HEADER RNA BINDING PROTEIN 18-FEB-22 7YYJ TITLE TETRAGONAL CRYSTAL STRUCTURE OF YTHDF1 YTH DOMAIN (544AVV546 MUTANT) 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MRNA BINDING AND STABILITY, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.DALLE VEDOVE,G.CAZZANELLI,G.LOLLI REVDAT 3 13-MAR-24 7YYJ 1 JRNL REVDAT 2 07-FEB-24 7YYJ 1 REMARK REVDAT 1 01-MAR-23 7YYJ 0 JRNL AUTH G.CAZZANELLI,A.DALLE VEDOVE,G.SPAGNOLLI,L.TERRUZZI, JRNL AUTH 2 E.COLASURDO,A.BOLDRINI,A.PATSILINAKOS,M.STURLESE,A.GROTTESI, JRNL AUTH 3 E.BIASINI,A.PROVENZANI,A.QUATTRONE,G.LOLLI JRNL TITL PLIABILITY IN THE M 6 A-BINDING REGION EXTENDS DRUGGABILITY JRNL TITL 2 OF YTH DOMAINS. JRNL REF J.CHEM.INF.MODEL. 2024 JRNL REFN ESSN 1549-960X JRNL PMID 38417111 JRNL DOI 10.1021/ACS.JCIM.4C00051 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 34741 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1721 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 48.1340 - 4.8066 1.00 2997 134 0.1781 0.1940 REMARK 3 2 4.8066 - 3.8157 1.00 2819 149 0.1607 0.1766 REMARK 3 3 3.8157 - 3.3335 1.00 2764 163 0.1910 0.2571 REMARK 3 4 3.3335 - 3.0287 1.00 2776 147 0.2139 0.2230 REMARK 3 5 3.0287 - 2.8117 1.00 2754 147 0.2342 0.2712 REMARK 3 6 2.8117 - 2.6459 1.00 2756 143 0.2342 0.3042 REMARK 3 7 2.6459 - 2.5134 1.00 2741 137 0.2159 0.2850 REMARK 3 8 2.5134 - 2.4040 1.00 2731 142 0.2203 0.2729 REMARK 3 9 2.4040 - 2.3115 1.00 2740 135 0.2256 0.2566 REMARK 3 10 2.3115 - 2.2317 0.94 2538 144 0.3578 0.4453 REMARK 3 11 2.2317 - 2.1619 1.00 2721 125 0.2543 0.2548 REMARK 3 12 2.1619 - 2.1001 0.99 2683 155 0.2862 0.3289 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.34 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 : 0.009 3168 REMARK 3 ANGLE : 0.935 4257 REMARK 3 CHIRALITY : 0.059 441 REMARK 3 PLANARITY : 0.007 545 REMARK 3 DIHEDRAL : 16.455 1924 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 363 THROUGH 389 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6389 -49.2544 -3.2509 REMARK 3 T TENSOR REMARK 3 T11: 0.5041 T22: 0.5014 REMARK 3 T33: 0.3596 T12: 0.0764 REMARK 3 T13: -0.0139 T23: 0.0774 REMARK 3 L TENSOR REMARK 3 L11: 8.4055 L22: 8.8085 REMARK 3 L33: 4.9398 L12: 5.4218 REMARK 3 L13: -0.6128 L23: 0.7444 REMARK 3 S TENSOR REMARK 3 S11: -0.6215 S12: 0.8464 S13: -0.3344 REMARK 3 S21: -1.2050 S22: 0.1821 S23: -0.3565 REMARK 3 S31: 0.4980 S32: -0.0171 S33: 0.4100 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 390 THROUGH 398 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.9930 -37.1931 11.2449 REMARK 3 T TENSOR REMARK 3 T11: 0.4922 T22: 0.4604 REMARK 3 T33: 0.5192 T12: -0.0730 REMARK 3 T13: -0.0094 T23: 0.0466 REMARK 3 L TENSOR REMARK 3 L11: 8.6957 L22: 4.1594 REMARK 3 L33: 2.9664 L12: 5.2125 REMARK 3 L13: -1.9373 L23: 0.4475 REMARK 3 S TENSOR REMARK 3 S11: 0.0116 S12: -0.0764 S13: 0.8212 REMARK 3 S21: 0.3888 S22: 0.1134 S23: 0.0618 REMARK 3 S31: -0.3144 S32: 0.1456 S33: -0.3439 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 399 THROUGH 457 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.4209 -36.3057 6.2907 REMARK 3 T TENSOR REMARK 3 T11: 0.4330 T22: 0.3830 REMARK 3 T33: 0.3772 T12: -0.0480 REMARK 3 T13: -0.0850 T23: 0.0170 REMARK 3 L TENSOR REMARK 3 L11: 6.2025 L22: 8.1542 REMARK 3 L33: 4.0207 L12: 2.7200 REMARK 3 L13: -0.1753 L23: -2.2088 REMARK 3 S TENSOR REMARK 3 S11: -0.1213 S12: 0.0972 