HEADER VIRAL PROTEIN/IMMUNE SYSTEM 08-FEB-21 7E39 TITLE SARS-COV-2 SPIKE IN COMPLEX WITH THE AB4 NEUTRALIZING ANTIBODY (STATE TITLE 2 3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LIGHT CHAIN OF AB4; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HEAVY CHAIN OF AB4; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_COMMON: HUMAN; SOURCE 19 ORGANISM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 21 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 22 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SPIKE, SARS-COV-2, ANTIBODY, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE KEYWDS 2 SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR C.LIU REVDAT 1 01-SEP-21 7E39 0 JRNL AUTH J.NIE,J.XIE,S.LIU,J.WU,C.LIU,J.LI,Y.LIU,M.WANG,H.ZHAO, JRNL AUTH 2 Y.ZHANG,J.YAO,L.CHEN,Y.SHEN,Y.YANG,H.W.WANG,Y.WANG,W.HUANG JRNL TITL THREE EPITOPE-DISTINCT HUMAN ANTIBODIES FROM RENMAB MICE JRNL TITL 2 NEUTRALIZE SARS-COV-2 AND COOPERATIVELY MINIMIZE THE ESCAPE JRNL TITL 3 OF MUTANTS. JRNL REF CELL DISCOV V. 7 53 2021 JRNL REFN ESSN 2056-5968 JRNL PMID 34285195 JRNL DOI 10.1038/S41421-021-00292-Z REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.700 REMARK 3 NUMBER OF PARTICLES : 108702 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7E39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1300020681. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : COMPLEX OF SPIKE PROTEIN TRIMER REMARK 245 WITH THREE AB4 ANTIBODIES; REMARK 245 SPIKE PROTEIN S1; LIGHT CHAIN REMARK 245 OF AB4; HEAVY CHAIN OF AB4 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS B 107 REMARK 465 ARG B 108 REMARK 465 THR B 109 REMARK 465 VAL B 110 REMARK 465 ALA B 111 REMARK 465 ALA B 112 REMARK 465 PRO B 113 REMARK 465 SER B 114 REMARK 465 VAL B 115 REMARK 465 PHE B 116 REMARK 465 ILE B 117 REMARK 465 PHE B 118 REMARK 465 PRO B 119 REMARK 465 PRO B 120 REMARK 465 SER B 121 REMARK 465 ASP B 122 REMARK 465 GLU B 123 REMARK 465 GLN B 124 REMARK 465 LEU B 125 REMARK 465 LYS B 126 REMARK 465 SER B 127 REMARK 465 GLY B 128 REMARK 465 THR B 129 REMARK 465 ALA B 130 REMARK 465 SER B 131 REMARK 465 VAL B 132 REMARK 465 VAL B 133 REMARK 465 CYS B 134 REMARK 465 LEU B 135 REMARK 465 LEU B 136 REMARK 465 ASN B 137 REMARK 465 ASN B 138 REMARK 465 PHE B 139 REMARK 465 TYR B 140 REMARK 465 PRO B 141 REMARK 465 ARG B 142 REMARK 465 GLU B 143 REMARK 465 ALA B 144 REMARK 465 LYS B 145 REMARK 465 VAL B 146 REMARK 465 GLN B 147 REMARK 465 TRP B 148 REMARK 465 LYS B 149 REMARK 465 VAL B 150 REMARK 465 ASP B 151 REMARK 465 ASN B 152 REMARK 465 ALA B 153 REMARK 465 LEU B 154 REMARK 465 GLN B 155 REMARK 465 SER B 156 REMARK 465 GLY B 157 