0.031653 0.011072 0.006550 0.000000 0.030858 0.008104 0.000000 0.000000 0.022948 0.00000 0.00000 0.00000 6 6 2.310 1.020 1.589 0.865 20.844 10.208 0.569 51.651 0.216 1 1 0.493 0.323 0.140 0.041 10.511 26.126 3.142 57.800 0.003 7 7 12.222 3.135 2.014 1.167 0.006 9.893 28.997 0.583 -11.538 8 8 3.049 2.287 1.546 0.867 13.277 5.701 0.324 32.909 0.251 16 16 6.905 5.203 1.438 1.586 1.468 22.215 0.254 56.172 1.049 0000-0002-3619-3057 Cottee, M.A. 0000-0002-6763-3852 Taylor, I.A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 101.641 96.351 109.279 31.593 34.332 45.333 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 C3 H7 N O2 S 121.158 y CYSTEINE L-peptide 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 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 N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O 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 H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O 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 N N 75 R C N 76 N C N 77 N O N 78 N C N 79 N S N 80 N O N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N N N 89 S C N 90 N C N 91 N O N 92 N C N 93 N C N 94 N C N 95 N O N 96 N N N 97 N O N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N N N 109 S C N 110 N C N 111 N O N 112 N C N 113 N C N 114 N C N 115 N O N 116 N O N 117 N O N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N N N 128 N C N 129 N C N 130 N O N 131 N O N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N N N 138 S C N 139 N C N 140 N O N 141 N C Y 142 N C Y 143 N N Y 144 N C Y 145 N C Y 146 N N N 147 N O N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N O N 159 N H N 160 N H N 161 N N N 162 S C N 163 N C N 164 N O N 165 S C N 166 N C N 167 N C N 168 N C N 169 N O 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 N N 184 S C N 185 N C N 186 N O N 187 N C N 188 N C N 189 N C N 190 N C N 191 N O N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N N N 206 S C N 207 N C N 208 N O N 209 N C N 210 N C N 211 N C N 212 N C N 213 N N N 214 N O N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N N N 231 S C N 232 N C N 233 N O N 234 N C N 235 N C N 236 N S N 237 N C N 238 N O N 239 N H N 240 N H 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 N N 251 S C N 252 N C N 253 N O N 254 N C Y 255 N C Y 256 N C Y 257 N C Y 258 N C Y 259 N C Y 260 N C N 261 N O N 262 N H N 263 N H N 264 N H N 265 N H 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 N N 274 S C N 275 N C N 276 N O N 277 N C N 278 N C N 279 N C N 280 N O 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 H N 289 N H N 290 N N N 291 S C N 292 N C N 293 N O N 294 N C N 295 N O N 296 N O N 297 N H N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N N N 305 S C N 306 N C N 307 N O