S13: 0.6669 REMARK 3 S21: 0.0008 S22: -0.1057 S23: 0.1996 REMARK 3 S31: -0.6391 S32: 0.2362 S33: 0.2389 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 458 THROUGH 475 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.7878 -32.8452 10.8475 REMARK 3 T TENSOR REMARK 3 T11: 0.8792 T22: 0.7927 REMARK 3 T33: 0.8760 T12: 0.0229 REMARK 3 T13: -0.0310 T23: -0.0831 REMARK 3 L TENSOR REMARK 3 L11: 7.3016 L22: 7.4047 REMARK 3 L33: 2.9640 L12: 1.0604 REMARK 3 L13: -4.5589 L23: -1.4577 REMARK 3 S TENSOR REMARK 3 S11: -0.1509 S12: -1.0468 S13: 0.5626 REMARK 3 S21: 1.6012 S22: -0.1164 S23: 1.2290 REMARK 3 S31: -0.5470 S32: -1.5367 S33: 0.7704 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 476 THROUGH 531 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.7355 -42.6644 6.1926 REMARK 3 T TENSOR REMARK 3 T11: 0.4114 T22: 0.5555 REMARK 3 T33: 0.4703 T12: -0.0675 REMARK 3 T13: -0.0332 T23: 0.1456 REMARK 3 L TENSOR REMARK 3 L11: 5.5320 L22: 6.7517 REMARK 3 L33: 3.2653 L12: 1.8403 REMARK 3 L13: 0.2652 L23: -0.0609 REMARK 3 S TENSOR REMARK 3 S11: -0.0658 S12: 0.0502 S13: -0.1285 REMARK 3 S21: 0.1045 S22: -0.2683 S23: -0.9499 REMARK 3 S31: -0.1974 S32: 0.7282 S33: 0.3176 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 532 THROUGH 558 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.4081 -48.5466 18.7914 REMARK 3 T TENSOR REMARK 3 T11: 0.3679 T22: 0.5412 REMARK 3 T33: 0.5148 T12: -0.0143 REMARK 3 T13: -0.0413 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 8.2210 L22: 7.7066 REMARK 3 L33: 9.6650 L12: -3.7677 REMARK 3 L13: -5.4661 L23: 5.7386 REMARK 3 S TENSOR REMARK 3 S11: -0.0782 S12: -0.6129 S13: -0.2115 REMARK 3 S21: -0.0493 S22: -0.3211 S23: 0.9586 REMARK 3 S31: -0.3065 S32: -0.5781 S33: 0.3558 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 364 THROUGH 374 ) REMARK 3 ORIGIN FOR THE GROUP (A): 51.9003 -2.7884 -2.3859 REMARK 3 T TENSOR REMARK 3 T11: 0.6621 T22: 0.7578 REMARK 3 T33: 0.4902 T12: -0.0602 REMARK 3 T13: 0.0898 T23: 0.1752 REMARK 3 L TENSOR REMARK 3 L11: 4.1121 L22: 2.8355 REMARK 3 L33: 9.6187 L12: 0.2777 REMARK 3 L13: 5.5810 L23: 2.7686 REMARK 3 S TENSOR REMARK 3 S11: -0.4965 S12: 1.2138 S13: 0.8142 REMARK 3 S21: -1.4446 S22: 0.4505 S23: -0.3319 REMARK 3 S31: -0.3971 S32: -0.2441 S33: 0.0537 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 375 THROUGH 388 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.9747 -1.1485 -8.0608 REMARK 3 T TENSOR REMARK 3 T11: 0.9088 T22: 1.1450 REMARK 3 T33: 0.6878 T12: -0.2062 REMARK 3 T13: -0.1784 T23: 0.2960 REMARK 3 L TENSOR REMARK 3 L11: 1.7807 L22: 4.1845 REMARK 3 L33: 3.7042 L12: -0.3007 REMARK 3 L13: 1.2266 L23: 0.5744 REMARK 3 S TENSOR REMARK 3 S11: 0.1361 S12: 1.9808 S13: 0.4113 REMARK 3 S21: -1.0932 S22: 0.1080 S23: 0.5623 REMARK 3 S31: -0.3298 S32: -0.7688 S33: -0.1244 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 389 THROUGH 398 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.6425 -8.6306 9.5625 REMARK 3 T TENSOR REMARK 3 T11: 0.5675 T22: 1.0222 REMARK 3 T33: 0.6475 T12: -0.2403 REMARK 3 T13: -0.0977 T23: 0.2843 REMARK 3 L TENSOR REMARK 3 L11: 4.8576 L22: 6.0091 REMARK 3 L33: 5.4252 L12: 5.3970 REMARK 3 L13: 5.1323 L23: 5.7143 REMARK 3 S TENSOR REMARK 3 S11: 0.4663 S12: -1.2436 S13: -0.4139 REMARK 3 S21: -0.2051 S22: 0.2182 S23: 0.7083 REMARK 3 S31: 1.1728 S32: -1.8659 S33: -0.6845 