1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 van Pee, K. Neuhaus, A. D'Imprima, E. Mills, D.J. Kuehlbrandt, W. Yildiz, O. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.0 90.0 90.0 1.0 1.0 1.0 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 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 US Elife 2050-084X 6 10.7554/eLife.23644 28323617 CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin. 2017 AB INITIO MODEL A 1-471 5AOD 5LY6 6461 4.5 FSC 0.143 CUT-OFF POINT 7 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 1 Pneumolysin pore complex 0 RECOMBINANT ORGANELLE OR CELLULAR COMPONENT MEGADALTONS 2.2 1313 Streptococcus pneumoniae 511693 Escherichia coli BL21 pET15 PARTICLE 1 1 SINGLE PARTICLE 6 1.02 COUNTING GATAN K2 SUMMIT (4k x 4k) 300 FIELD EMISSION GUN FLOOD BEAM FEI POLARA 300 BRIGHT FIELD 1 5LY6 C42 PARTICLE SELECTION 1 RELION 1.4 IMAGE ACQUISITION 1 RELION 1.4 MASKING CTF CORRECTION 1 CTFFIND 3 LAYERLINE INDEXING DIFFRACTION INDEXING MODEL FITTING 1 Coot 8.4 OTHER INITIAL EULER ASSIGNMENT 1 RELION 1.4 FINAL EULER ASSIGNMENT 1 RELION 1.4 CLASSIFICATION 1 RELION 1.4 RECONSTRUCTION 1 RELION 1.4 MODEL REFINEMENT 1 Coot 8.4 1 NO NO NO YES ETHANE 5LY6 52866.066 Pneumolysin 1 man polymer Thiol-activated cytolysin no no MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDE TLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQ LKVKFGSDFEKAANSLDIDFNAVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSV AYGRQVYLKLETTSKSDEVQAAFEAAILGVKVAPQTQWKQILDNTEVKAVILGGDPSSGARVVTGKVDMVEDLIQEGSRF TADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRN GQDLTAHFTTSIPLKGNVRNLSVKIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDE TLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQ LKVKFGSDFEKAANSLDIDFNAVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSV AYGRQVYLKLETTSKSDEVQAAFEAAILGVKVAPQTQWKQILDNTEVKAVILGGDPSSGARVVTGKVDMVEDLIQEGSRF TADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRN GQDLTAHFTTSIPLKGNVRNLSVKIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n sample 1 471 ply, SPD_1726 373153 Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) 469008 Escherichia coli BL21(DE3) Biological sequence em_image_scans em_software em_admin pdbx_data_processing_status pdbx_database_proc pdbx_validate_close_contact struct_conn struct_conn_type atom_sites cell repository Initial release Data collection Advisory Data collection Derived calculations Data collection Other 1 0 2017-04-05 1 1 2017-08-02 1 2 2019-02-20 1 3 2019-10-02 _em_software.name _em_admin.last_update _atom_sites.fract_transf_matrix[1][1] _atom_sites.fract_transf_matrix[2][2] _atom_sites.fract_transf_matrix[3][3] _cell.length_a _cell.length_b _cell.length_c Germany Max Planck Society Biophysics/Structural Biology CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A N PDBE Y PDBE 2016-09-24 REL MET 1 n 1 MET 1 B ALA 2 n 2 ALA 2 B ASN 3 n 3 ASN 3 B LYS 4 n 4 LYS 4 B ALA 5 n 5 ALA 5 B VAL 6 n 6 VAL 6 B ASN 7 n 7 ASN 7 B ASP 8 n 8 ASP 8 B PHE 9 n 9 PHE 9 B ILE 10 n 10 ILE 10 B LEU 11 n 11 LEU 11 B ALA 12 n 12 ALA 12 B MET 13 n 13 MET 13 B ASN 14 n 14 ASN 14 B TYR 15 n 15 TYR 15 B ASP 16 n 16 ASP 16 B LYS 17 n 17 LYS 17 B LYS 18 n 18 LYS 18 B LYS 19 n 19 LYS 19 B LEU 20 n 20 LEU 20 B LEU 21 n 21 LEU 21 B THR 22 n 22 THR 22 B HIS 23 n 23 HIS 23 B GLN 24 n 24 GLN 24 B GLY 25 n 25 GLY 25 B GLU 26 n 26 GLU 26 B SER 27 n 27 SER 27 B ILE 28 n 28 ILE 28 B GLU 29 n 29 GLU 29 B ASN 30 n 30 ASN 30 B ARG 31 n 31 ARG 31 B PHE 32 n 32 PHE 32 B ILE 33 n 33 ILE 33 B LYS 34 n 34 LYS 34 B GLU 35 n 35 GLU 35 B GLY 36 n 36 GLY 36 B ASN 37 n 37 ASN 37 B GLN 38 n 38 GLN 38 B LEU 39 n 39 LEU 39 B PRO 40 n 40 PRO 40 B ASP 41 n 41 ASP 41 B GLU 42 n 42 GLU 42 B PHE 43 n 43 PHE 43 B VAL 44 n 44 VAL 44 B VAL 45 n 45 VAL 45 B ILE 46 n 46 ILE 46 B GLU 47 n 47 GLU 47 B ARG 48 n 48 ARG 48 B LYS 49 n 49 LYS 49 B LYS 50 n 50 LYS 50 B ARG 51 n 51 ARG 51 B SER 52 n 52 SER 52 B LEU 53 n 53 LEU 53 B SER 54 n 54 SER 54 B THR 55 n 55 THR 55 B ASN 56 n 56 ASN 56 B THR 57 n 57 THR 57 B SER 58 n 58 SER 58 B ASP 59 n 59 ASP 59 B ILE 60 n 60 ILE 60 B SER 61 n 61 SER 61 B VAL 62 n 62 VAL 62 B THR 63 n 63 THR 63 B ALA 64 n 64 ALA 64 B THR 65 n 65 THR 65 B ASN 66 n 66 ASN 66 B ASP 67 n 67 ASP 67 B SER 68 n 68 SER 68 B ARG 69 n 69 ARG 69 B LEU 70 n 70 LEU 70 B TYR 71 n 71 TYR 71 B PRO 72 n 72 PRO 72 B GLY 73 n 73 GLY 73 B ALA 74 n 74 ALA 74 B LEU 75 n 75 LEU 75 B LEU 76 n 76 LEU 76 B VAL 77 n 77 VAL 77 B VAL 78 n 78 VAL 78 B ASP 79 n 79 ASP 79 B GLU 80 n 80 GLU 80 B THR 81 n 81 THR 81 B LEU 82 n 82 LEU 82 B LEU 83 n 83 LEU 83 B GLU 84 n 84 GLU 84 B ASN 85 n 85 ASN 85 B ASN 86 n 86 ASN 86 B PRO 87 n 87 PRO 87 B THR 88 n 88 THR 88 B LEU 89 n 89 LEU 89 B LEU 90 n 90 LEU 90 B ALA 91 n 91 ALA 91 B VAL 92 n 92 VAL 92 B ASP 93 n 93 ASP 93 B ARG 94 n 94 ARG 94 B ALA 95 n 95 ALA 95 B PRO 96 n 96 PRO 96 B MET 97 n 97 MET 97 B THR 98 n 98 THR 98 B TYR 99 n 99 TYR 99 B SER 100 n 100 SER 100 B ILE 101 n 101 ILE 101 B ASP 102 n 102 ASP 102 B LEU 103 n 103 LEU 103 B PRO 104 n 104 PRO 104 B GLY 105 n 105 GLY 105 B LEU 106 n 106 LEU 106 B ALA 107 n 107 ALA 107 B SER 108 n 108 SER 108 B SER 109 n 109 SER 