HEADER RNA BINDING PROTEIN 18-DEC-21 7QKN TITLE CRYSTAL STRUCTURE OF YTHDF1 YTH DOMAIN IN COMPLEX WITH THE EBSULFUR TITLE 2 DERIVATIVE COMPOUND 7 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 7QKN 1 REMARK REVDAT 1 23-NOV-22 7QKN 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. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 31689 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1521 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 44.2760 - 4.7799 1.00 2931 159 0.1607 0.1773 REMARK 3 2 4.7799 - 3.7946 1.00 2822 114 0.1507 0.1655 REMARK 3 3 3.7946 - 3.3151 1.00 2757 138 0.1867 0.2360 REMARK 3 4 3.3151 - 3.0121 1.00 2734 145 0.2037 0.2564 REMARK 3 5 3.0121 - 2.7962 1.00 2720 145 0.2179 0.2261 REMARK 3 6 2.7962 - 2.6314 1.00 2709 123 0.2122 0.2306 REMARK 3 7 2.6314 - 2.4996 1.00 2743 125 0.2062 0.2672 REMARK 3 8 2.4996 - 2.3908 1.00 2679 143 0.2015 0.2291 REMARK 3 9 2.3908 - 2.2988 1.00 2712 137 0.2064 0.2292 REMARK 3 10 2.2988 - 2.2195 1.00 2694 131 0.2305 0.2498 REMARK 3 11 2.2195 - 2.1501 1.00 2667 161 0.2444 0.2756 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.19 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 3216 REMARK 3 ANGLE : 0.974 4311 REMARK 3 CHIRALITY : 0.060 445 REMARK 3 PLANARITY : 0.006 549 REMARK 3 DIHEDRAL : 19.726 1930 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 363 THROUGH 374 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.2814 -55.2953 1.8767 REMARK 3 T TENSOR REMARK 3 T11: 0.5623 T22: 0.4747 REMARK 3 T33: 0.4884 T12: -0.0246 REMARK 3 T13: 0.0301 T23: -0.0433 REMARK 3 L TENSOR REMARK 3 L11: 3.8014 L22: 8.4518 REMARK 3 L33: 2.7980 L12: 5.1330 REMARK 3 L13: -2.8439 L23: -2.9459 REMARK 3 S TENSOR REMARK 3 S11: -0.3654 S12: -0.1826 S13: -0.7168 REMARK 3 S21: -0.9869 S22: -0.3498 S23: 0.2581 REMARK 3 S31: 1.6750 S32: 0.0711 S33: 0.5825 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 375 THROUGH 398 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.5062 -41.0892 -0.2483 REMARK 3 T TENSOR REMARK 3 T11: 0.3549 T22: 0.4422 REMARK 3 T33: 0.3337 T12: -0.0108 REMARK 3 T13: -0.0119 T23: 0.0924 REMARK 3 L TENSOR REMARK 3 L11: 6.3787 L22: 4.6799 REMARK 3 L33: 3.0934 L12: 2.0985 REMARK 3 L13: -1.1100 L23: 0.3725 REMARK 3 S TENSOR REMARK 3 S11: -0.1664 S12: 0.7024 S13: 0.0845 REMARK 3 S21: -0.4324 S22: 0.1704 S23: -0.2489 REMARK 3 S31: -0.0936 S32: 0.7700 S33: -0.0793 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 399 THROUGH 440 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4834 -34.5413 6.2063 REMARK 3 T TENSOR REMARK 3 T11: 0.3335 T22: 0.2773 REMARK 3 T33: 0.3090 T12: -0.0363 REMARK 3 T13: -0.0088 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 6.2892 L22: 7.1577 REMARK 3 L33: 4.8190 L12: 1.8227 REMARK 3 L13: 0.7524 L23: -1.8186 REMARK 3 S TENSOR REMARK 3 S11: -0.0524 S12: 0.2360 S13: 0.5553 REMARK 3 S21: -0.0443 S22: 0.0043 S23: 0.0899 REMARK 3 S31: -0.4346 S32: 0.1775 S33: 0.0771 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 441 THROUGH 475 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9352 -36.3035 6.7651 REMARK 3 T TENSOR REMARK 3 T11: 0.2515 T22: 0.3155 REMARK 3 T33: 0.2894 T12: -0.1029 REMARK 3 T13: -0.0108 T23: -0.0262 REMARK 3 L TENSOR REMARK 3 L11: 7.9907 