REMARK 465 ASN B 158 REMARK 465 SER B 159 REMARK 465 GLN B 160 REMARK 465 GLU B 161 REMARK 465 SER B 162 REMARK 465 VAL B 163 REMARK 465 THR B 164 REMARK 465 GLU B 165 REMARK 465 GLN B 166 REMARK 465 ASP B 167 REMARK 465 SER B 168 REMARK 465 LYS B 169 REMARK 465 ASP B 170 REMARK 465 SER B 171 REMARK 465 THR B 172 REMARK 465 TYR B 173 REMARK 465 SER B 174 REMARK 465 LEU B 175 REMARK 465 SER B 176 REMARK 465 SER B 177 REMARK 465 THR B 178 REMARK 465 LEU B 179 REMARK 465 THR B 180 REMARK 465 LEU B 181 REMARK 465 SER B 182 REMARK 465 LYS B 183 REMARK 465 ALA B 184 REMARK 465 ASP B 185 REMARK 465 TYR B 186 REMARK 465 GLU B 187 REMARK 465 LYS B 188 REMARK 465 HIS B 189 REMARK 465 LYS B 190 REMARK 465 VAL B 191 REMARK 465 TYR B 192 REMARK 465 ALA B 193 REMARK 465 CYS B 194 REMARK 465 GLU B 195 REMARK 465 VAL B 196 REMARK 465 THR B 197 REMARK 465 HIS B 198 REMARK 465 GLN B 199 REMARK 465 GLY B 200 REMARK 465 LEU B 201 REMARK 465 SER B 202 REMARK 465 SER B 203 REMARK 465 PRO B 204 REMARK 465 VAL B 205 REMARK 465 THR B 206 REMARK 465 LYS B 207 REMARK 465 SER B 208 REMARK 465 PHE B 209 REMARK 465 ASN B 210 REMARK 465 ARG B 211 REMARK 465 GLY B 212 REMARK 465 GLU B 213 REMARK 465 CYS B 214 REMARK 465 LEU C 86 REMARK 465 ARG C 87 REMARK 465 ALA C 88 REMARK 465 SER C 118 REMARK 465 ALA C 119 REMARK 465 SER C 120 REMARK 465 THR C 121 REMARK 465 LYS C 122 REMARK 465 GLY C 123 REMARK 465 PRO C 124 REMARK 465 SER C 125 REMARK 465 VAL C 126 REMARK 465 PHE C 127 REMARK 465 PRO C 128 REMARK 465 LEU C 129 REMARK 465 ALA C 130 REMARK 465 PRO C 131 REMARK 465 SER C 132 REMARK 465 SER C 133 REMARK 465 LYS C 134 REMARK 465 SER C 135 REMARK 465 THR C 136 REMARK 465 SER C 137 REMARK 465 GLY C 138 REMARK 465 GLY C 139 REMARK 465 THR C 140 REMARK 465 ALA C 141 REMARK 465 ALA C 142 REMARK 465 LEU C 143 REMARK 465 GLY C 144 REMARK 465 CYS C 145 REMARK 465 LEU C 146 REMARK 465 VAL C 147 REMARK 465 LYS C 148 REMARK 465 ASP C 149 REMARK 465 TYR C 150 REMARK 465 PHE C 151 REMARK 465 PRO C 152 REMARK 465 GLU C 153 REMARK 465 PRO C 154 REMARK 465 VAL C 155 REMARK 465 THR C 156 REMARK 465 VAL C 157 REMARK 465 SER C 158 REMARK 465 TRP C 159 REMARK 465 ASN C 160 REMARK 465 SER C 161 REMARK 465 GLY C 162 REMARK 465 ALA C 163 REMARK 465 LEU C 164 REMARK 465 THR C 165 REMARK 465 SER C 166 REMARK 465 GLY C 167 REMARK 465 VAL C 168 REMARK 465 HIS C 169 REMARK 465 THR C 170 REMARK 465 PHE C 171 REMARK 465 PRO C 172 REMARK 465 ALA C 173 REMARK 465 VAL C 174 REMARK 465 LEU C 175 REMARK 465 GLN C 176 REMARK 465 SER C 177 REMARK 465 SER C 178 REMARK 465 GLY C 179 REMARK 465 LEU C 180 REMARK 465 TYR C 181 REMARK 465 SER C 182 REMARK 465 LEU C 183 REMARK 465 SER C 