109 B ASP 110 n 110 ASP 110 B SER 111 n 111 SER 111 B PHE 112 n 112 PHE 112 B LEU 113 n 113 LEU 113 B GLN 114 n 114 GLN 114 B VAL 115 n 115 VAL 115 B GLU 116 n 116 GLU 116 B ASP 117 n 117 ASP 117 B PRO 118 n 118 PRO 118 B SER 119 n 119 SER 119 B ASN 120 n 120 ASN 120 B SER 121 n 121 SER 121 B SER 122 n 122 SER 122 B VAL 123 n 123 VAL 123 B ARG 124 n 124 ARG 124 B GLY 125 n 125 GLY 125 B ALA 126 n 126 ALA 126 B VAL 127 n 127 VAL 127 B ASN 128 n 128 ASN 128 B ASP 129 n 129 ASP 129 B LEU 130 n 130 LEU 130 B LEU 131 n 131 LEU 131 B ALA 132 n 132 ALA 132 B LYS 133 n 133 LYS 133 B TRP 134 n 134 TRP 134 B HIS 135 n 135 HIS 135 B GLN 136 n 136 GLN 136 B ASP 137 n 137 ASP 137 B TYR 138 n 138 TYR 138 B GLY 139 n 139 GLY 139 B GLN 140 n 140 GLN 140 B VAL 141 n 141 VAL 141 B ASN 142 n 142 ASN 142 B ASN 143 n 143 ASN 143 B VAL 144 n 144 VAL 144 B PRO 145 n 145 PRO 145 B ALA 146 n 146 ALA 146 B ARG 147 n 147 ARG 147 B MET 148 n 148 MET 148 B GLN 149 n 149 GLN 149 B TYR 150 n 150 TYR 150 B GLU 151 n 151 GLU 151 B LYS 152 n 152 LYS 152 B ILE 153 n 153 ILE 153 B THR 154 n 154 THR 154 B ALA 155 n 155 ALA 155 B HIS 156 n 156 HIS 156 B SER 157 n 157 SER 157 B MET 158 n 158 MET 158 B GLU 159 n 159 GLU 159 B GLN 160 n 160 GLN 160 B LEU 161 n 161 LEU 161 B LYS 162 n 162 LYS 162 B VAL 163 n 163 VAL 163 B LYS 164 n 164 LYS 164 B PHE 165 n 165 PHE 165 B GLY 166 n 166 GLY 166 B SER 167 n 167 SER 167 B ASP 168 n 168 ASP 168 B PHE 169 n 169 PHE 169 B GLU 170 n 170 GLU 170 B LYS 171 n 171 LYS 171 B ALA 172 n 172 ALA 172 B ALA 173 n 173 ALA 173 B ASN 174 n 174 ASN 174 B SER 175 n 175 SER 175 B LEU 176 n 176 LEU 176 B ASP 177 n 177 ASP 177 B ILE 178 n 178 ILE 178 B ASP 179 n 179 ASP 179 B PHE 180 n 180 PHE 180 B ASN 181 n 181 ASN 181 B ALA 182 n 182 ALA 182 B VAL 183 n 183 VAL 183 B HIS 184 n 184 HIS 184 B SER 185 n 185 SER 185 B GLY 186 n 186 GLY 186 B GLU 187 n 187 GLU 187 B LYS 188 n 188 LYS 188 B GLN 189 n 189 GLN 189 B ILE 190 n 190 ILE 190 B GLN 191 n 191 GLN 191 B ILE 192 n 192 ILE 192 B VAL 193 n 193 VAL 193 B ASN 194 n 194 ASN 194 B PHE 195 n 195 PHE 195 B LYS 196 n 196 LYS 196 B GLN 197 n 197 GLN 197 B ILE 198 n 198 ILE 198 B TYR 199 n 199 TYR 199 B TYR 200 n 200 TYR 200 B THR 201 n 201 THR 201 B VAL 202 n 202 VAL 202 B SER 203 n 203 SER 203 B VAL 204 n 204 VAL 204 B ASP 205 n 205 ASP 205 B ALA 206 n 206 ALA 206 B VAL 207 n 207 VAL 207 B LYS 208 n 208 LYS 208 B ASN 209 n 209 ASN 209 B PRO 210 n 210 PRO 210 B GLY 211 n 211 GLY 211 B ASP 212 n 212 ASP 212 B VAL 213 n 213 VAL 213 B PHE 214 n 214 PHE 214 B GLN 215 n 215 GLN 215 B ASP 216 n 216 ASP 216 