0.013410 0.000000 0.000000 0.000000 0.008660 0.000000 0.000000 0.000000 0.025031 0.00000 0.00000 0.00000 3.54356 2.42580 25.62398 1.50364 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 4.01032 2.96436 19.97189 1.75589 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 4.49882 3.47563 15.80542 1.70748 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 9.51135 5.44231 1.42069 35.72801 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. 9.55732 6.39887 1.23737 29.19336 0.0 2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. Bedi, R.K. Caflisch, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 74.570 115.469 39.951 343999.018 C11 H16 N5 O6 P 345.248 n N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE DNA linking C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C Y 18 N N Y 19 N C Y 20 N N Y 21 N C N 22 N N N 23 N C N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N N N 41 S C N 42 N C N 43 N O N 44 N C N 45 N O N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N H N 52 N H N 53 N N N 54 S C N 55 N C N 56 N O N 57 N C N 58 N C N 59 N C N 60 N N N 61 N C N 62 N N N 63 N N N 64 N O N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N N N 81 S C N 82 N C N 83 N O N 84 N C N 85 N C N 86 N O N 87 N N N 88 N O N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N N N 98 S C N 99 N C N 100 N O N 101 N C N 102 N C N 103 N O N 104 N O N 105 N O N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N O N 114 N P N 115 N O N 116 N O N 117 N O N 118 N C N 119 R C N 120 N O N 121 S C N 122 N O N 123 N C N 124 R C Y 125 N N Y 126 N C Y 127 N N Y 128 N C Y 129 N C N 130 N N Y 131 N N Y 132 N C Y 133 N N Y 134 N C N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N O N 150 N P N 151 N O N 152 N O N 153 N O N 154 N C N 155 R C N 156 N O N 157 S C N 158 N O N 159 N C N 160 R C N 161 N N N 162 N C N 163 N O N 164 N N N 165 N C N 166 N N N 167 N C N 168 N C N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N O N 184 N P N 185 N O N 186 N O N 187 N O N 188 N C N 189 R C N 190 N O N 191 S C N 192 N O N 193 N C N 194 R C Y 195 N N Y 196 N C Y 197 N N Y 198 N C N 199 N C N 200 N O N 201 N N N 202 N C N 203 N N N 204 N N Y 205 N C N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N O N 221 N P N 222 N O N 223 N O N 224 N O N 225 N C N 226 R C N 227 N O N 228 S C N 229 N O N 230 N C N 231 R C N 232 N N N 233 N C N 234 N O N 235 N N N 236 N C N 237 N O N 238 N C N 239 N C N 240 N C N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N N N 257 S C N 258 N C N 259 N O N 260 N C N 261 N C N 262 N C N 263 N O N 264 N N N 265 N O N 266 N H N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N N N 277 S C N 278 N C N 279 N O N 280 N C N 281 N C N 282 N C N 283 N O N 284 N O N 285 N O N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N N N 296 N C N 297 N C N 298 N O N 299 N O N 300 N H N 301 N H N 302 N H N 303 N H N 304 N H N 305 N N N 306 S C N 307 N C N 308 N O N 309 N C Y 310 N C