L22: 9.3067 REMARK 3 L33: 6.0033 L12: -0.9598 REMARK 3 L13: 1.5891 L23: -2.9993 REMARK 3 S TENSOR REMARK 3 S11: -0.1321 S12: -0.3168 S13: 0.4428 REMARK 3 S21: 0.1395 S22: 0.1279 S23: 0.4506 REMARK 3 S31: -0.3624 S32: -0.0650 S33: 0.0744 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 476 THROUGH 531 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.1453 -41.9349 6.4173 REMARK 3 T TENSOR REMARK 3 T11: 0.3243 T22: 0.4254 REMARK 3 T33: 0.4069 T12: -0.0467 REMARK 3 T13: 0.0147 T23: 0.0665 REMARK 3 L TENSOR REMARK 3 L11: 5.3378 L22: 6.3779 REMARK 3 L33: 2.9170 L12: 1.1873 REMARK 3 L13: 0.6884 L23: 0.0876 REMARK 3 S TENSOR REMARK 3 S11: 0.0369 S12: -0.0162 S13: -0.0120 REMARK 3 S21: 0.0750 S22: -0.1828 S23: -0.9549 REMARK 3 S31: -0.0381 S32: 0.4840 S33: 0.1268 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 532 THROUGH 558 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.6349 -48.0783 19.0637 REMARK 3 T TENSOR REMARK 3 T11: 0.3379 T22: 0.3678 REMARK 3 T33: 0.3769 T12: -0.0297 REMARK 3 T13: -0.0313 T23: 0.0298 REMARK 3 L TENSOR REMARK 3 L11: 7.9455 L22: 5.8868 REMARK 3 L33: 9.1695 L12: -4.9482 REMARK 3 L13: -6.7730 L23: 5.9567 REMARK 3 S TENSOR REMARK 3 S11: -0.1074 S12: -0.1098 S13: -0.1208 REMARK 3 S21: -0.0028 S22: -0.0221 S23: 0.5012 REMARK 3 S31: -0.0081 S32: -0.2175 S33: 0.0382 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 364 THROUGH 452 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.7797 -33.9907 37.2396 REMARK 3 T TENSOR REMARK 3 T11: 0.5550 T22: 0.4274 REMARK 3 T33: 0.3400 T12: -0.1785 REMARK 3 T13: 0.0418 T23: -0.0379 REMARK 3 L TENSOR REMARK 3 L11: 2.5615 L22: 5.6914 REMARK 3 L33: 3.6205 L12: -0.1383 REMARK 3 L13: -1.3357 L23: 1.1912 REMARK 3 S TENSOR REMARK 3 S11: 0.3347 S12: -0.3022 S13: 0.3943 REMARK 3 S21: 0.1308 S22: -0.1500 S23: -0.1114 REMARK 3 S31: -1.0033 S32: 0.4573 S33: -0.1116 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 453 THROUGH 468 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9165 -39.6152 33.4478 REMARK 3 T TENSOR REMARK 3 T11: 0.7759 T22: 1.1792 REMARK 3 T33: 0.7800 T12: -0.2992 REMARK 3 T13: 0.1017 T23: -0.1793 REMARK 3 L TENSOR REMARK 3 L11: 5.8598 L22: 2.2456 REMARK 3 L33: 4.6883 L12: -1.1011 REMARK 3 L13: 0.9112 L23: -0.7531 REMARK 3 S TENSOR REMARK 3 S11: -0.4102 S12: 1.1262 S13: -1.1021 REMARK 3 S21: -0.3608 S22: 0.3110 S23: -0.7132 REMARK 3 S31: 1.1154 S32: 1.1202 S33: 0.5224 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 469 THROUGH 558 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.0641 -35.2584 31.0403 REMARK 3 T TENSOR REMARK 3 T11: 0.5153 T22: 0.2945 REMARK 3 T33: 0.4318 T12: -0.0373 REMARK 3 T13: 0.0272 T23: 0.0476 REMARK 3 L TENSOR REMARK 3 L11: 2.1820 L22: 3.2389 REMARK 3 L33: 4.8399 L12: -0.0545 REMARK 3 L13: -1.4225 L23: 2.0789 REMARK 3 S TENSOR REMARK 3 S11: 0.3637 S12: -0.0805 S13: 0.4640 REMARK 3 S21: -0.3200 S22: -0.1818 S23: 0.1203 REMARK 3 S31: -0.9959 S32: 0.0484 S33: -0.1289 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 AND (RESID 364 THROUGH 458 OR REMARK 3 RESID 471 THROUGH 558)) REMARK 3 ATOM PAIRS NUMBER : 1797 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7QKN 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_1292119875. 