0.015089 0.008711 0.000000 0.000000 0.017423 0.000000 0.000000 0.000000 0.028413 0.00000 0.00000 0.00000 Yang, X. Huang, Y. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 66.275 66.275 35.195 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA 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 C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA 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 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 C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA 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 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 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 N N 39 S C N 40 N C N 41 N O N 42 N C N 43 N O N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N N N 52 S C N 53 N C N 54 N O N 55 N C N 56 N C N 57 N C N 58 N N N 59 N C N 60 N N N 61 N N N 62 N O N 63 N H N 64 N H 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 N N 79 S C N 80 N C N 81 N O N 82 N C N 83 N C N 84 N O N 85 N N N 86 N O N 87 N H N 88 N H 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 N N 96 S C N 97 N C N 98 N O N 99 N C N 100 N C N 101 N O N 102 N O N 103 N O N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N O N 112 N P N 113 N O N 114 N O N 115 N O N 116 N C N 117 R C N 118 N O N 119 S C N 120 N O N 121 R C N 122 N O N 123 R C N 124 N N N 125 N C N 126 N O N 127 N N N 128 N C N 129 N N N 130 N C N 131 N C N 132 N H N 133 N H N 134 N H 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 N N 147 S C N 148 N C N 149 N O N 150 N C N 151 N C N 152 N C N 153 N O N 154 N N N 155 N O N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N N N 167 S C N 168 N C N 169 N O N 170 N C N 171 N C N 172 N C N 173 N O N 174 N O N 175 N O 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 H N 184 N H N 185 N N N 186 N C N 187 N C N 188 N O N 189 N O N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N N N 196 S C N 197 N C N 198 N O N 199 N C Y 200 N C Y 201 N N Y 202 N C Y 203 N C Y 204 N N N 205 N O 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 O N 217 N H N 218 N H N 219 N N N 220 S C N 221 N C N 222 N O N 223 S C N 224 N C N 225 N C N 226 N C N 227 N O N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N N N 242 S C N 243 N C N 244 N O N 245 N C N 246 N C N 247 N C N 248 N C N 249 N O 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 H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N N N 264 S C N 265 N C N 266 N O N 267 N C N 268 N C N 269 N C N 270 N C N 271 N N N 272 N O N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 N H N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N N N 289 S C N 290 N C N 291 N O N 292 N C Y 293 N C Y 294 N C Y 295 N C Y 296 N C Y 297 N C Y 298 N C 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 H N 306 N H N 307 N H N 308 N H N 309 N H N 310 N H N 311 N N N 312 S C N 313 N C N 314 N O N 315 N C N 316 N C N 317 N C N 318 N O 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 H N 327 N H N 328 N N N 329 S C N 330 N C N 331 N O N 332 N C N 333 N O N 334 N O N 335 N H N 336 N H N 337 N H N 338 N H N 339 N H N 340 N H N 341 N H N 342 N N N 343 S C N 344 N C N 345 N O N 346 R C N 347 N O N 348 N C N 349 N O N 350 N H N 351 N H N 352 N H N 353 N H N 354 N H N 355 N H N 356 N H N 357 N H N 358 N H N 359 N N N 360 S C N 361 N C N 362 N O N 363 N C Y 364 N C Y 365 N C Y 366 N C Y 367 N N Y 368 N C Y 369 N C Y 370 N C Y 371 N C Y 372 N C N 373 N O N 374 N H N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N N N 387 S C N 388 N C N 389 N O N 390 N C Y 391 N C Y 392 N C Y 393 N C Y 394 N C Y 