Y 311 N N Y 312 N C Y 313 N C Y 314 N N N 315 N O N 316 N H N 317 N H N 318 N H N 319 N H N 320 N H N 321 N H N 322 N H N 323 N H N 324 N H N 325 N H N 326 N O N 327 N H N 328 N H N 329 N N N 330 S C N 331 N C N 332 N O N 333 S C N 334 N C N 335 N C N 336 N C N 337 N O N 338 N H N 339 N H N 340 N H N 341 N H N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N N N 352 S C N 353 N C N 354 N O N 355 N C N 356 N C N 357 N C N 358 N C N 359 N O N 360 N H N 361 N H N 362 N H N 363 N H N 364 N H N 365 N H N 366 N H N 367 N H N 368 N H N 369 N H N 370 N H N 371 N H N 372 N H N 373 N N N 374 S C N 375 N C N 376 N O N 377 N C N 378 N C N 379 N C N 380 N C N 381 N N N 382 N O N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N H N 390 N H N 391 N H N 392 N H N 393 N H N 394 N H N 395 N H N 396 N H N 397 N H N 398 N N N 399 S C N 400 N C N 401 N O N 402 N C N 403 N C N 404 N S N 405 N C N 406 N O N 407 N H N 408 N H N 409 N H N 410 N H N 411 N H N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N H N 418 N N N 419 S C N 420 N C N 421 N O N 422 N C Y 423 N C Y 424 N C Y 425 N C Y 426 N C Y 427 N C Y 428 N C N 429 N O N 430 N H N 431 N H N 432 N H N 433 N H N 434 N H N 435 N H N 436 N H N 437 N H N 438 N H N 439 N H N 440 N H N 441 N N N 442 S C N 443 N C N 444 N O N 445 N C N 446 N C N 447 N C N 448 N O N 449 N H N 450 N H N 451 N H N 452 N H N 453 N H N 454 N H N 455 N H N 456 N H N 457 N H N 458 N N N 459 S C N 460 N C N 461 N O N 462 N C N 463 N O N 464 N O N 465 N H N 466 N H N 467 N H N 468 N H N 469 N H N 470 N H N 471 N H N 472 N N N 473 S C N 474 N C N 475 N O N 476 R C N 477 N O N 478 N C N 479 N O N 480 N H N 481 N H N 482 N H N 483 N H N 484 N H N 485 N H N 486 N H N 487 N H N 488 N H N 489 N N N 490 S C N 491 N C N 492 N O N 493 N C Y 494 N C Y 495 N C Y 496 N C Y 497 N N Y 498 N C Y 499 N C Y 500 N C Y 501 N C Y 502 N C N 503 N O N 504 N H N 505 N H N 506 N H N 507 N H N 508 N H N 509 N H N 510 N H N 511 N H N 512 N H N 513 N H N 514 N H N 515 N H N 516 N N N 517 S C N 518 N C N 519 N O N 520 N C Y 521 N C Y 522 N C Y 523 N C Y 524 N C Y 525 N C Y 526 N C N 527 N O N 528 N O N 529 N H N 530 N H N 531 N H N 532 N H N 533 N H N 534 N H N 535 N H N 536 N H N 537 N H N 538 N H N 539 N H N 540 N N N 541 S C N 542 N C N 543 N O N 544 N C N 545 N C N 546 N C N 547 N O N 548 N H N 549 N H N 550 N H N 551 N H N 552 N H N 553 N H N 554 N H N 555 N H N 556 N H N 557 N H N 558 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub Y 31 N doub N 32 N sing Y 33 N sing Y 34 N doub N 35 N sing Y 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N doub N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N doub N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N doub N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N doub N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N doub N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N doub N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing Y 134 