B THR 217 n 217 THR 217 B VAL 218 n 218 VAL 218 B THR 219 n 219 THR 219 B VAL 220 n 220 VAL 220 B GLU 221 n 221 GLU 221 B ASP 222 n 222 ASP 222 B LEU 223 n 223 LEU 223 B LYS 224 n 224 LYS 224 B GLN 225 n 225 GLN 225 B ARG 226 n 226 ARG 226 B GLY 227 n 227 GLY 227 B ILE 228 n 228 ILE 228 B SER 229 n 229 SER 229 B ALA 230 n 230 ALA 230 B GLU 231 n 231 GLU 231 B ARG 232 n 232 ARG 232 B PRO 233 n 233 PRO 233 B LEU 234 n 234 LEU 234 B VAL 235 n 235 VAL 235 B TYR 236 n 236 TYR 236 B ILE 237 n 237 ILE 237 B SER 238 n 238 SER 238 B SER 239 n 239 SER 239 B VAL 240 n 240 VAL 240 B ALA 241 n 241 ALA 241 B TYR 242 n 242 TYR 242 B GLY 243 n 243 GLY 243 B ARG 244 n 244 ARG 244 B GLN 245 n 245 GLN 245 B VAL 246 n 246 VAL 246 B TYR 247 n 247 TYR 247 B LEU 248 n 248 LEU 248 B LYS 249 n 249 LYS 249 B LEU 250 n 250 LEU 250 B GLU 251 n 251 GLU 251 B THR 252 n 252 THR 252 B THR 253 n 253 THR 253 B SER 254 n 254 SER 254 B LYS 255 n 255 LYS 255 B SER 256 n 256 SER 256 B ASP 257 n 257 ASP 257 B GLU 258 n 258 GLU 258 B VAL 259 n 259 VAL 259 B GLN 260 n 260 GLN 260 B ALA 261 n 261 ALA 261 B ALA 262 n 262 ALA 262 B PHE 263 n 263 PHE 263 B GLU 264 n 264 GLU 264 B ALA 265 n 265 ALA 265 B ALA 266 n 266 ALA 266 B ILE 267 n 267 ILE 267 B LEU 268 n 268 LEU 268 B GLY 269 n 269 GLY 269 B VAL 270 n 270 VAL 270 B LYS 271 n 271 LYS 271 B VAL 272 n 272 VAL 272 B ALA 273 n 273 ALA 273 B PRO 274 n 274 PRO 274 B GLN 275 n 275 GLN 275 B THR 276 n 276 THR 276 B GLN 277 n 277 GLN 277 B TRP 278 n 278 TRP 278 B LYS 279 n 279 LYS 279 B GLN 280 n 280 GLN 280 B ILE 281 n 281 ILE 281 B LEU 282 n 282 LEU 282 B ASP 283 n 283 ASP 283 B ASN 284 n 284 ASN 284 B THR 285 n 285 THR 285 B GLU 286 n 286 GLU 286 B VAL 287 n 287 VAL 287 B LYS 288 n 288 LYS 288 B ALA 289 n 289 ALA 289 B VAL 290 n 290 VAL 290 B ILE 291 n 291 ILE 291 B LEU 292 n 292 LEU 292 B GLY 293 n 293 GLY 293 B GLY 294 n 294 GLY 294 B ASP 295 n 295 ASP 295 B PRO 296 n 296 PRO 296 B SER 297 n 297 SER 297 B SER 298 n 298 SER 298 B GLY 299 n 299 GLY 299 B ALA 300 n 300 ALA 300 B ARG 301 n 301 ARG 301 B VAL 302 n 302 VAL 302 B VAL 303 n 303 VAL 303 B THR 304 n 304 THR 304 B GLY 305 n 305 GLY 305 B LYS 306 n 306 LYS 306 B VAL 307 n 307 VAL 307 B ASP 308 n 308 ASP 308 B MET 309 n 309 MET 309 B VAL 310 n 310 VAL 310 B GLU 311 n 311 GLU 311 B ASP 312 n 312 ASP 312 B LEU 313 n 313 LEU 313 B ILE 314 n 314 ILE 314 B GLN 315 n 315 GLN 315 B GLU 316 n 316 GLU 316 B GLY 317 n 317 GLY 317 B SER 318 n 318 SER 318 B ARG 319 n 319 ARG 319 B PHE 320 n 320 PHE 320 B THR 321 n 321 THR 321 B ALA 322 n 322 ALA 322 B ASP 323 n 323 ASP 323 B