N 308 R C N 309 N O N 310 N C N 311 N O N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N H N 319 N H N 320 N H N 321 N N N 322 S C N 323 N C N 324 N O N 325 N C Y 326 N C Y 327 N C Y 328 N C Y 329 N C Y 330 N C Y 331 N C N 332 N O N 333 N O N 334 N H 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 H N 343 N H N 344 N H N 345 N N N 346 S C N 347 N C N 348 N O N 349 N C N 350 N C N 351 N C N 352 N O 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 H N 360 N H N 361 N H N 362 N H N 363 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub 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 doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 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 doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub 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 sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub 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 sing N 75 N sing N 76 N doub 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 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 doub N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N doub 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 doub 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 sing N 138 N sing N 139 N sing Y 140 N sing Y 141 N doub Y 142 N doub N 143 N sing Y 144 N sing N 145 N sing Y 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing 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 doub 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 sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N doub 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 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 doub N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 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 sing N 221 N sing N 222 N sing N 223 N sing N 224 N doub 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 sing N 242 N sing N 243 N doub N 244 N sing N 245 N sing N 246 N sing N 247 N sing Y 248 N doub Y 249 N sing Y 250 N sing N 251 N sing Y 252 N doub N 253 N sing Y 254 N doub N 255 N sing Y 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 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 doub N 284 N sing N 285 N sing 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 sing N 294 N sing N 295 N sing N 296 N doub 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 sing 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 doub Y 318 N sing Y 319 N sing N 320 N sing Y 321 N doub N 322 N sing Y 323 N doub N 324 N sing Y 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 sing N 336 N doub 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 US Plos Genet. 