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 399 THROUGH 414 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.9648 -10.4253 7.8635 REMARK 3 T TENSOR REMARK 3 T11: 0.6401 T22: 0.6139 REMARK 3 T33: 0.3959 T12: -0.1356 REMARK 3 T13: -0.0276 T23: 0.0983 REMARK 3 L TENSOR REMARK 3 L11: 2.2999 L22: 5.2475 REMARK 3 L33: 4.3471 L12: 2.5571 REMARK 3 L13: -1.7123 L23: -2.2912 REMARK 3 S TENSOR REMARK 3 S11: 0.0658 S12: -0.4655 S13: 0.0883 REMARK 3 S21: -0.3670 S22: 0.0420 S23: -0.0850 REMARK 3 S31: 1.3341 S32: -0.6910 S33: -0.0525 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 415 THROUGH 475 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.7866 -13.9662 3.9552 REMARK 3 T TENSOR REMARK 3 T11: 0.7090 T22: 0.8771 REMARK 3 T33: 0.5576 T12: -0.3295 REMARK 3 T13: -0.1305 T23: 0.1884 REMARK 3 L TENSOR REMARK 3 L11: 5.5869 L22: 5.3458 REMARK 3 L33: 4.1937 L12: 0.0851 REMARK 3 L13: 1.7211 L23: -0.0252 REMARK 3 S TENSOR REMARK 3 S11: 0.0417 S12: -0.0984 S13: -0.5610 REMARK 3 S21: -0.6579 S22: 0.4806 S23: 0.7777 REMARK 3 S31: 1.0262 S32: -1.1596 S33: -0.3943 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 476 THROUGH 531 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.2986 0.5929 5.5092 REMARK 3 T TENSOR REMARK 3 T11: 0.5011 T22: 1.1130 REMARK 3 T33: 0.8533 T12: 0.0291 REMARK 3 T13: -0.0604 T23: 0.2125 REMARK 3 L TENSOR REMARK 3 L11: 5.4747 L22: 5.2730 REMARK 3 L33: 3.5715 L12: 1.4681 REMARK 3 L13: 0.9066 L23: -1.0147 REMARK 3 S TENSOR REMARK 3 S11: -0.1931 S12: -0.4530 S13: 0.9708 REMARK 3 S21: 0.0411 S22: 0.4558 S23: 1.2280 REMARK 3 S31: -0.1852 S32: -1.7099 S33: -0.2471 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 532 THROUGH 558 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.7630 -10.0390 15.6040 REMARK 3 T TENSOR REMARK 3 T11: 0.4987 T22: 0.4495 REMARK 3 T33: 0.5019 T12: 0.0556 REMARK 3 T13: 0.0951 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 6.1127 L22: 6.4433 REMARK 3 L33: 3.9991 L12: -2.5285 REMARK 3 L13: 3.0136 L23: -4.7125 REMARK 3 S TENSOR REMARK 3 S11: -0.1249 S12: 0.0217 S13: -0.0164 REMARK 3 S21: -0.1975 S22: -0.1297 S23: -0.2173 REMARK 3 S31: 0.2825 S32: 0.2754 S33: 0.3820 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 396 OR REMARK 3 RESID 398 THROUGH 403 OR RESID 405 REMARK 3 THROUGH 458 OR RESID 472 THROUGH 517 OR REMARK 3 RESID 519 THROUGH 558)) REMARK 3 SELECTION : (CHAIN B AND (RESID 364 THROUGH 396 OR REMARK 3 RESID 398 THROUGH 403 OR RESID 405 REMARK 3 THROUGH 458 OR RESID 472 THROUGH 517 OR REMARK 3 RESID 519 THROUGH 558)) REMARK 3 ATOM PAIRS NUMBER : 1721 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7YYJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292121211. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-20 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) : 0.9998 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 : 35009 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 79.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 23.50 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.60 REMARK 200 R MERGE FOR SHELL (I) : 1.79300 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 (%): 60.