N sing Y 135 N sing Y 136 N doub N 137 N sing Y 138 N sing Y 139 N sing Y 140 N doub N 141 N sing Y 142 N doub N 143 N sing N 144 N sing Y 145 N sing Y 146 N doub N 147 N sing Y 148 N sing N 149 N sing N 150 N sing N 151 N doub N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N doub N 175 N sing N 176 N doub N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N doub N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N doub N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing Y 207 N sing Y 208 N sing Y 209 N doub N 210 N sing Y 211 N sing N 212 N sing Y 213 N doub N 214 N doub N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N doub N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N doub N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N doub N 249 N sing N 250 N sing N 251 N sing N 252 N doub N 253 N sing N 254 N sing N 255 N doub N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N doub N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N doub N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N doub N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N doub N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N doub N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N doub N 313 N sing N 314 N sing N 315 N sing N 316 N sing Y 317 N sing Y 318 N doub Y 319 N doub N 320 N sing Y 321 N sing N 322 N sing Y 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N doub N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N doub N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N doub N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N sing N 394 N sing N 395 N sing N 396 N sing N 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N doub N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 409 N sing N 410 N sing N 411 N sing N 412 N sing N 413 N sing N 414 N sing N 415 N sing N 416 N sing N 417 N sing N 418 N sing N 419 N sing N 420 N doub N 421 N sing N 422 N sing N 423 N sing N 424 N sing Y 425 N doub Y 426 N sing Y 427 N sing N 428 N sing Y 429 N doub N 430 N sing Y 431 N doub N 432 N sing Y 433 N sing N 434 N sing N 435 N sing N 436 N sing N 437 N sing N 438 N sing N 439 N sing N 440 N sing N 441 N sing N 442 N sing N 443 N doub N 444 N sing N 445 N sing N 446 N sing N 447 N sing N 448 N sing N 449 N sing N 450 N sing N 451 N sing N 452 N sing N 453 N sing N 454 N sing N 455 N sing N 456 N sing N 457 N sing N 458 N sing N 459 N sing N 460 N doub N 461 N sing N 462 N sing N 463 N sing N 464 N sing N 465 N sing N 466 N sing N 467 N sing N 468 N sing N 469 N sing N 470 N sing N 471 N sing N 472 N sing N 473 N doub N 474 N sing N 475 N sing N 476 N sing N 477 N sing N 478 N sing N 479 N sing N 480 N sing N 481 N sing N 482 N sing N 483 N sing N 484 N sing N 485 N sing N 486 N sing N 487 N sing N 488 N sing N 489 N doub N 490 N sing N 491 N sing N 492 N sing N 493 N sing Y 494 N doub Y 495 N sing Y 496 N sing N 497 N sing Y 498 N doub Y 499 N sing Y 500 N sing N 