HIS 324 n 324 HIS 324 B PRO 325 n 325 PRO 325 B GLY 326 n 326 GLY 326 B LEU 327 n 327 LEU 327 B PRO 328 n 328 PRO 328 B ILE 329 n 329 ILE 329 B SER 330 n 330 SER 330 B TYR 331 n 331 TYR 331 B THR 332 n 332 THR 332 B THR 333 n 333 THR 333 B SER 334 n 334 SER 334 B PHE 335 n 335 PHE 335 B LEU 336 n 336 LEU 336 B ARG 337 n 337 ARG 337 B ASP 338 n 338 ASP 338 B ASN 339 n 339 ASN 339 B VAL 340 n 340 VAL 340 B VAL 341 n 341 VAL 341 B ALA 342 n 342 ALA 342 B THR 343 n 343 THR 343 B PHE 344 n 344 PHE 344 B GLN 345 n 345 GLN 345 B ASN 346 n 346 ASN 346 B SER 347 n 347 SER 347 B THR 348 n 348 THR 348 B ASP 349 n 349 ASP 349 B TYR 350 n 350 TYR 350 B VAL 351 n 351 VAL 351 B GLU 352 n 352 GLU 352 B THR 353 n 353 THR 353 B LYS 354 n 354 LYS 354 B VAL 355 n 355 VAL 355 B THR 356 n 356 THR 356 B ALA 357 n 357 ALA 357 B TYR 358 n 358 TYR 358 B ARG 359 n 359 ARG 359 B ASN 360 n 360 ASN 360 B GLY 361 n 361 GLY 361 B ASP 362 n 362 ASP 362 B LEU 363 n 363 LEU 363 B LEU 364 n 364 LEU 364 B LEU 365 n 365 LEU 365 B ASP 366 n 366 ASP 366 B HIS 367 n 367 HIS 367 B SER 368 n 368 SER 368 B GLY 369 n 369 GLY 369 B ALA 370 n 370 ALA 370 B TYR 371 n 371 TYR 371 B VAL 372 n 372 VAL 372 B ALA 373 n 373 ALA 373 B GLN 374 n 374 GLN 374 B TYR 375 n 375 TYR 375 B TYR 376 n 376 TYR 376 B ILE 377 n 377 ILE 377 B THR 378 n 378 THR 378 B TRP 379 n 379 TRP 379 B ASP 380 n 380 ASP 380 B GLU 381 n 381 GLU 381 B LEU 382 n 382 LEU 382 B SER 383 n 383 SER 383 B TYR 384 n 384 TYR 384 B ASP 385 n 385 ASP 385 B HIS 386 n 386 HIS 386 B GLN 387 n 387 GLN 387 B GLY 388 n 388 GLY 388 B LYS 389 n 389 LYS 389 B GLU 390 n 390 GLU 390 B VAL 391 n 391 VAL 391 B LEU 392 n 392 LEU 392 B THR 393 n 393 THR 393 B PRO 394 n 394 PRO 394 B LYS 395 n 395 LYS 395 B ALA 396 n 396 ALA 396 B TRP 397 n 397 TRP 397 B ASP 398 n 398 ASP 398 B ARG 399 n 399 ARG 399 B ASN 400 n 400 ASN 400 B GLY 401 n 401 GLY 401 B GLN 402 n 402 GLN 402 B ASP 403 n 403 ASP 403 B LEU 404 n 404 LEU 404 B THR 405 n 405 THR 405 B ALA 406 n 406 ALA 406 B HIS 407 n 407 HIS 407 B PHE 408 n 408 PHE 408 B THR 409 n 409 THR 409 B THR 410 n 410 THR 410 B SER 411 n 411 SER 411 B ILE 412 n 412 ILE 412 B PRO 413 n 413 PRO 413 B LEU 414 n 414 LEU 414 B LYS 415 n 415 LYS 415 B GLY 416 n 416 GLY 416 B ASN 417 n 417 ASN 417 B VAL 418 n 418 VAL 418 B ARG 419 n 419 ARG 419 B ASN 420 n 420 ASN 420 B LEU 421 n 421 LEU 421 B SER 422 n 422 SER 422 B VAL 423 n 423 VAL 423 B LYS 424 n 424 LYS 424 B ILE 425 n 425 ILE 425 B ARG 426 n 426 ARG 426 B GLU 427 n 427 GLU 427 B CYS 428 n 428 CYS 428 B THR 429 n 429 THR 429 B GLY 430 n 430 GLY 430 B LEU 