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6-12% PEG3350, 0.2 M KSCN, PH 9.5, REMARK 280 VAPOR 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 39.81800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 60.42050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 60.42050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.72700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 60.42050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 60.42050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.90900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 60.42050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.42050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 59.72700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 60.42050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.42050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.90900 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 39.81800 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 LYS A 471 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 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 LYS B 471 REMARK 465 GLN B 559 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 387 CD CE NZ REMARK 470 TYR A 397 CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 558 CG CD CE NZ REMARK 470 SER B 364 OG REMARK 470 GLU B 383 CG CD OE1 OE2 REMARK 470 ASN B 385 CG OD1 ND2 REMARK 470 LEU B 386 CD1 CD2 REMARK 470 LYS B 387 CG CD CE NZ REMARK 470 SER B 388 OG REMARK 470 VAL B 391 CG2 REMARK 470 TYR B 397 CD1 CD2 CE1 CE2 CZ OH REMARK 470 MET B 428 SD CE REMARK 470 LYS B 431 CG CD CE NZ REMARK 470 LEU B 494 CG CD1 CD2 REMARK 470 GLU B 495 CG CD OE1 OE2 REMARK 470 LEU B 513 CD1 CD2 REMARK 470 LYS B 515 CD CE NZ REMARK 470 GLN B 518 CG CD OE1 NE2 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 SER A 376 76.05 -105.78 REMARK 500 SER A 430 15.68 57.81 REMARK 500 LYS A 482 144.92 -172.74 REMARK 500 SER B 376 79.92 -112.58 REMARK 500 LYS B 482 146.95 -172.15 REMARK 500 ASN B 497 51.33 -144.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7YYE RELATED DB: PDB REMARK 900 7YYE CONTAINS THE SAME PROTEIN IN A DIFFERENT SPACE GROUP. REMARK 900 RELATED ID: 7YYF RELATED DB: PDB REMARK 900 7YYF CONTAINS THE SAME PROTEIN IN A DIFFERENT SPACE GROUP. DBREF 7YYJ A 361 559 UNP Q9BYJ9 YTHD1_HUMAN 361 559 DBREF 7YYJ B 361 559 UNP Q9BYJ9 YTHD1_HUMAN 361 559 SEQADV 7YYJ GLY A 360 UNP Q9BYJ9 EXPRESSION TAG SEQADV 7YYJ ALA A 544 UNP Q9BYJ9 GLU 544 ENGINEERED MUTATION SEQADV 7YYJ VAL A 545 UNP Q9BYJ9 GLU 545 ENGINEERED MUTATION SEQADV 7YYJ VAL A 546 UNP Q9BYJ9 GLU 546 ENGINEERED MUTATION SEQADV 7YYJ GLY B 360 UNP Q9BYJ9 EXPRESSION TAG SEQADV 7YYJ ALA B 544 UNP Q9BYJ9 GLU 544 ENGINEERED MUTATION SEQADV 7YYJ VAL B 545 UNP Q9BYJ9 GLU 545 ENGINEERED MUTATION SEQADV 7YYJ 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 EDO A 601 4 HET EDO A 602 4 HET SCN A 603 3 HET EDO A 604 4 HET SCN B 601 3 HET EDO B 602 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM SCN THIOCYANATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 4(C2 H6 O2) FORMUL 5 SCN 2(C N S 1-) FORMUL 9 HOH *62(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 CYS B 427 1 14 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 VAL B 449 O ILE B 479 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 1555 2.07 CRYST1 120.841 120.841 79.636 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 0.008275 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008275 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012557 0.00000