1553-7404 21 e1011898 e1011898 10.1371/journal.pgen.1011898 41066520 Probing the molecular determinants of Ty1 retrotransposon restriction specificity in yeast. 2025 0000-0001-6559-1030 0000-0002-3619-3057 0000-0002-4435-5167 0009-0006-0703-1434 0009-0008-4746-1556 0009-0006-9496-6819 0000-0003-3377-323X 0000-0002-6763-3852 0000-0001-6234-2426 10.2210/pdb9rxw/pdb pdb_00009rxw 100 1 N PIXEL 2020-12-16 DECTRIS EIGER2 XE 16M double crystal SINGLE WAVELENGTH M x-ray 1 0.97625 1.0 I03 Diamond 0.97625 SYNCHROTRON DIAMOND BEAMLINE I03 11127.427 Capsid protein 2 man polymer 18.015 water 74 nat water CA,Gag-p45,p54 no no MQSDTQEVNDITTLATLHYNGSTPADAFEAEVTNILDRLNNNGIPINNKVACQFIMRGLSGEYKFLRYARHRCIHMTVAD LFSDIHSMYEEQQPLEH MQSDTQEVNDITTLATLHYNGSTPADAFEAEVTNILDRLNNNGIPINNKVACQFIMRGLSGEYKFLRYARHRCIHMTVAD LFSDIHSMYEEQQPLEH A,B polypeptide(L) 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 brewer's yeast RefSeq: NC_001134 sample 1 97 204508 TY1A-MR1, YMRCTy1-3 GAG, YMR046C, YM9532.11C 4932 Saccharomyces cerevisiae 511693 Escherichia coli BL21 Biological sequence 1 2.00 38.65 Typically small angular shards, approx 70x30um. Grew overnight, harvested after 1 day VAPOR DIFFUSION, SITTING DROP 4.2 150 nL protein (12 mg/ml (1.067mM) in 20 mM Tris pH 8.5, 150mM NaCl, 1mM TCEP) mixed with 50 nL well solution (0.2M NaCl, 10% PEG3K, 0.1M Na Phos Citrate pH4.2) 293 citation citation_author repository Initial release Database references 1 0 2025-10-08 1 1 2025-10-22 _citation.country _citation.journal_abbrev _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation_author.identifier_ORCID United Kingdom Cancer Research UK CC2029 United Kingdom Medical Research Council (MRC, United Kingdom) CC2029 United Kingdom Wellcome Trust CC2029 Ian.taylor@crick.ac.uk 0000-0002-6763-3852 Ian Taylor A principal investigator/group leader N PDBE Y PDBE 2025-07-13 REL REL HOH water N 7NLH Polyalanine model PDB experimental model HOH 24 2 HOH HOH 401 A HOH 57 2 HOH HOH 402 A HOH 34 2 HOH HOH 403 A HOH 27 2 HOH HOH 404 A HOH 47 2 HOH HOH 405 A HOH 25 2 HOH HOH 406 A HOH 43 2 HOH HOH 407 A HOH 38 2 HOH HOH 408 A HOH 8 2 HOH HOH 409 A HOH 11 2 HOH HOH 410 A HOH 10 2 HOH HOH 411 A HOH 46 2 HOH HOH 412 A HOH 2 2 HOH HOH 413 A HOH 16 2 HOH HOH 414 A HOH 4 2 HOH HOH 415 A HOH 67 2 HOH HOH 416 A HOH 39 2 HOH HOH 417 A HOH 56 2 HOH HOH 418 A HOH 15 2 HOH HOH 419 A HOH 41 2 HOH HOH 420 A HOH 31 2 HOH HOH 421 A HOH 23 2 HOH HOH 422 A HOH 45 2 HOH HOH 423 A HOH 29 2 HOH HOH 424 A HOH 33 2 HOH HOH 425 A HOH 48 2 HOH HOH 426 A HOH 19 2 HOH HOH 427 A HOH 14 2 HOH HOH 428 A HOH 54 2 HOH HOH 429 A HOH 73 2 HOH HOH 430 A HOH 72 2 HOH HOH 431 A HOH 66 2 HOH HOH 432 A HOH 44 2 HOH HOH 433 A HOH 65 2 HOH HOH 434 A HOH 55 2 HOH HOH 401 B HOH 35 2 HOH HOH 402 B HOH 9 2 HOH HOH 403 B HOH 63 2 HOH HOH 404 B HOH 30 2 HOH HOH 405 B HOH 61 2 HOH