431 n 431 LEU 431 B ALA 432 n 432 ALA 432 B TRP 433 n 433 TRP 433 B GLU 434 n 434 GLU 434 B TRP 435 n 435 TRP 435 B TRP 436 n 436 TRP 436 B ARG 437 n 437 ARG 437 B THR 438 n 438 THR 438 B VAL 439 n 439 VAL 439 B TYR 440 n 440 TYR 440 B GLU 441 n 441 GLU 441 B LYS 442 n 442 LYS 442 B THR 443 n 443 THR 443 B ASP 444 n 444 ASP 444 B LEU 445 n 445 LEU 445 B PRO 446 n 446 PRO 446 B LEU 447 n 447 LEU 447 B VAL 448 n 448 VAL 448 B ARG 449 n 449 ARG 449 B LYS 450 n 450 LYS 450 B ARG 451 n 451 ARG 451 B THR 452 n 452 THR 452 B ILE 453 n 453 ILE 453 B SER 454 n 454 SER 454 B ILE 455 n 455 ILE 455 B TRP 456 n 456 TRP 456 B GLY 457 n 457 GLY 457 B THR 458 n 458 THR 458 B THR 459 n 459 THR 459 B LEU 460 n 460 LEU 460 B TYR 461 n 461 TYR 461 B PRO 462 n 462 PRO 462 B GLN 463 n 463 GLN 463 B VAL 464 n 464 VAL 464 B GLU 465 n 465 GLU 465 B ASP 466 n 466 ASP 466 B LYS 467 n 467 LYS 467 B VAL 468 n 468 VAL 468 B GLU 469 n 469 GLU 469 B ASN 470 n 470 ASN 470 B ASP 471 n 471 ASP 471 B software_defined_assembly PISA 1 monomeric 0 0 29420 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 B O GLU 29 A O GLU 29 B N ILE 46 A N ILE 46 B O PHE 43 A O PHE 43 B N ALA 357 A N ALA 357 B O SER 100 A O SER 100 B N SER 203 A N SER 203 B O ARG 147 A O ARG 147 B N ILE 198 A N ILE 198 B O ASN 181 A O ASN 181 B N GLN 260 A N GLN 260 B O LYS 249 A O LYS 249 B N LYS 288 A N LYS 288 B O ILE 153 A O ILE 153 B N ILE 192 A N ILE 192 B O TYR 236 A O TYR 236 B N SER 334 A N SER 334 B O TYR 331 A O TYR 331 B N GLN 345 A N GLN 345 B O ALA 261 A O ALA 261 B N THR 276 A N THR 276 B O PHE 408 A O PHE 408 B N HIS 367 A N HIS 367 B O ASP 362 A O ASP 362 B N ARG 451 A N ARG 451 B O LYS 450 A O LYS 450 B N GLU 469 A N GLU 469 B O VAL 372 A O VAL 372 B N CYS 428 A N CYS 428 B O SER 383 A O SER 383 B N VAL 391 A N VAL 391 B O TYR 440 A O TYR 440 B N ILE 425 A N ILE 425 B O ARG 419 A O ARG 419 B N ASP 380 A N ASP 380 1 B B CG1 CD VAL PRO 78 233 1.53 1 B B OD2 ND1 ASP HIS 295 324 1.81 1 B B CG2 CD1 VAL LEU 302 313 1.85 1 B B N O LEU VAL 76 235 1.88 1 B B CG1 CG VAL PRO 78 233 1.89 1 B B O N TYR SER 236 334 2.02 1 B B OH CD1 TYR ILE 371 455 2.07 1 B B N O TYR SER 236 334 2.08 1 B B O CB ALA TYR 74 236 2.09 1 B B CG2 CE1 VAL PHE 235 335 2.10 1 B B CB CA ARG GLY 244 293 2.11 1 B B O OG1 VAL THR 62 65 2.11 1 B B O OG1 ILE THR 60 63 2.11 1 B B CB NH2 PRO ARG 233 337 2.12 1 B B OH NE TYR ARG 199 244 2.12 1 B B CE1 CB HIS ALA 135 322 2.16 1 B B CB CZ PRO ARG 233 337 2.18 1 B B OG1 CB THR PRO 81 87 2.18 1 B B O N LEU HIS 161 184 2.18 1 B B O OG SER SER 58 61 2.18 1 B B OG1 CA THR PRO 81 