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 : 31749 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 119.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 24.00 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.70 REMARK 200 R MERGE FOR SHELL (I) : 1.66600 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 (%): 59.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 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 39.35250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 59.87450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 59.87450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.02875 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 59.87450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 59.87450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.67625 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 59.87450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.87450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 59.02875 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 59.87450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.87450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.67625 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 39.35250 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 SER B 466 REMARK 465 GLN B 467 REMARK 465 GLN B 559 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 482 142.11 -174.67 REMARK 500 ASN A 497 59.97 -143.61 REMARK 500 SER B 429 29.85 49.35 REMARK 500 LYS B 482 144.22 -173.84 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 DBREF 7QKN A 361 559 UNP Q9BYJ9 YTHD1_HUMAN 361 559 DBREF 7QKN B 361 559 UNP Q9BYJ9 YTHD1_HUMAN 361 559 SEQADV 7QKN GLY A 360 UNP Q9BYJ9 EXPRESSION TAG SEQADV 7QKN ALA A 544 UNP Q9BYJ9 GLU 544 ENGINEERED MUTATION SEQADV 7QKN VAL A 545 UNP Q9BYJ9 GLU 545 ENGINEERED MUTATION SEQADV 7QKN VAL A 546 UNP Q9BYJ9 GLU 546 ENGINEERED MUTATION SEQADV 7QKN GLY B 360 UNP Q9BYJ9 EXPRESSION TAG SEQADV 7QKN ALA B 544 UNP Q9BYJ9 GLU 544 ENGINEERED MUTATION SEQADV 7QKN VAL B 545 UNP Q9BYJ9 GLU 545 ENGINEERED MUTATION SEQADV 7QKN 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 JVF A 601 17 HET EDO A 602 4 HET EDO A 603 4 HET SCN A 604 3 HET JVF B 601 17 HET EDO B 602 4 HET SCN B 603 3 HETNAM JVF ~{N}-[2-(DIETHYLAMINO)ETHYL]-2-SULFANYL-BENZAMIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM SCN THIOCYANATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 JVF 2(C13 H20 N2 O S) FORMUL 4 EDO 3(C2 H6 O2) FORMUL 6 SCN 2(C N S 1-) FORMUL 10 HOH *106(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 ASP B 468 GLY B 472 5 5 HELIX 14 AB5 ASN B 487 LEU B 489 5 3 HELIX 15 AB6 LEU B 494 ASP B 498 5 5 HELIX 16 AB7 PRO B 501 SER B 505 5 5 HELIX 17 AB8 PRO B 512 TYR B 526 1 15 HELIX 18 AB9 SER B 531 ASP B 534 5 4 HELIX 19 AC1 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 PHE A 446 O VAL A 484 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 S17 JVF A 601 1555 1555 2.04 LINK SG CYS B 412 S17 JVF B 601 1555 1555 2.03 CRYST1 119.749 119.749 78.705 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 0.008351 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008351 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012706 0.00000