501 N sing Y 502 N sing Y 503 N doub N 504 N sing Y 505 N doub N 506 N sing Y 507 N sing N 508 N sing N 509 N sing N 510 N sing N 511 N sing N 512 N sing N 513 N sing N 514 N sing N 515 N sing N 516 N sing N 517 N doub N 518 N sing N 519 N sing N 520 N sing N 521 N sing Y 522 N doub Y 523 N sing Y 524 N sing N 525 N sing Y 526 N doub N 527 N sing Y 528 N doub N 529 N sing Y 530 N sing N 531 N sing N 532 N sing N 533 N sing N 534 N sing N 535 N sing N 536 N sing N 537 N sing N 538 N sing N 539 N sing N 540 N sing N 541 N doub N 542 N sing N 543 N sing N 544 N sing N 545 N sing N 546 N sing N 547 N sing N 548 N sing N 549 N sing N 550 N sing N 551 N sing N 552 N sing GE Chembiochem 1439-7633 27 e202500897 e202500897 10.1002/cbic.202500897 41863816 A DNA-Based Binding Assay for the m 6 A-RNA Reader Proteins. 2026 0000-0002-2317-6792 10.2210/pdb9szp/pdb pdb_00009szp 100 1 N PIXEL 2025-06-20 DECTRIS EIGER X 16M SINGLE WAVELENGTH M x-ray 1 1.05965 1.0 P13 (MX1) PETRA III, EMBL c/o DESY 1.05965 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 18683.969 3'-5' RNA helicase YTHDC2 3.6.4.13 1 man polymer 1847.269 DNA (5'-D(*GP*GP*(6MA)P*CP*TP*A)-3') 1 syn polymer 18.015 water 173 nat water YTH domain-containing protein 2,hYTHDC2 no no MGSSHHHHHHSQDPENLYFQGNMPVRYFIMKSSNLRNLEISQQKGIWSTTPSNERKLNRAFWESSIVYLVFSVQGSGHFQ GFSRMSSEIGREKSQDWGSAGLGGVFKVEWIRKESLPFQFAHHLLNPWNDNKKVQISRDGQELEPLVGEQLLQLWERLPL G MGSSHHHHHHSQDPENLYFQGNMPVRYFIMKSSNLRNLEISQQKGIWSTTPSNERKLNRAFWESSIVYLVFSVQGSGHFQ GFSRMSSEIGREKSQDWGSAGLGGVFKVEWIRKESLPFQFAHHLLNPWNDNKKVQISRDGQELEPLVGEQLLQLWERLPL G A polypeptide(L) no yes (DG)(DG)(6MA)(DC)(DT)(DA) GGACTA B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human sample 1 161 YTHDC2 9606 Homo sapiens 562 Escherichia coli Biological sequence 1 2.09 41.27 VAPOR DIFFUSION, HANGING DROP 20% PEG 3350, 200 mM KNO3 295 repository Initial release 1 0 2026-04-01 Switzerland Swiss National Science Foundation 310030B_189363 caflisch@bioc.uzh.ch 0000-0002-2317-6792 Amedeo Caflisch principal investigator/group leader N PDBE Y PDBE 2025-10-15 REL REL 6MA 6MA SUBJECT OF INVESTIGATION HOH water 2853804 DNA molecule sample 1 6 Y N 4R3I PDB experimental model HOH 10 3 HOH HOH 1501 A HOH 164 3 HOH HOH 1502 A HOH 13 3 HOH HOH 1503 A HOH 2 3 HOH HOH 1504 A HOH 39 3 HOH HOH 1505 A HOH 5 3 HOH HOH 1506 A HOH 131 3 HOH HOH 1507 A HOH 3 3 HOH HOH 1508 A HOH 109 3 HOH HOH 1509 A HOH 75 3 HOH HOH 1510 A HOH 124 3 HOH HOH 1511 A HOH 68 3 HOH HOH 1512 A HOH 15 3 HOH HOH 1513 A HOH 24 3 HOH HOH 1514 A HOH 19 3 HOH HOH 1515 A HOH 26 3 HOH HOH 1516 A HOH 58 3 HOH HOH 1517 A HOH 94 3 HOH HOH 1518 A HOH 74 3 HOH HOH 1519 A HOH 86 3 HOH HOH 1520 A HOH 55 3 HOH HOH 1521 A HOH 117 3 HOH HOH 1522 A HOH 44 3 HOH HOH 1523 A HOH 8 3 HOH HOH 1524 A HOH 316 3 HOH HOH 1525 A HOH 216 3 HOH HOH 1526 A HOH 141 3 HOH HOH 1527 A HOH 23 3 HOH HOH 1528 A HOH 36 3 HOH HOH 1529 A HOH 48 3 HOH HOH 1530 A HOH 76 3 HOH HOH 1531 A HOH 72 3 HOH HOH 1532 A HOH 60 3 HOH