HOH 406 B HOH 20 2 HOH HOH 407 B HOH 7 2 HOH HOH 408 B HOH 18 2 HOH HOH 409 B HOH 5 2 HOH HOH 410 B HOH 17 2 HOH HOH 411 B HOH 21 2 HOH HOH 412 B HOH 53 2 HOH HOH 413 B HOH 58 2 HOH HOH 414 B HOH 3 2 HOH HOH 415 B HOH 26 2 HOH HOH 416 B HOH 13 2 HOH HOH 417 B HOH 37 2 HOH HOH 418 B HOH 22 2 HOH HOH 419 B HOH 70 2 HOH HOH 420 B HOH 51 2 HOH HOH 421 B HOH 40 2 HOH HOH 422 B HOH 62 2 HOH HOH 423 B HOH 42 2 HOH HOH 424 B HOH 59 2 HOH HOH 425 B HOH 68 2 HOH HOH 426 B HOH 49 2 HOH HOH 427 B HOH 6 2 HOH HOH 428 B HOH 32 2 HOH HOH 429 B HOH 52 2 HOH HOH 430 B HOH 12 2 HOH HOH 431 B HOH 71 2 HOH HOH 432 B HOH 64 2 HOH HOH 433 B HOH 28 2 HOH HOH 434 B HOH 1 2 HOH HOH 435 B HOH 36 2 HOH HOH 436 B HOH 75 2 HOH HOH 437 B HOH 60 2 HOH HOH 438 B HOH 74 2 HOH HOH 439 B HOH 50 2 HOH HOH 440 B n 1 259 A n 2 260 A SER 261 n 3 SER 261 A ASP 262 n 4 ASP 262 A THR 263 n 5 THR 263 A GLN 264 n 6 GLN 264 A GLU 265 n 7 GLU 265 A VAL 266 n 8 VAL 266 A ASN 267 n 9 ASN 267 A ASP 268 n 10 ASP 268 A ILE 269 n 11 ILE 269 A THR 270 n 12 THR 270 A THR 271 n 13 THR 271 A LEU 272 n 14 LEU 272 A ALA 273 n 15 ALA 273 A THR 274 n 16 THR 274 A LEU 275 n 17 LEU 275 A HIS 276 n 18 HIS 276 A TYR 277 n 19 TYR 277 A ASN 278 n 20 ASN 278 A GLY 279 n 21 GLY 279 A SER 280 n 22 SER 280 A THR 281 n 23 THR 281 A PRO 282 n 24 PRO 282 A ALA 283 n 25 ALA 283 A ASP 284 n 26 ASP 284 A ALA 285 n 27 ALA 285 A PHE 286 n 28 PHE 286 A GLU 287 n 29 GLU 287 A ALA 288 n 30 ALA 288 A GLU 289 n 31 GLU 289 A VAL 290 n 32 VAL 290 A THR 291 n 33 THR 291 A ASN 292 n 34 ASN 292 A ILE 293 n 35 ILE 293 A LEU 294 n 36 LEU 294 A ASP 295 n 37 ASP 295 A ARG 296 n 38 ARG 296 A LEU 297 n 39 LEU 297 A ASN 298 n 40 ASN 298 A ASN 299 n 41 ASN 299 A ASN 300 n 42 ASN 300 A GLY 301 n 43 GLY 301 A ILE 302 n 44 ILE 302 A PRO 303 n 45 PRO 303 A ILE 304 n 46 ILE 304 A ASN 305 n 47 ASN 305 A ASN 306 n 48 ASN 306 A LYS 307 n 49 LYS 307 A VAL 308 n 50 VAL 308 A ALA 309 n 51 ALA 309 A CYS 310 n 52 CYS 310 A GLN 311 n 53 GLN 311 A PHE 312 n 54 PHE 312 A ILE 313 n 55 ILE 313 A MET 314 n 56 MET 314 A ARG 315 n 57 ARG 315 A GLY 316 n 58 GLY 316 A LEU 317 n 59 LEU 317 A SER 318 n 60 SER 318 A GLY 319 n 61 GLY 319 A GLU 320 n 62 GLU 320 A TYR 321 n 63 TYR 321 A LYS 322 n 64 LYS 322 A PHE 323 n 65 PHE 323 A LEU 324 n 66 LEU 324 A ARG 325 n 67 ARG 325 A TYR 326 n 68 TYR 326 A ALA 327 n 69 ALA 327 A ARG 328 n 70 ARG 328 A HIS 329 n 71 HIS 329 A n 72 330 A CYS 331 n 73 CYS 331 A ILE 332 n 74 ILE 332 A HIS 333 n 75 HIS 333 A MET 334 n 76 MET 334 A THR 335 n 77 THR 335 A VAL 336 n 78 VAL 336 A ALA 337 n 79 ALA 337 A ASP 338 n 80 ASP 338 A LEU 339 n 81 LEU 339 A PHE 340 n 82 PHE 340 A SER 341 n 83 SER 341 A ASP 342 n 84 ASP 342 A ILE 343 n 85 ILE 343 A HIS 344 n 86 HIS 344 A SER 345 n 87 SER 345 A MET 346 n 88 MET 346 A TYR 