184 REMARK 465 SER C 185 REMARK 465 VAL C 186 REMARK 465 VAL C 187 REMARK 465 THR C 188 REMARK 465 VAL C 189 REMARK 465 PRO C 190 REMARK 465 SER C 191 REMARK 465 SER C 192 REMARK 465 SER C 193 REMARK 465 LEU C 194 REMARK 465 GLY C 195 REMARK 465 THR C 196 REMARK 465 GLN C 197 REMARK 465 THR C 198 REMARK 465 TYR C 199 REMARK 465 ILE C 200 REMARK 465 CYS C 201 REMARK 465 ASN C 202 REMARK 465 VAL C 203 REMARK 465 ASN C 204 REMARK 465 HIS C 205 REMARK 465 LYS C 206 REMARK 465 PRO C 207 REMARK 465 SER C 208 REMARK 465 ASN C 209 REMARK 465 THR C 210 REMARK 465 LYS C 211 REMARK 465 VAL C 212 REMARK 465 ASP C 213 REMARK 465 LYS C 214 REMARK 465 LYS C 215 REMARK 465 VAL C 216 REMARK 465 GLU C 217 REMARK 465 PRO C 218 REMARK 465 LYS C 219 REMARK 465 SER C 220 REMARK 465 CYS C 221 REMARK 465 ASP C 222 REMARK 465 LYS C 223 REMARK 465 THR C 224 REMARK 465 HIS C 225 REMARK 465 THR C 226 REMARK 465 CYS C 227 REMARK 465 PRO C 228 REMARK 465 PRO C 229 REMARK 465 CYS C 230 REMARK 465 PRO C 231 REMARK 465 ALA C 232 REMARK 465 PRO C 233 REMARK 465 GLU C 234 REMARK 465 ALA C 235 REMARK 465 ALA C 236 REMARK 465 GLY C 237 REMARK 465 GLY C 238 REMARK 465 PRO C 239 REMARK 465 SER C 240 REMARK 465 VAL C 241 REMARK 465 PHE C 242 REMARK 465 LEU C 243 REMARK 465 PHE C 244 REMARK 465 PRO C 245 REMARK 465 PRO C 246 REMARK 465 LYS C 247 REMARK 465 PRO C 248 REMARK 465 LYS C 249 REMARK 465 ASP C 250 REMARK 465 THR C 251 REMARK 465 LEU C 252 REMARK 465 MET C 253 REMARK 465 ILE C 254 REMARK 465 SER C 255 REMARK 465 ARG C 256 REMARK 465 THR C 257 REMARK 465 PRO C 258 REMARK 465 GLU C 259 REMARK 465 VAL C 260 REMARK 465 THR C 261 REMARK 465 CYS C 262 REMARK 465 VAL C 263 REMARK 465 VAL C 264 REMARK 465 VAL C 265 REMARK 465 ASP C 266 REMARK 465 VAL C 267 REMARK 465 SER C 268 REMARK 465 HIS C 269 REMARK 465 GLU C 270 REMARK 465 ASP C 271 REMARK 465 PRO C 272 REMARK 465 GLU C 273 REMARK 465 VAL C 274 REMARK 465 LYS C 275 REMARK 465 PHE C 276 REMARK 465 ASN C 277 REMARK 465 TRP C 278 REMARK 465 TYR C 279 REMARK 465 VAL C 280 REMARK 465 ASP C 281 REMARK 465 GLY C 282 REMARK 465 VAL C 283 REMARK 465 GLU C 284 REMARK 465 VAL C 285 REMARK 465 HIS C 286 REMARK 465 ASN C 287 REMARK 465 ALA C 288 REMARK 465 LYS C 289 REMARK 465 THR C 290 REMARK 465 LYS C 291 REMARK 465 PRO C 292 REMARK 465 ARG C 293 REMARK 465 GLU C 294 REMARK 465 GLU C 295 REMARK 465 GLN C 296 REMARK 465 TYR C 297 REMARK 465 ASN C 298 REMARK 465 SER C 299 REMARK 465 THR C 300 REMARK 465 TYR C 301 REMARK 465 ARG C 302 REMARK 465 VAL C 303 REMARK 465 VAL C 304 REMARK 465 SER C 305 REMARK 465 VAL C 306 REMARK 465 LEU C 307 REMARK 465 THR C 308 REMARK 465 VAL C 309 REMARK 465 LEU C 310 REMARK 465 