HOH 1533 A HOH 32 3 HOH HOH 1534 A HOH 31 3 HOH HOH 1535 A HOH 64 3 HOH HOH 1536 A HOH 17 3 HOH HOH 1537 A HOH 54 3 HOH HOH 1538 A HOH 37 3 HOH HOH 1539 A HOH 82 3 HOH HOH 1540 A HOH 57 3 HOH HOH 1541 A HOH 38 3 HOH HOH 1542 A HOH 22 3 HOH HOH 1543 A HOH 129 3 HOH HOH 1544 A HOH 174 3 HOH HOH 1545 A HOH 120 3 HOH HOH 1546 A HOH 59 3 HOH HOH 1547 A HOH 107 3 HOH HOH 1548 A HOH 12 3 HOH HOH 1549 A HOH 4 3 HOH HOH 1550 A HOH 21 3 HOH HOH 1551 A HOH 193 3 HOH HOH 1552 A HOH 135 3 HOH HOH 1553 A HOH 132 3 HOH HOH 1554 A HOH 96 3 HOH HOH 1555 A HOH 125 3 HOH HOH 1556 A HOH 197 3 HOH HOH 1557 A HOH 115 3 HOH HOH 1558 A HOH 319 3 HOH HOH 1559 A HOH 87 3 HOH HOH 1560 A HOH 65 3 HOH HOH 1561 A HOH 14 3 HOH HOH 1562 A HOH 221 3 HOH HOH 1563 A HOH 6 3 HOH HOH 1564 A HOH 25 3 HOH HOH 1565 A HOH 186 3 HOH HOH 1566 A HOH 91 3 HOH HOH 1567 A HOH 112 3 HOH HOH 1568 A HOH 113 3 HOH HOH 1569 A HOH 20 3 HOH HOH 1570 A HOH 18 3 HOH HOH 1571 A HOH 159 3 HOH HOH 1572 A HOH 62 3 HOH HOH 1573 A HOH 119 3 HOH HOH 1574 A HOH 173 3 HOH HOH 1575 A HOH 139 3 HOH HOH 1576 A HOH 138 3 HOH HOH 1577 A HOH 49 3 HOH HOH 1578 A HOH 16 3 HOH HOH 1579 A HOH 110 3 HOH HOH 1580 A HOH 199 3 HOH HOH 1581 A HOH 222 3 HOH HOH 1582 A HOH 9 3 HOH HOH 1583 A HOH 33 3 HOH HOH 1584 A HOH 101 3 HOH HOH 1585 A HOH 246 3 HOH HOH 1586 A HOH 45 3 HOH HOH 1587 A HOH 63 3 HOH HOH 1588 A HOH 98 3 HOH HOH 1589 A HOH 66 3 HOH HOH 1590 A HOH 185 3 HOH HOH 1591 A HOH 43 3 HOH HOH 1592 A HOH 315 3 HOH HOH 1593 A HOH 318 3 HOH HOH 1594 A HOH 196 3 HOH HOH 1595 A HOH 35 3 HOH HOH 1596 A HOH 27 3 HOH HOH 1597 A HOH 100 3 HOH HOH 1598 A HOH 41 3 HOH HOH 1599 A HOH 34 3 HOH HOH 1600 A HOH 265 3 HOH HOH 1601 A HOH 40 3 HOH HOH 1602 A HOH 205 3 HOH HOH 1603 A HOH 258 3 HOH HOH 1604 A HOH 70 3 HOH HOH 1605 A HOH 46 3 HOH HOH 1606 A HOH 47 3 HOH HOH 1607 A HOH 245 3 HOH HOH 1608 A HOH 317 3 HOH HOH 1609 A HOH 105 3 HOH HOH 1610 A HOH 202 3 HOH HOH 1611 A HOH 253 3 HOH HOH 1612 A HOH 148 3 HOH HOH 1613 A HOH 127 3 HOH HOH 1614 A HOH 325 3 HOH HOH 1615 A HOH 322 3 HOH HOH 1616 A HOH 73 3 HOH HOH 1617 A HOH 83 3 HOH HOH 1618 A HOH 244 3 HOH HOH 1619 A HOH 133 3 HOH HOH 1620 A HOH 42 3 HOH HOH 1621 A HOH 88 3 HOH HOH 1622 A HOH 84 3 HOH HOH 1623 A HOH 142 3 HOH HOH 1624 A HOH 95 3 HOH HOH 1625 A HOH 85 3 HOH HOH 1626 A HOH 323 3 HOH HOH 1627 A HOH 231 3 HOH HOH 1628 A HOH 92 3 HOH HOH 1629 A HOH 326 3 HOH HOH 1630 A HOH 236 3 HOH HOH 1631 A HOH 274 3 HOH HOH 1632 A HOH 321 3 HOH HOH 1633 A HOH 152 3 HOH HOH 1634 A HOH 153 3 HOH HOH 1635 A HOH 93 3 HOH HOH 1636 A HOH 69 3 HOH HOH 1637 A HOH 53 3 HOH HOH 1638 A HOH 89 3 HOH HOH 1639 A HOH 77 3 HOH HOH 1640 A HOH 314 3 HOH HOH 1641 A HOH 78 3 HOH HOH 1642 A HOH 121 3 HOH HOH 1643 A HOH 61 3 HOH HOH 1644 A HOH 51 3 HOH HOH 1645 A HOH 149 3 HOH HOH 1646 A HOH 250 3 HOH HOH 1647 A HOH 313 3 HOH HOH 1648 A HOH 175 3 HOH HOH 1649 A HOH 162 3 HOH HOH 1650 A HOH 320 3 HOH HOH 1651 A HOH 56 3 HOH HOH 1652 A HOH 97 3 HOH HOH 1653 A HOH 130 3 HOH HOH 