395 N C Y 396 N C N 397 N O N 398 N O N 399 N H N 400 N H N 401 N H N 402 N H N 403 N H N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 N H N 410 N O N 411 N P N 412 N O N 413 N O N 414 N O N 415 N C N 416 R C N 417 N O N 418 S C N 419 N O N 420 R C N 421 N O N 422 R C N 423 N N N 424 N C N 425 N O N 426 N N N 427 N C N 428 N O N 429 N C N 430 N C 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 H N 442 N H N 443 N H N 444 N N N 445 S C N 446 N C N 447 N O N 448 N C N 449 N C N 450 N C N 451 N O 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 H N 459 N H N 460 N H N 461 N H N 462 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 N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 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 doub N 47 N sing N 48 N sing 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 doub N 59 N sing N 60 N sing 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 doub N 73 N sing N 74 N sing 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 doub N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N doub N 90 N sing N 91 N sing 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 doub N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N doub N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N doub N 112 N sing N 113 N sing 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 N 134 N sing N 135 N doub N 136 N sing N 137 N doub N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 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 doub 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 doub N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N doub N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N doub 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 doub N 198 N sing N 199 N sing N 200 N sing N 201 N sing Y 202 N sing Y 203 N doub Y 204 N doub N 205 N sing Y 206 N sing N 207 N sing Y 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N doub N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing 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 doub 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 sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing 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 doub N 263 N sing N 264 N sing N 265 N sing N 266 N sing 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 sing 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 sing N 286 N doub N 287 N sing N 288 N sing N 289 N sing N 290 N sing Y 291 N doub Y 292 N sing Y 293 N sing N 294 N sing Y 295 N doub N 296 N sing Y 297 N doub N 298 N sing Y 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N doub N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N doub 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 sing N 336 N sing N 337 N sing N 338 N sing N 339 N doub 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 doub N 356 N sing N 357 N sing N 358 N sing N 359 N sing Y 360 N doub Y 361 N sing Y 362 N sing N 363 N sing Y 364 N doub Y 365 N sing Y 366 N sing N 367 N sing Y 368 N sing Y 369 N doub N 370 N sing Y 371 N doub N 372 N sing Y 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N doub N 384 N sing N 385 N sing N 386 N sing N 387 N sing Y 388 N doub Y 389 N sing Y 390 N sing N 391 N sing Y 392 N doub N 393 N sing Y 394 N doub N 395 N sing Y 396 N sing N 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N doub 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 sing N 421 N sing N 422 N sing N 423 N sing N 424 N sing N 425 N sing N 426 N sing N 427 N doub N 428 N sing N 429 N sing N 430 N sing N 431 N doub N 432 N sing N 433 N doub 