347 n 89 TYR 347 A GLU 348 n 90 GLU 348 A GLU 349 n 91 GLU 349 A GLN 350 n 92 GLN 350 A GLN 351 n 93 GLN 351 A n 94 352 A n 95 353 A n 96 354 A n 97 355 A n 1 259 B n 2 260 B n 3 261 B ASP 262 n 4 ASP 262 B THR 263 n 5 THR 263 B GLN 264 n 6 GLN 264 B GLU 265 n 7 GLU 265 B VAL 266 n 8 VAL 266 B ASN 267 n 9 ASN 267 B ASP 268 n 10 ASP 268 B ILE 269 n 11 ILE 269 B THR 270 n 12 THR 270 B THR 271 n 13 THR 271 B LEU 272 n 14 LEU 272 B ALA 273 n 15 ALA 273 B THR 274 n 16 THR 274 B LEU 275 n 17 LEU 275 B HIS 276 n 18 HIS 276 B TYR 277 n 19 TYR 277 B ASN 278 n 20 ASN 278 B GLY 279 n 21 GLY 279 B SER 280 n 22 SER 280 B THR 281 n 23 THR 281 B PRO 282 n 24 PRO 282 B ALA 283 n 25 ALA 283 B ASP 284 n 26 ASP 284 B ALA 285 n 27 ALA 285 B PHE 286 n 28 PHE 286 B GLU 287 n 29 GLU 287 B ALA 288 n 30 ALA 288 B GLU 289 n 31 GLU 289 B VAL 290 n 32 VAL 290 B THR 291 n 33 THR 291 B ASN 292 n 34 ASN 292 B ILE 293 n 35 ILE 293 B LEU 294 n 36 LEU 294 B ASP 295 n 37 ASP 295 B ARG 296 n 38 ARG 296 B LEU 297 n 39 LEU 297 B ASN 298 n 40 ASN 298 B ASN 299 n 41 ASN 299 B ASN 300 n 42 ASN 300 B GLY 301 n 43 GLY 301 B ILE 302 n 44 ILE 302 B PRO 303 n 45 PRO 303 B ILE 304 n 46 ILE 304 B ASN 305 n 47 ASN 305 B ASN 306 n 48 ASN 306 B LYS 307 n 49 LYS 307 B VAL 308 n 50 VAL 308 B ALA 309 n 51 ALA 309 B CYS 310 n 52 CYS 310 B GLN 311 n 53 GLN 311 B PHE 312 n 54 PHE 312 B ILE 313 n 55 ILE 313 B MET 314 n 56 MET 314 B ARG 315 n 57 ARG 315 B GLY 316 n 58 GLY 316 B LEU 317 n 59 LEU 317 B SER 318 n 60 SER 318 B GLY 319 n 61 GLY 319 B GLU 320 n 62 GLU 320 B TYR 321 n 63 TYR 321 B LYS 322 n 64 LYS 322 B PHE 323 n 65 PHE 323 B LEU 324 n 66 LEU 324 B ARG 325 n 67 ARG 325 B TYR 326 n 68 TYR 326 B ALA 327 n 69 ALA 327 B ARG 328 n 70 ARG 328 B HIS 329 n 71 HIS 329 B ARG 330 n 72 ARG 330 B CYS 331 n 73 CYS 331 B ILE 332 n 74 ILE 332 B HIS 333 n 75 HIS 333 B MET 334 n 76 MET 334 B THR 335 n 77 THR 335 B VAL 336 n 78 VAL 336 B ALA 337 n 79 ALA 337 B ASP 338 n 80 ASP 338 B LEU 339 n 81 LEU 339 B PHE 340 n 82 PHE 340 B SER 341 n 83 SER 341 B ASP 342 n 84 ASP 342 B ILE 343 n 85 ILE 343 B HIS 344 n 86 HIS 344 B SER 345 n 87 SER 345 B MET 346 n 88 MET 346 B TYR 347 n 89 TYR 347 B GLU 348 n 90 GLU 348 B GLU 349 n 91 GLU 349 B GLN 350 n 92 GLN 350 B GLN 351 n 93 GLN 351 B PRO 352 n 94 PRO 352 B n 95 353 B n 96 354 B n 97 355 B 1.5974 0.5737 1.0431 1.7273 -0.3399 2.0945 0.0480 -0.0741 0.0880 0.1493 -0.0522 0.0379 -0.0306 -0.0293 0.0042 0.0163 0.0002 0.0102 0.0103 0.0051 0.0219 refined 0.3610 -10.2419 7.3129 X-RAY DIFFRACTION 0.7123 0.2530 0.1777 1.6577 1.0866 2.1445 -0.0495 0.0258 0.0371 -0.1466 0.0238 0.1315 -0.1148 0.0597 0.0257 0.0166 -0.0021 -0.0092 0.0186 0.0216 0.0408 refined -11.4591 -27.9007 -8.0865 X-RAY DIFFRACTION A 261 A 351 X-RAY DIFFRACTION 1 ALL B 262 B 352 X-RAY DIFFRACTION 