HIS C 311 REMARK 465 GLN C 312 REMARK 465 ASP C 313 REMARK 465 TRP C 314 REMARK 465 LEU C 315 REMARK 465 ASN C 316 REMARK 465 GLY C 317 REMARK 465 LYS C 318 REMARK 465 GLU C 319 REMARK 465 TYR C 320 REMARK 465 LYS C 321 REMARK 465 CYS C 322 REMARK 465 LYS C 323 REMARK 465 VAL C 324 REMARK 465 SER C 325 REMARK 465 ASN C 326 REMARK 465 LYS C 327 REMARK 465 ALA C 328 REMARK 465 LEU C 329 REMARK 465 PRO C 330 REMARK 465 ALA C 331 REMARK 465 PRO C 332 REMARK 465 ILE C 333 REMARK 465 GLU C 334 REMARK 465 LYS C 335 REMARK 465 THR C 336 REMARK 465 ILE C 337 REMARK 465 SER C 338 REMARK 465 LYS C 339 REMARK 465 ALA C 340 REMARK 465 LYS C 341 REMARK 465 GLY C 342 REMARK 465 GLN C 343 REMARK 465 PRO C 344 REMARK 465 ARG C 345 REMARK 465 GLU C 346 REMARK 465 PRO C 347 REMARK 465 GLN C 348 REMARK 465 VAL C 349 REMARK 465 TYR C 350 REMARK 465 THR C 351 REMARK 465 LEU C 352 REMARK 465 PRO C 353 REMARK 465 PRO C 354 REMARK 465 SER C 355 REMARK 465 ARG C 356 REMARK 465 GLU C 357 REMARK 465 GLU C 358 REMARK 465 MET C 359 REMARK 465 THR C 360 REMARK 465 LYS C 361 REMARK 465 ASN C 362 REMARK 465 GLN C 363 REMARK 465 VAL C 364 REMARK 465 SER C 365 REMARK 465 LEU C 366 REMARK 465 THR C 367 REMARK 465 CYS C 368 REMARK 465 LEU C 369 REMARK 465 VAL C 370 REMARK 465 LYS C 371 REMARK 465 GLY C 372 REMARK 465 PHE C 373 REMARK 465 TYR C 374 REMARK 465 PRO C 375 REMARK 465 SER C 376 REMARK 465 ASP C 377 REMARK 465 ILE C 378 REMARK 465 ALA C 379 REMARK 465 VAL C 380 REMARK 465 GLU C 381 REMARK 465 TRP C 382 REMARK 465 GLU C 383 REMARK 465 SER C 384 REMARK 465 ASN C 385 REMARK 465 GLY C 386 REMARK 465 GLN C 387 REMARK 465 PRO C 388 REMARK 465 GLU C 389 REMARK 465 ASN C 390 REMARK 465 ASN C 391 REMARK 465 TYR C 392 REMARK 465 LYS C 393 REMARK 465 THR C 394 REMARK 465 THR C 395 REMARK 465 PRO C 396 REMARK 465 PRO C 397 REMARK 465 VAL C 398 REMARK 465 LEU C 399 REMARK 465 ASP C 400 REMARK 465 SER C 401 REMARK 465 ASP C 402 REMARK 465 GLY C 403 REMARK 465 SER C 404 REMARK 465 PHE C 405 REMARK 465 PHE C 406 REMARK 465 LEU C 407 REMARK 465 TYR C 408 REMARK 465 SER C 409 REMARK 465 LYS C 410 REMARK 465 LEU C 411 REMARK 465 THR C 412 REMARK 465 VAL C 413 REMARK 465 ASP C 414 REMARK 465 LYS C 415 REMARK 465 SER C 416 REMARK 465 ARG C 417 REMARK 465 TRP C 418 REMARK 465 GLN C 419 REMARK 465 GLN C 420 REMARK 465 GLY C 421 REMARK 465 ASN C 422 REMARK 465 VAL C 423 REMARK 465 PHE C 424 REMARK 465 SER C 425 REMARK 465 CYS C 426 REMARK 465 SER C 427 REMARK 465 VAL C 428 REMARK 465 MET C 429 REMARK 465 HIS C 430 REMARK 465 GLU C 431 REMARK 465 ALA C 432 REMARK 465 LEU C 433 REMARK 465 HIS C 434 REMARK 465 ASN C 435 REMARK 465 HIS C 436 REMARK 465 TYR C 437 REMARK 