1654 A HOH 324 3 HOH HOH 1655 A HOH 145 3 HOH HOH 1656 A HOH 30 3 HOH HOH 1657 A HOH 114 3 HOH HOH 1658 A HOH 106 3 HOH HOH 101 B HOH 134 3 HOH HOH 102 B HOH 11 3 HOH HOH 103 B HOH 28 3 HOH HOH 104 B HOH 71 3 HOH HOH 105 B HOH 154 3 HOH HOH 106 B HOH 52 3 HOH HOH 107 B HOH 122 3 HOH HOH 108 B HOH 7 3 HOH HOH 109 B HOH 168 3 HOH HOH 110 B HOH 158 3 HOH HOH 111 B HOH 165 3 HOH HOH 112 B HOH 80 3 HOH HOH 113 B HOH 289 3 HOH HOH 114 B HOH 90 3 HOH HOH 115 B n 1 1264 A n 2 1265 A n 3 1266 A n 4 1267 A n 5 1268 A n 6 1269 A n 7 1270 A n 8 1271 A n 9 1272 A n 10 1273 A n 11 1274 A n 12 1275 A n 13 1276 A n 14 1277 A n 15 1278 A n 16 1279 A n 17 1280 A n 18 1281 A n 19 1282 A n 20 1283 A n 21 1284 A n 22 1285 A n 23 1286 A PRO 1287 n 24 PRO 1287 A VAL 1288 n 25 VAL 1288 A ARG 1289 n 26 ARG 1289 A TYR 1290 n 27 TYR 1290 A PHE 1291 n 28 PHE 1291 A ILE 1292 n 29 ILE 1292 A MET 1293 n 30 MET 1293 A LYS 1294 n 31 LYS 1294 A SER 1295 n 32 SER 1295 A SER 1296 n 33 SER 1296 A ASN 1297 n 34 ASN 1297 A LEU 1298 n 35 LEU 1298 A ARG 1299 n 36 ARG 1299 A ASN 1300 n 37 ASN 1300 A LEU 1301 n 38 LEU 1301 A GLU 1302 n 39 GLU 1302 A ILE 1303 n 40 ILE 1303 A SER 1304 n 41 SER 1304 A GLN 1305 n 42 GLN 1305 A GLN 1306 n 43 GLN 1306 A LYS 1307 n 44 LYS 1307 A GLY 1308 n 45 GLY 1308 A ILE 1309 n 46 ILE 1309 A TRP 1310 n 47 TRP 1310 A SER 1311 n 48 SER 1311 A THR 1312 n 49 THR 1312 A THR 1313 n 50 THR 1313 A PRO 1314 n 51 PRO 1314 A SER 1315 n 52 SER 1315 A ASN 1316 n 53 ASN 1316 A GLU 1317 n 54 GLU 1317 A ARG 1318 n 55 ARG 1318 A LYS 1319 n 56 LYS 1319 A LEU 1320 n 57 LEU 1320 A ASN 1321 n 58 ASN 1321 A ARG 1322 n 59 ARG 1322 A ALA 1323 n 60 ALA 1323 A PHE 1324 n 61 PHE 1324 A TRP 1325 n 62 TRP 1325 A GLU 1326 n 63 GLU 1326 A SER 1327 n 64 SER 1327 A SER 1328 n 65 SER 1328 A ILE 1329 n 66 ILE 1329 A VAL 1330 n 67 VAL 1330 A TYR 1331 n 68 TYR 1331 A LEU 1332 n 69 LEU 1332 A VAL 1333 n 70 VAL 1333 A PHE 1334 n 71 PHE 1334 A SER 1335 n 72 SER 1335 A VAL 1336 n 73 VAL 1336 A GLN 1337 n 74 GLN 1337 A GLY 1338 n 75 GLY 1338 A SER 1339 n 76 SER 1339 A GLY 1340 n 77 GLY 1340 A HIS 1341 n 78 HIS 1341 A PHE 1342 n 79 PHE 1342 A GLN 1343 n 80 GLN 1343 A GLY 1344 n 81 GLY 1344 A PHE 1345 n 82 PHE 1345 A SER 1346 n 83 SER 1346 A ARG 1347 n 84 ARG 1347 A MET 1348 n 85 MET 1348 A SER 1349 n 86 SER 1349 A SER 1350 n 87 SER 1350 A GLU 1351 n 88 GLU 1351 A ILE 1352 n 89 ILE 1352 A GLY 1353 n 90 GLY 1353 A ARG 1354 n 91 ARG 1354 A GLU 1355 n 92 GLU 1355 A LYS 1356 n 93 LYS 1356 A SER 1357 n 94 SER 1357 A GLN 1358 n 95 GLN 1358 A ASP 1359 n 96 ASP 1359 A TRP 1360 n 97 TRP 1360 A GLY 1361 n 98 GLY 1361 A SER 1362 n 99 SER 1362 A ALA 1363 n 100 ALA 1363 A GLY 1364 n 101 GLY 1364 A LEU 1365 n 102 LEU 1365 A GLY 1366 n 103 GLY 1366 A GLY 1367 n 104 GLY 1367 A VAL 1368 n 105 VAL 1368 A PHE 1369 n 106 PHE 1369 A LYS 1370 n 107 LYS 1370 A VAL 1371 n 108 VAL 1371 A GLU 1372 n 109 GLU 1372 A TRP 1373 n 110 TRP 1373 A ILE 1374 n 111 ILE 1374 A ARG 1375 n 112 ARG 1375 A LYS 