2 ALL author_and_software_defined_assembly PISA 2 dimeric Gel filtration shows single oligomeric species in solution, consistent with crystallographic dimer, and closely related orthologues gel filtration 1470 -5 9590 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 1 A CZ ARG 328 A CZ ARG 70 1 Y 1 A NH1 ARG 328 A NH1 ARG 70 1 Y 1 A NH2 ARG 328 A NH2 ARG 70 1 Y 1 A CG HIS 329 A CG HIS 71 1 Y 1 A ND1 HIS 329 A ND1 HIS 71 1 Y 1 A CD2 HIS 329 A CD2 HIS 71 1 Y 1 A CE1 HIS 329 A CE1 HIS 71 1 Y 1 A NE2 HIS 329 A NE2 HIS 71 1 Y 1 A SG CYS 331 A SG CYS 73 1 Y 1 A CG1 ILE 332 A CG1 ILE 74 1 Y 1 A CG2 ILE 332 A CG2 ILE 74 1 Y 1 A CD1 ILE 332 A CD1 ILE 74 1 Y 1 B CG ARG 330 B CG ARG 72 1 Y 1 B CD ARG 330 B CD ARG 72 1 Y 1 B NE ARG 330 B NE ARG 72 1 Y 1 B CZ ARG 330 B CZ ARG 72 1 Y 1 B NH1 ARG 330 B NH1 ARG 72 1 Y 1 B NH2 ARG 330 B NH2 ARG 72 1 Y 1 B SG CYS 331 B SG CYS 73 1 Y 1 B CG1 ILE 332 B CG1 ILE 74 1 Y 1 B CG2 ILE 332 B CG2 ILE 74 1 Y 1 B CD1 ILE 332 B CD1 ILE 74 1 Y 1 B CG HIS 333 B CG HIS 75 1 Y 1 B ND1 HIS 333 B ND1 HIS 75 1 Y 1 B CD2 HIS 333 B CD2 HIS 75 1 Y 1 B CE1 HIS 333 B CE1 HIS 75 1 Y 1 B NE2 HIS 333 B NE2 HIS 75 1 Y 1 A MET 259 A MET 1 1 Y 1 A GLN 260 A GLN 2 1 Y 1 A ARG 330 A ARG 72 1 Y 1 A PRO 352 A PRO 94 1 Y 1 A LEU 353 A LEU 95 1 Y 1 A GLU 354 A GLU 96 1 Y 1 A HIS 355 A HIS 97 1 Y 1 B MET 259 B MET 1 1 Y 1 B GLN 260 B GLN 2 1 Y 1 B SER 261 B SER 3 1 Y 1 B LEU 353 B LEU 95 1 Y 1 B GLU 354 B GLU 96 1 Y 1 B HIS 355 B HIS 97 1 Y 1 A ARG 328 -114.74 58.02 23.523 0.695 -0.722 -1.663 0.886 -0.925 0.062 0.964 0.960 Hydrogens have been added in their riding positions 0.2022 0.1798 0.181 1.600 43.577 978 17855 18833 5.193 82.496 5.719 0.086 Random selection 1 FREE R-VALUE MOLECULAR REPLACEMENT 0.114 0.103 0.800 0.800 1.200 MASK BULK SOLVENT 1.600 43.577 74 1491 0 0 1417 0.008 0.012 1508 0.001 0.016 1338 1.375 1.635 2057 0.489 1.561 3084 4.987 5.000 194 32.370 23.913 23 14.425 10.332 241 14.900 10.000 65 0.068 0.200 230 0.008 0.020 1836 0.001 0.020 356 0.239 0.200 388 0.194 0.200 1254 0.186 0.200 812 0.072 0.200 818 0.141 0.200 44 0.254 0.200 1 0.192 0.200 18 0.138 0.200 38 0.041 0.200 6 1.786 1.849 754 1.785 1.848 754 2.928 2.737 946 2.929 2.740 947 2.759 2.120 754 2.757 2.122 755 4.082 3.079 1107 4.080 3.080 1108 6.442 29.693 1816 6.411 29.255 1814 0.099 0.050 2959 1 A 1 X-RAY DIFFRACTION Local ncs 0.09939 0.05009 2 A 1 X-RAY DIFFRACTION Local ncs 0.09939 0.05009 0.331 0.356 0.355 1.641 36 508 1701 0.909 0.899 20 31.9812 0.354 0.320 0.339 0.338 1.686 28 631 1653 0.932 0.922 20 39.8669 0.335 0.365 0.308 0.311 1.735 38 764 1598 0.912 0.924 20 50.1877 0.296 0.267 0.303 0.301 1.788 48 982 1534 0.939 0.939 20 67.1447 0.287 0.287 0.257 0.259 1.847 66 1261 1490 0.940 0.954 20 89.0604 0.230 0.260 0.203 0.206 1.912 80 1339 