL LEU LYS ILE ILE SER SER TYR LYS HIS SEQRES 14 A 200 THR THR SER ILE PHE ASP ASP PHE ALA HIS TYR GLU LYS SEQRES 15 A 200 ARG GLN ALA VAL VAL GLU VAL VAL ARG LYS GLU ARG GLN SEQRES 16 A 200 SER ARG ASN LYS GLN SEQRES 1 B 200 GLY SER VAL GLU SER HIS PRO VAL LEU GLU LYS LEU LYS SEQRES 2 B 200 ALA ALA HIS SER TYR ASN PRO LYS GLU PHE GLU TRP ASN SEQRES 3 B 200 LEU LYS SER GLY ARG VAL PHE ILE ILE LYS SER TYR SER SEQRES 4 B 200 GLU ASP ASP ILE HIS ARG SER ILE LYS TYR SER ILE TRP SEQRES 5 B 200 CYS SER THR GLU HIS GLY ASN LYS ARG LEU ASP SER ALA SEQRES 6 B 200 PHE ARG CYS MET SER SER LYS GLY PRO VAL TYR LEU LEU SEQRES 7 B 200 PHE SER VAL ASN GLY SER GLY HIS PHE CYS GLY VAL ALA SEQRES 8 B 200 GLU MET LYS SER PRO VAL ASP TYR GLY THR SER ALA GLY SEQRES 9 B 200 VAL TRP SER GLN ASP LYS TRP LYS GLY LYS PHE ASP VAL SEQRES 10 B 200 GLN TRP ILE PHE VAL LYS ASP VAL PRO ASN ASN GLN LEU SEQRES 11 B 200 ARG HIS ILE ARG LEU GLU ASN ASN ASP ASN LYS PRO VAL SEQRES 12 B 200 THR ASN SER ARG ASP THR GLN GLU VAL PRO LEU GLU LYS SEQRES 13 B 200 ALA LYS GLN VAL LEU LYS ILE ILE SER SER TYR LYS HIS SEQRES 14 B 200 THR THR SER ILE PHE ASP ASP PHE ALA HIS TYR GLU LYS SEQRES 15 B 200 ARG GLN ALA VAL VAL GLU VAL VAL ARG LYS GLU ARG GLN SEQRES 16 B 200 SER ARG ASN LYS GLN HET E3J A 601 18 HET EDO A 602 4 HET SCN A 603 3 HET E3J B 601 18 HET SCN B 602 3 HETNAM E3J ~{N}-(2-MORPHOLIN-4-YLETHYL)-2-SULFANYL-BENZAMIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM SCN THIOCYANATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 E3J 2(C13 H18 N2 O2 S) FORMUL 4 EDO C2 H6 O2 FORMUL 5 SCN 2(C N S 1-) FORMUL 8 HOH *31(H2 O) HELIX 1 AA1 HIS A 365 HIS A 375 1 11 HELIX 2 AA2 SER A 398 SER A 409 1 12 HELIX 3 AA3 THR A 414 SER A 429 1 16 HELIX 4 AA4 ASN A 487 LEU A 489 5 3 HELIX 5 AA5 LEU A 494 ASP A 498 5 5 HELIX 6 AA6 PRO A 501 SER A 505 5 5 HELIX 7 AA7 PRO A 512 TYR A 526 1 15 HELIX 8 AA8 SER A 531 ASP A 534 5 4 HELIX 9 AA9 ASP A 535 ASN A 557 1 23 HELIX 10 AB1 HIS B 365 HIS B 375 1 11 HELIX 11 AB2 SER B 398 SER B 409 1 12 HELIX 12 AB3 THR B 414 SER B 429 1 16 HELIX 13 AB4 ASN B 487 LEU B 489 5 3 HELIX 14 AB5 LEU B 494 ASP B 498 5 5 HELIX 15 AB6 PRO B 501 SER B 505 5 5 HELIX 16 AB7 PRO B 512 TYR B 526 1 15 HELIX 17 AB8 SER B 531 ASP B 534 5 4 HELIX 18 AB9 ASP B 535 ASN B 557 1 23 SHEET 1 AA1 6 ILE A 410 TRP A 411 0 SHEET 2 AA1 6 PHE A 474 PRO A 485 -1 O PHE A 474 N TRP A 411 SHEET 3 AA1 6 HIS A 445 MET A 452 -1 N VAL A 449 O ILE A 479 SHEET 4 AA1 6 VAL A 434 VAL A 440 -1 N LEU A 436 O ALA A 450 SHEET 5 AA1 6 ARG A 390 SER A 396 1 N ILE A 394 O LEU A 437 SHEET 6 AA1 6 GLU A 510 VAL A 511 -1 O VAL A 511 N VAL A 391 SHEET 1 AA2 6 ILE B 410 TRP B 411 0 SHEET 2 AA2 6 PHE B 474 PRO B 485 -1 O PHE B 474 N TRP B 411 SHEET 3 AA2 6 HIS B 445 MET B 452 -1 N GLU B 451 O GLN B 477 SHEET 4 AA2 6 VAL B 434 VAL B 440 -1 N LEU B 436 O ALA B 450 SHEET 5 AA2 6 ARG B 390 SER B 396 1 N ILE B 394 O LEU B 437 SHEET 6 AA2 6 GLU B 510 VAL B 511 -1 O VAL B 511 N VAL B 391 SSBOND 1 CYS A 427 CYS B 427 1555 8555 2.06 LINK SG CYS A 412 S18 E3J A 601 1555 1555 2.05 LINK SG CYS B 412 S18 E3J B 601 1555 1555 2.03 CRYST1 119.854 119.854 78.306 90.00 90.00 90.00 P 43 21 2 16 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 0.008343 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008343 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012770 0.00000