1376 n 113 LYS 1376 A GLU 1377 n 114 GLU 1377 A SER 1378 n 115 SER 1378 A LEU 1379 n 116 LEU 1379 A PRO 1380 n 117 PRO 1380 A PHE 1381 n 118 PHE 1381 A GLN 1382 n 119 GLN 1382 A PHE 1383 n 120 PHE 1383 A ALA 1384 n 121 ALA 1384 A HIS 1385 n 122 HIS 1385 A HIS 1386 n 123 HIS 1386 A LEU 1387 n 124 LEU 1387 A LEU 1388 n 125 LEU 1388 A ASN 1389 n 126 ASN 1389 A PRO 1390 n 127 PRO 1390 A TRP 1391 n 128 TRP 1391 A ASN 1392 n 129 ASN 1392 A ASP 1393 n 130 ASP 1393 A ASN 1394 n 131 ASN 1394 A LYS 1395 n 132 LYS 1395 A LYS 1396 n 133 LYS 1396 A VAL 1397 n 134 VAL 1397 A GLN 1398 n 135 GLN 1398 A ILE 1399 n 136 ILE 1399 A SER 1400 n 137 SER 1400 A ARG 1401 n 138 ARG 1401 A ASP 1402 n 139 ASP 1402 A GLY 1403 n 140 GLY 1403 A GLN 1404 n 141 GLN 1404 A GLU 1405 n 142 GLU 1405 A LEU 1406 n 143 LEU 1406 A GLU 1407 n 144 GLU 1407 A PRO 1408 n 145 PRO 1408 A LEU 1409 n 146 LEU 1409 A VAL 1410 n 147 VAL 1410 A GLY 1411 n 148 GLY 1411 A GLU 1412 n 149 GLU 1412 A GLN 1413 n 150 GLN 1413 A LEU 1414 n 151 LEU 1414 A LEU 1415 n 152 LEU 1415 A GLN 1416 n 153 GLN 1416 A LEU 1417 n 154 LEU 1417 A TRP 1418 n 155 TRP 1418 A GLU 1419 n 156 GLU 1419 A ARG 1420 n 157 ARG 1420 A LEU 1421 n 158 LEU 1421 A PRO 1422 n 159 PRO 1422 A n 160 1423 A n 161 1424 A DG 1 n 1 DG 1 B DG 2 n 2 DG 2 B 6MA 3 n 3 6MA 3 B DC 4 n 4 DC 4 B DT 5 n 5 DT 5 B DA 6 n 6 DA 6 B author_and_software_defined_assembly PISA 2 dimeric none 1580 3 7460 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N PHE 1291 A N PHE 28 A O VAL 1333 A O VAL 70 A N VAL 1330 A N VAL 67 A O MET 1348 A O MET 85 A N PHE 1342 A N PHE 79 A O LEU 1379 A O LEU 116 A O PHE 1369 A O PHE 106 A N TRP 1310 A N TRP 47 1 A HOH 1514 C HOH 1 A HOH 1657 C HOH 1 A CE LYS 1319 A CE LYS 56 1 Y 1 A CG ARG 1354 A CG ARG 91 1 Y 1 A CD ARG 1354 A CD ARG 91 1 Y 1 A NE ARG 1354 A NE ARG 91 1 Y 1 A CZ ARG 1354 A CZ ARG 91 1 Y 1 A NH1 ARG 1354 A NH1 ARG 91 1 Y 1 A NH2 ARG 1354 A NH2 ARG 91 1 Y 1 A CG GLU 1355 A CG GLU 92 1 Y 1 A CD GLU 1355 A CD GLU 92 1 Y 1 A OE1 GLU 1355 A OE1 GLU 92 1 Y 1 A OE2 GLU 1355 A OE2 GLU 92 1 Y 1 A CE LYS 1370 A CE LYS 107 1 Y 1 A NZ LYS 1370 A NZ LYS 107 1 Y 1 B O5' DG 1 B O5' DG 1 1 Y 1 B C5' DG 1 B C5' DG 1 1 Y 1 A MET 1264 A MET 1 1 Y 1 A GLY 1265 A GLY 2 1 Y 1 A SER 1266 A SER 3 1 Y 1 A SER 1267 A SER 4 1 Y 1 A HIS 1268 A HIS 5 1 Y 1 A HIS 1269 A HIS 6 1 Y 1 A HIS 1270 A HIS 7 1 Y 1 A HIS 1271 A HIS 8 1 Y 1 A HIS 1272 A HIS 9 1 Y 1 A HIS 1273 A HIS 10 1 Y 1 A SER 1274 A SER 11 1 Y 1 A GLN 1275 A GLN 12 1 Y 1 A ASP 1276 A ASP 13 1 Y 1 A PRO 1277 A PRO 14 1 Y 1 A GLU 1278 A GLU 15 1 Y 1 A ASN 1279 A ASN 16 1 Y 1 A LEU 1280 A LEU 17 1 Y 1 A TYR 1281 A TYR 18 1 Y 1 A PHE 1282 A PHE 19 1 Y 1 A GLN 1283 A GLN 20 1 Y 1 A GLY 1284 A GLY 21 1 Y 1 A ASN 1285 A ASN 22 1 Y 1 A MET 1286 A MET 23 1 Y 1 A LEU 1423 A LEU 160 1 Y 1 A GLY 1424 A GLY 161 1 Y 1 A ARG 1347 0.116 SIDE CHAIN 1 1.96 0.30 108.30 110.26 B B B O4' C1' N9 DG DG DG 1 1 1 N 1 A LYS 1356 -113.97 68.76 22.51 0.2310 0.1993 0.2008 1.58 