1490 0.963 0.972 20 95.2349 0.173 0.180 0.193 0.192 1.984 67 1275 1399 0.978 0.974 20 95.9257 0.167 0.261 0.180 0.184 2.064 66 1227 1340 0.963 0.979 20 96.4925 0.155 0.203 0.173 0.175 2.156 70 1213 1316 0.974 0.982 20 97.4924 0.148 0.240 0.156 0.159 2.261 56 1140 1230 0.956 0.986 20 97.2358 0.134 0.164 0.158 0.158 2.383 60 1093 1179 0.982 0.985 20 97.7947 0.138 0.189 0.152 0.154 2.527 48 1038 1111 0.981 0.986 20 97.7498 0.129 0.205 0.157 0.159 2.701 56 967 1046 0.973 0.985 20 97.8011 0.138 0.223 0.152 0.155 2.916 42 931 986 0.977 0.986 20 98.6815 0.136 0.212 0.162 0.165 3.193 39 838 896 0.977 0.984 20 97.8795 0.147 0.126 0.153 0.151 3.568 55 735 806 0.989 0.987 20 98.0149 0.144 0.172 0.168 0.168 4.115 41 662 709 0.985 0.983 20 99.1537 0.165 0.198 0.178 0.179 5.029 37 570 611 0.981 0.981 20 99.3453 0.184 0.283 0.263 0.264 7.065 26 430 463 0.968 0.972 20 98.4881 0.264 0.191 0.182 0.182 43.577 19 251 271 0.973 0.975 20 99.6310 0.208 20.42 1.6 43.59 9RXW 18863 0.999 0.034 0.067 1 20.0 3.4 82.6 1.60 1.63 361 0.492 0.833 1.524 1 3.1 31.26 data reduction xia2 0.7.107-g95bc1153-dials-3.2 data reduction DIALS 3.2.3-gcbf1028a5-release data scaling TRUNCATE CCP4 7.1.008 phasing PHASER 2.8.3 model building ARP/wARP 8.0 patch 1 model building Coot 0.9.8.1 refinement REFMAC 5.8.0340 N Ty1 Prime Retrotransposon Capsid C-Terminal Domain, wt 1 N N 1 N N 2 N N 2 N N A THR 263 A THR 5 HELX_P A THR 274 A THR 16 1 AA1 12 A PRO 282 A PRO 24 HELX_P A ASN 300 A ASN 42 1 AA2 19 A ASN 305 A ASN 47 HELX_P A GLY 316 A GLY 58 1 AA3 12 A LEU 317 A LEU 59 HELX_P A GLU 320 A GLU 62 5 AA4 4 A TYR 321 A TYR 63 HELX_P A ARG 328 A ARG 70 1 AA5 8 A THR 335 A THR 77 HELX_P A GLN 351 A GLN 93 1 AA6 17 B THR 263 B THR 5 HELX_P B THR 274 B THR 16 1 AA7 12 B PRO 282 B PRO 24 HELX_P B ASN 300 B ASN 42 1 AA8 19 B ASN 305 B ASN 47 HELX_P B LEU 317 B LEU 59 1 AA9 13 B SER 318 B SER 60 HELX_P B GLU 320 B GLU 62 5 AB1 3 B TYR 321 B TYR 63 HELX_P B HIS 329 B HIS 71 1 AB2 9 B THR 335 B THR 77 HELX_P B GLN 351 B GLN 93 1 AB3 17 VIRUS LIKE PARTICLE Capsid, Gag, Retrotransposon, VIRUS LIKE PARTICLE A A A ASP 262 A ASP 4 A GLN 350 A GLN 92 A ASP 262 A ASP 4 A GLN 350 A GLN 92 Local NCS retraints between domains: 1 2 YM13A_YEAST UNP 1 259 Q04215 MQSDTQEVNDITTLATLHYNGSTPADAFEAEVTNILDRLNNNGIPINNKVACQFIMRGLSGEYKFLRYARHRCIHMTVAD LFSDIHSMYEEQQ 259 351 9RXW 259 351 Q04215 A 1 1 93 259 351 9RXW 259 351 Q04215 B 1 1 93 1 expression tag PRO 352 9RXW A Q04215 UNP 94 1 expression tag LEU 353 9RXW A Q04215 UNP 95 1 expression tag GLU 354 9RXW A Q04215 UNP 96 1 expression tag HIS 355 9RXW A Q04215 UNP 97 2 expression tag PRO 352 9RXW B Q04215 UNP 94 2 expression tag LEU 353 9RXW B Q04215 UNP 95 2 expression tag GLU 354 9RXW B Q04215 UNP 96 2 expression tag HIS 355 9RXW B Q04215 UNP 97 1 P 1