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 doub N 443 N sing 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 US J.Biol.Chem. JBCHA3 0071 1083-351X 294 10998 11010 10.1074/jbc.RA119.007545 31160337 Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA. 2019 0000-0002-6647-8491 0000-0002-1999-4776 0000-0002-2806-2874 10.2210/pdb5ytv/pdb pdb_00005ytv 100 1 CCD 2011-03-06 ADSC QUANTUM 315 SINGLE WAVELENGTH M x-ray 1 0.979 1.0 BL17U1 SSRF 0.979 SYNCHROTRON SSRF BEAMLINE BL17U1 8997.026 Nuclease-sensitive element-binding protein 1 1 man polymer 1813.109 RNA (5'-R(P*UP*CP*AP*UP*CP*U)-3') 1 syn polymer 18.015 water 53 nat water CCAAT-binding transcription factor I subunit A,CBF-A,DNA-binding protein B,DBPB,Enhancer factor I subunit A,EFI-A,Y-box transcription factor,Y-box-binding protein 1,YB-1 no no GSGDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTG PGG GSGDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTG PGG A polypeptide(L) no no UCAUCU UCAUCU B polyribonucleotide 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 83 YBX1, NSEP1, YB1 9606 Homo sapiens 562 Escherichia coli Biological sequence 1 2.06 40.41 VAPOR DIFFUSION, HANGING DROP 4.5 30 % (v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, pH 4.5, 25 % (w/v) PEG 1500 290 citation citation_author citation citation_author chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model repository Initial release Data collection Database references Data collection Database references Data collection Database references Refinement description 1 0 2018-12-05 1 1 2019-06-19 1 2 2019-07-24 1 3 2023-11-22 _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _database_2.pdbx_DOI _database_2.pdbx_database_accession China National Natural Science Foundation of China 91640102 China Strategic Priority Research Program of the Chinese Academy of Sciences XDB08010202 N PDBJ Y PDBJ 2017-11-20 REL REL HOH water 32630 synthetic construct sample 1 6 3PF5 PDB experimental model HOH 46 3 HOH HOH 201 A HOH 45 3 HOH HOH 202 A HOH 53 3 HOH HOH 203 A HOH 27 3 HOH HOH 204 A HOH 48 3 HOH HOH 205 A HOH 21 3 HOH HOH 206 A HOH 3 3 HOH HOH 207 A HOH 14 3 HOH HOH 208 A HOH 13 3 HOH HOH 209 A HOH 8 3 HOH HOH 210 A HOH 10 3 HOH HOH 211 A HOH 4 3 HOH HOH 212 A HOH 51 3 HOH HOH 213 A HOH 12 3 HOH HOH 214 A HOH 49 3 HOH HOH 215 A HOH 7 3 HOH HOH 216 A HOH 31 3 HOH HOH 217 A HOH 30 3 HOH HOH 218 A HOH 1 3 HOH HOH 219 A HOH 2 3 HOH HOH 220 A HOH 42 3 HOH HOH 221 A HOH 33 3 HOH HOH 222 A HOH 20 3 HOH HOH 223 A HOH 16 3 HOH HOH 224 A HOH 32 3 HOH HOH 225 A HOH 9 3 HOH HOH 226 A HOH 24 3 HOH HOH 227 A HOH 19 3 HOH HOH 228 A HOH 22 3 HOH HOH 229 A HOH 15 3 HOH HOH 230 A HOH 26 3 HOH HOH 231 A HOH 6 3 HOH HOH 232 A HOH 25 3 HOH HOH 233 A HOH 18 3 HOH HOH 234 A HOH 11 3 HOH HOH 235 A HOH 52 3 HOH HOH 236 A HOH 40 3 HOH HOH 237 A HOH 37 3 HOH HOH 238 A HOH 29 3 HOH HOH 239 A HOH 28 3 HOH HOH 240 A HOH 50 3 HOH HOH 241 A HOH 23 3 HOH HOH 242 A HOH 35 3 HOH HOH 243 A HOH 47 3 HOH HOH 244 A HOH 41 3 HOH HOH 245 A HOH 36 3 HOH HOH 246 A HOH 43 3 HOH HOH 247 A HOH 34 3 HOH HOH 248 A HOH 44 3 HOH HOH 101 B HOH 39 3 HOH HOH 102 B HOH 17 3 HOH HOH 103 B HOH 5 3 HOH HOH 104 B HOH 38 3 HOH HOH 105 B n 1 48 A n 2 49 A n 3 50 A n 4 51 A LYS 52 n 5 LYS 52 A LYS 53 n 6 LYS 53 A VAL 54 n 7 VAL 54 A ILE 55 n 8 ILE 55 A ALA 56 n 9 ALA 56 A THR 57 n 10 THR 57 A LYS 58 n 11 LYS 58 A VAL 59 n 12 VAL 59 A LEU 60 n 13 LEU 60 A GLY 61 n 14 GLY 61 A THR 62 n 15 THR 62 A VAL 63 n 16 VAL 63 A LYS 64 n 17 LYS 64 A TRP 65 n 18 TRP 65 A PHE 66 n 19 PHE 66 A ASN 67 n 20 ASN 67 A VAL 68 n 21 VAL 68 A ARG 69 n 22 ARG 69 A ASN 70 n 23 ASN 70 A GLY 71 n 24 GLY 71 