87 2.19 1 -30.61 2.10 128.40 97.79 B B B C N CD LEU PRO PRO 39 40 40 Y 1 -11.32 1.60 122.70 111.38 B B B O C N THR THR SER 57 57 58 Y 1 -25.31 2.10 128.40 103.09 B B B C N CD TYR PRO PRO 71 72 72 Y 1 -13.83 2.10 128.40 114.57 B B B C N CD ASN PRO PRO 86 87 87 Y 1 -28.73 2.10 128.40 99.67 B B B C N CD ASP PRO PRO 117 118 118 Y 1 -14.01 2.10 128.40 114.39 B B B C N CD ASN PRO PRO 209 210 210 Y 1 -26.20 2.10 128.40 102.20 B B B C N CD ALA PRO PRO 273 274 274 Y 1 -19.61 2.10 128.40 108.79 B B B C N CD ASP PRO PRO 295 296 296 Y 1 -13.54 2.10 128.40 114.86 B B B C N CD LEU PRO PRO 445 446 446 Y 1 B B C N THR SER 57 58 0.261 0.023 1.336 1.597 Y 1 B HIS 23 -115.79 77.00 1 B GLU 26 -107.08 -145.68 1 B SER 27 -89.35 -94.71 1 B ILE 33 -161.23 116.70 1 B GLN 38 -160.02 -23.94 1 B LEU 39 -91.00 -101.31 1 B ASP 41 -160.29 113.66 1 B SER 52 -160.06 -68.53 1 B SER 54 -71.93 -82.04 1 B SER 68 -109.29 63.49 1 B ARG 69 -99.61 38.74 1 B LEU 75 -152.06 83.21 1 B ASP 79 -138.72 -73.06 1 B GLU 80 -138.65 -43.10 1 B ASN 86 -177.51 83.71 1 B PRO 87 -111.80 -165.46 1 B LEU 89 -109.99 41.28 1 B LEU 103 -142.01 -150.73 1 B LEU 113 -127.96 -136.64 1 B GLU 116 -93.00 -144.27 1 B ASN 120 -153.93 40.52 1 B GLN 136 -72.85 -70.76 1 B GLN 140 -150.54 -99.76 1 B VAL 141 49.80 -90.59 1 B ALA 172 -75.20 37.11 1 B ALA 173 -159.25 -63.93 1 B TYR 199 -114.09 -70.13 1 B ALA 206 -22.62 151.69 1 B ASN 209 -138.36 -152.27 1 B GLN 215 -92.51 -154.94 1 B ARG 226 -66.60 -74.83 1 B SER 229 -104.88 -150.77 1 B SER 238 -87.76 -100.07 1 B GLN 245 -160.21 110.61 1 B ALA 266 -161.56 62.14 1 B LEU 268 -67.93 92.78 1 B PRO 296 -137.24 -83.95 1 B LYS 306 -131.83 -99.75 1 B VAL 307 -131.67 -41.25 1 B ASP 308 -97.84 57.43 1 B MET 309 -99.87 -64.10 1 B ILE 314 -107.90 45.39 1 B GLN 315 -158.74 -25.94 1 B THR 321 -143.28 -69.64 1 B ALA 322 -146.44 -22.59 1 B ILE 329 -118.41 -79.60 1 B ARG 337 -153.61 -47.35 1 B ASP 338 -143.09 16.59 1 B VAL 340 -141.43 -63.82 1 B VAL 341 -54.72 105.20 1 B ASN 346 -109.41 -145.59 1 B TYR 376 -117.94 72.84 1 B LEU 382 -67.22 -166.95 1 B SER 383 168.59 144.52 1 B GLN 387 -60.65 -71.46 1 B ARG 399 -108.07 68.83 1 B GLN 402 176.36 153.67 1 B THR 410 -162.45 -163.44 1 B SER 411 174.51 127.91 1 B LEU 414 -69.62 -154.02 1 B LYS 415 -177.78 87.61 1 B ARG 419 176.70 125.28 1 B ASN 420 75.83 144.45 1 B LEU 421 -160.13 105.47 1 B LEU 431 49.93 -134.51 1 B ALA 432 -146.99 -28.66 1 B GLU 434 -100.51 -168.95 1 B TRP 435 -149.01 -44.89 1 B VAL 439 -81.64 -79.88 1 B LEU 447 -61.33 94.13 1 B THR 458 -106.50 -150.23 1 B LEU 460 -132.68 -53.03 1 B GLN 463 -101.25 54.80 N