34.20 1146 22572 23718 4.83 97.97 0.1969 1 FREE R-VALUE 1.35 MOLECULAR REPLACEMENT 26.2534 0.9000 1.1000 GeoStd + Monomer Library + CDL v1.2 FLAT BULK SOLVENT MODEL 1.58 34.20 173 1398 0 121 1104 0.0057 1292 0.8595 1773 0.0552 179 0.0150 207 16.4338 477 0.3432 0.3165 1.65 118 2446 85.67 0.2932 0.2397 1.74 149 2777 98.22 0.2392 0.2058 1.85 149 2827 99.97 0.2404 0.2044 1.99 141 2860 99.93 0.2486 0.1888 2.19 140 2852 99.97 0.2365 0.1955 2.50 141 2882 100.00 0.2409 0.2064 3.15 153 2899 99.90 0.1980 0.1822 34.20 155 3029 99.91 18.15 1.5 63 9SZP 26232 0.996 1 7.7 20 99.7 1.5 1.63 1011 0.477 1 data reduction XDS data scaling autoPROC phasing PHASER refinement PHENIX 1.21.2_5419 20 orthorhombic C 2 2 21 C 2c 2 x,y,z x,-y,-z -x,y,-z+1/2 -x,-y,z+1/2 x+1/2,y+1/2,z x+1/2,-y+1/2,-z -x+1/2,y+1/2,-z+1/2 -x+1/2,-y+1/2,z+1/2 N Crystal structure of the human YTHDC2 YTH domain in complex with m6A DNA 1 N N 2 N N 3 N N 3 N N A ASN 1297 A ASN 34 HELX_P A GLY 1308 A GLY 45 1 AA1 12 A THR 1313 A THR 50 HELX_P A SER 1327 A SER 64 1 AA2 15 A PHE 1381 A PHE 118 HELX_P A HIS 1385 A HIS 122 1 AA3 5 A ASN 1389 A ASN 126 HELX_P A ASP 1393 A ASP 130 5 AA4 5 A GLU 1407 A GLU 144 HELX_P A LEU 1417 A LEU 154 1 AA5 11 A TRP 1418 A TRP 155 HELX_P A LEU 1421 A LEU 158 5 AA6 4 covale 1.602 both B DG 2 B O3' DG 2 1_555 B 6MA 3 B P 6MA 3 1_555 covale 1.597 both B 6MA 3 B O3' 6MA 3 1_555 B DC 4 B P DC 4 1_555 RNA BINDING PROTEIN YTHDC2, DNA, m6A, RNA BINDING PROTEIN YTDC2_HUMAN UNP 1 1285 Q9H6S0 NMPVRYFIMKSSNLRNLEISQQKGIWSTTPSNERKLNRAFWESSIVYLVFSVQGSGHFQGFSRMSSEIGREKSQDWGSAG LGGVFKVEWIRKESLPFQFAHHLLNPWNDNKKVQISRDGQELEPLVGEQLLQLWERLPLG 9SZP PDB 2 1 9SZP 1285 1424 9SZP 1285 1424 Q9H6S0 A 1 22 161 1 6 9SZP 1 6 9SZP B 2 1 6 1 initiating methionine MET 1264 9SZP A Q9H6S0 UNP 1 1 expression tag GLY 1265 9SZP A Q9H6S0 UNP 2 1 expression tag SER 1266 9SZP A Q9H6S0 UNP 3 1 expression tag SER 1267 9SZP A Q9H6S0 UNP 4 1 expression tag HIS 1268 9SZP A Q9H6S0 UNP 5 1 expression tag HIS 1269 9SZP A Q9H6S0 UNP 6 1 expression tag HIS 1270 9SZP A Q9H6S0 UNP 7 1 expression tag HIS 1271 9SZP A Q9H6S0 UNP 8 1 expression tag HIS 1272 9SZP A Q9H6S0 UNP 9 1 expression tag HIS 1273 9SZP A Q9H6S0 UNP 10 1 expression tag SER 1274 9SZP A Q9H6S0 UNP 11 1 expression tag GLN 1275 9SZP A Q9H6S0 UNP 12 1 expression tag ASP 1276 9SZP A Q9H6S0 UNP 13 1 expression tag PRO 1277 9SZP A Q9H6S0 UNP 14 1 expression tag GLU 1278 9SZP A Q9H6S0 UNP 15 1 expression tag ASN 1279 9SZP A Q9H6S0 UNP 16 1 expression tag LEU 1280 9SZP A Q9H6S0 UNP 17 1 expression tag TYR 1281 9SZP A Q9H6S0 UNP 18 1 expression tag PHE 1282 9SZP A Q9H6S0 UNP 19 1 expression tag GLN 1283 9SZP A Q9H6S0 UNP 20 1 expression tag GLY 1284 9SZP A Q9H6S0 UNP 21 5 parallel anti-parallel anti-parallel anti-parallel A VAL 1288 A VAL 25 A SER 1295 A SER 32 A ILE 1329 A ILE 66 A VAL 1336 A VAL 73 A HIS 1341 A HIS 78 A MET 1348 A MET 85 A PHE 1369 A PHE 106 A PRO 1380 A PRO 117 A ILE 1309 A ILE 46 A TRP 1310 A TRP 47 20 C 2 2 21 C 2c 2