A TYR 72 n 25 TYR 72 A GLY 73 n 26 GLY 73 A PHE 74 n 27 PHE 74 A ILE 75 n 28 ILE 75 A ASN 76 n 29 ASN 76 A ARG 77 n 30 ARG 77 A ASN 78 n 31 ASN 78 A ASP 79 n 32 ASP 79 A THR 80 n 33 THR 80 A LYS 81 n 34 LYS 81 A GLU 82 n 35 GLU 82 A ASP 83 n 36 ASP 83 A VAL 84 n 37 VAL 84 A PHE 85 n 38 PHE 85 A VAL 86 n 39 VAL 86 A HIS 87 n 40 HIS 87 A GLN 88 n 41 GLN 88 A THR 89 n 42 THR 89 A ALA 90 n 43 ALA 90 A ILE 91 n 44 ILE 91 A LYS 92 n 45 LYS 92 A LYS 93 n 46 LYS 93 A ASN 94 n 47 ASN 94 A n 48 95 A n 49 96 A n 50 97 A LYS 98 n 51 LYS 98 A TYR 99 n 52 TYR 99 A LEU 100 n 53 LEU 100 A ARG 101 n 54 ARG 101 A SER 102 n 55 SER 102 A VAL 103 n 56 VAL 103 A GLY 104 n 57 GLY 104 A ASP 105 n 58 ASP 105 A GLY 106 n 59 GLY 106 A GLU 107 n 60 GLU 107 A THR 108 n 61 THR 108 A VAL 109 n 62 VAL 109 A GLU 110 n 63 GLU 110 A PHE 111 n 64 PHE 111 A ASP 112 n 65 ASP 112 A VAL 113 n 66 VAL 113 A VAL 114 n 67 VAL 114 A GLU 115 n 68 GLU 115 A GLY 116 n 69 GLY 116 A GLU 117 n 70 GLU 117 A LYS 118 n 71 LYS 118 A GLY 119 n 72 GLY 119 A ALA 120 n 73 ALA 120 A GLU 121 n 74 GLU 121 A ALA 122 n 75 ALA 122 A ALA 123 n 76 ALA 123 A ASN 124 n 77 ASN 124 A VAL 125 n 78 VAL 125 A THR 126 n 79 THR 126 A GLY 127 n 80 GLY 127 A PRO 128 n 81 PRO 128 A GLY 129 n 82 GLY 129 A n 83 130 A n 1 1 B C 2 n 2 C 2 B A 3 n 3 A 3 B U 4 n 4 U 4 B C 5 n 5 C 5 B n 6 6 B author_defined_assembly 2 dimeric YB1 can form homodimer in vivo immunoprecipitation 1090 -1 5170 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 THR 62 A N THR 15 A O ASN 76 A O ASN 29 A N ILE 75 A N ILE 28 A O VAL 84 A O VAL 37 A N PHE 85 A N PHE 38 A O ALA 122 A O ALA 75 A O GLU 121 A O GLU 74 A N VAL 114 A N VAL 67 A O VAL 113 A O VAL 66 A N ILE 55 A N ILE 8 1 B HOH 104 D HOH 1 A GLY 48 A GLY 1 1 Y 1 A SER 49 A SER 2 1 Y 1 A GLY 50 A GLY 3 1 Y 1 A ASP 51 A ASP 4 1 Y 1 A ASN 95 A ASN 48 1 Y 1 A PRO 96 A PRO 49 1 Y 1 A ARG 97 A ARG 50 1 Y 1 A GLY 130 A GLY 83 1 Y 1 B U 1 B U 1 1 Y 1 B U 6 B U 6 1 Y 1 A A OE1 O GLU HOH 115 201 1.99 1 A A O O ALA HOH 120 202 2.07 1 A A NZ O LYS HOH 53 203 2.12 1 A A NZ O LYS HOH 98 204 2.15 1 A B O O HOH HOH 242 105 2.18 1 A B O O HOH HOH 237 105 1.86 1_555 5_454 1 A A O O HOH HOH 204 222 2.11 1_555 6_665 1 A A O O HOH HOH 241 244 2.12 1_555 3_565 0.2276 0.1961 0.1992 1.700 30.003 976 9677 10.09 98.28 0.17 1 FREE R-VALUE 1.66 MOLECULAR REPLACEMENT 24.65 0.90 1.11 3PF5 1.700 30.003 53 717 0 82 582 0.007 680 1.071 929 12.701 259 0.060 108 0.004 106 0.2823 0.2315 1.7898 123 1111 88.00 0.2269 0.2008 1.9019 137 1240 100.00 0.2517 0.1885 2.0487 139 1257 100.00 0.2135 0.1811 2.2548 143 1254 100.00 0.2268 0.1894 2.5810 142 1258 100.00 0.2182 0.2096 3.2511 145 1276 100.00 0.2258 0.1923 30.0080 147 1305 100.00 1.7 30.003 5YTV 9693 1 30.0 16.6 100.00 1.70 1.76 1 refinement PHENIX 1.9_1692 data reduction HKL-2000 data scaling HKL-2000 phasing PHENIX N Crystal structure of YB1 cold-shock domain in complex with UCAUCU 1 N N 2 N N 3 N N 3 N N A THR 89 A THR 42 HELX_P A ILE 91 A ILE 44 5 AA1 3 RNA BINDING PROTEIN/RNA YB1, cold-shock domain, CAUC, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex YBOX1_HUMAN UNP 1 50 P67809 GDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPG G 5YTV PDB 2 1 5YTV 50 130 5YTV 50 130 P67809 A 1 3 83 1 6 5YTV 1 6 5YTV B 2 1 6 1 expression tag GLY 48 5YTV A P67809 UNP 1 1 expression tag SER 49 5YTV A P67809 UNP 2 6 anti-parallel anti-parallel parallel anti-parallel anti-parallel A VAL 54 A VAL 7 A ASN 67 A ASN 20 A TYR 72 A TYR 25 A ARG 77 A ARG 30 A ASP 83 A ASP 36 A HIS 87 A HIS 40 A GLY 119 A GLY 72 A THR 126 A THR 79 A THR 108 A THR 61 A GLY 116 A GLY 69 A VAL 54 A VAL 7 A ASN 67 A ASN 20 171 P 62