Pneumolysin CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A 1 N N B ALA 2 A ALA 2 HELX_P B ALA 12 A ALA 12 1 1 11 B LYS 17 A LYS 17 HELX_P B LEU 21 A LEU 21 1 2 5 B ASP 59 A ASP 59 HELX_P B ASP 67 A ASP 67 1 3 9 B SER 122 A SER 122 HELX_P B ASP 137 A ASP 137 1 4 16 B ASP 222 A ASP 222 HELX_P B GLY 227 A GLY 227 1 5 6 B SER 297 A SER 297 HELX_P B THR 304 A THR 304 1 6 8 B VAL 310 A VAL 310 HELX_P B LEU 313 A LEU 313 1 7 4 TOXIN Bacterial toxins, pore complex, cryoEM structure, cholesterol-dependent cytolysin, Pneumolysin, membrane pore, TOXIN B ALA 406 A ALA 406 1 B HIS 407 A HIS 407 0.00 TACY_STRP2 UNP 1 1 Q04IN8 MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDE TLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQ LKVKFGSDFEKTGNSLDIDFNSVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSV AYGRQVYLKLETTSKSDEVEAAFEALIKGVKVAPQTEWKQILDNTEVKAVILGGDPSSGARVVTGKVDMVEDLIQEGSRF TADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRN GQDLTAHFTTSIPLKGNVRNLSVKIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND 1 471 5LY6 1 471 Q04IN8 B 1 1 471 1 THR conflict ALA 172 5LY6 B Q04IN8 UNP 172 172 1 GLY conflict ALA 173 5LY6 B Q04IN8 UNP 173 173 1 SER conflict ALA 182 5LY6 B Q04IN8 UNP 182 182 1 GLU conflict GLN 260 5LY6 B Q04IN8 UNP 260 260 1 LEU conflict ALA 266 5LY6 B Q04IN8 UNP 266 266 1 LYS conflict LEU 268 5LY6 B Q04IN8 UNP 268 268 1 GLU conflict GLN 277 5LY6 B Q04IN8 UNP 277 277 3 2 4 2 3 2 4 2 2 3 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel B ILE 28 A ILE 28 B ARG 31 A ARG 31 B PHE 43 A PHE 43 B ARG 48 A ARG 48 B GLU 352 A GLU 352 B ALA 357 A ALA 357 B TYR 99 A TYR 99 B ILE 101 A ILE 101 B VAL 202 A VAL 202 B VAL 204 A VAL 204 B ARG 147 A ARG 147 B GLN 149 A GLN 149 B PHE 180 A PHE 180 B ILE 198 A ILE 198 B GLY 243 A GLY 243 B ALA 261 A ALA 261 B ILE 281 A ILE 281 B LYS 288 A LYS 288 B LYS 152 A LYS 152 B PHE 165 A PHE 165 B PHE 180 A PHE 180 B VAL 193 A VAL 193 B VAL 235 A VAL 235 B ILE 237 A ILE 237 B TYR 331 A TYR 331 B PHE 335 A PHE 335 B ALA 342 A ALA 342 B GLN 345 A GLN 345 B ALA 261 A ALA 261 B GLU 264 A GLU 264 B ALA 273 A ALA 273 B THR 276 A THR 276 B PHE 408 A PHE 408 B PRO 413 A PRO 413 B ASP 362 A ASP 362 B GLY 369 A GLY 369 B LYS 450 A LYS 450 B GLY 457 A GLY 457 B GLN 463 A GLN 463 B GLU 469 A GLU 469 B VAL 372 A VAL 372 B GLN 374 A GLN 374 B ARG 426 A ARG 426 B CYS 428 A CYS 428 B LEU 382 A LEU 382 B TYR 384 A TYR 384 B GLU 390 A GLU 390 B LEU 392 A LEU 392 B TYR 440 A TYR 440 B LYS 442 A LYS 442 B ARG 419 A ARG 419 B ILE 425 A ILE 425 B ILE 377 A ILE 377 B ASP 380 A ASP 380 1 P 1