465 THR C 438 REMARK 465 GLN C 439 REMARK 465 LYS C 440 REMARK 465 SER C 441 REMARK 465 LEU C 442 REMARK 465 SER C 443 REMARK 465 LEU C 444 REMARK 465 SER C 445 REMARK 465 PRO C 446 REMARK 465 GLY C 447 REMARK 465 LYS C 448 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN C 1 CG CD OE1 NE2 REMARK 470 VAL C 2 CG1 CG2 REMARK 470 GLN C 3 CG CD OE1 NE2 REMARK 470 LEU C 4 CG CD1 CD2 REMARK 470 VAL C 5 CG1 CG2 REMARK 470 GLU C 6 CG CD OE1 OE2 REMARK 470 SER C 7 OG REMARK 470 VAL C 11 CG1 CG2 REMARK 470 VAL C 12 CG1 CG2 REMARK 470 GLN C 13 CG CD OE1 NE2 REMARK 470 PRO C 14 CG CD REMARK 470 ARG C 16 CG CD NE CZ NH1 NH2 REMARK 470 SER C 17 OG REMARK 470 LEU C 18 CG CD1 CD2 REMARK 470 ARG C 19 CG CD NE CZ NH1 NH2 REMARK 470 LEU C 20 CG CD1 CD2 REMARK 470 SER C 21 OG REMARK 470 SER C 25 OG REMARK 470 PHE C 27 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE C 28 CG1 CG2 CD1 REMARK 470 PHE C 29 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER C 30 OG REMARK 470 MET C 34 CG SD CE REMARK 470 LYS C 43 CG CD CE NZ REMARK 470 VAL C 48 CG1 CG2 REMARK 470 VAL C 50 CG1 CG2 REMARK 470 ILE C 51 CG1 CG2 CD1 REMARK 470 ASP C 54 CG OD1 OD2 REMARK 470 SER C 56 OG REMARK 470 TYR C 60 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP C 62 CG OD1 OD2 REMARK 470 SER C 63 OG REMARK 470 VAL C 64 CG1 CG2 REMARK 470 LYS C 65 CG CD CE NZ REMARK 470 ARG C 67 CG CD NE CZ NH1 NH2 REMARK 470 PHE C 68 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR C 69 OG1 CG2 REMARK 470 ILE C 70 CG1 CG2 CD1 REMARK 470 SER C 71 OG REMARK 470 ARG C 72 CG CD NE CZ NH1 NH2 REMARK 470 ASP C 73 CG OD1 OD2 REMARK 470 ASN C 74 CG OD1 ND2 REMARK 470 SER C 75 OG REMARK 470 LYS C 76 CG CD CE NZ REMARK 470 ASN C 77 CG OD1 ND2 REMARK 470 THR C 78 OG1 CG2 REMARK 470 LEU C 79 CG CD1 CD2 REMARK 470 TYR C 80 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU C 81 CG CD1 CD2 REMARK 470 GLN C 82 CG CD OE1 NE2 REMARK 470 MET C 83 CG SD CE REMARK 470 ASN C 84 CG OD1 ND2 REMARK 470 SER C 85 OG REMARK 470 TYR C 103 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 THR C 112 OG1 CG2 REMARK 470 THR C 115 OG1 CG2 REMARK 470 VAL C 116 CG1 CG2 REMARK 470 SER C 117 OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS B 39 O GLU B 81 2.13 REMARK 500 OG SER B 63 OG1 THR B 74 2.16 REMARK 500 NZ LYS B 39 OE2 GLU B 81 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 341 -61.98 -122.75 REMARK 500 ALA A 372 10.05 58.86 REMARK 500 ALA A 411 146.37 -172.21 REMARK 500 ASP A 428 35.35 -99.90 REMARK 500 ASN A 460 -168.22 -76.96 REMARK 500 GLU A 484 49.53 -83.89 REMARK 500 ASN A 487 -3.76 68.54 REMARK 500 LEU A 518 -163.73 -124.62 REMARK 500 ASN B 31 -18.12 -141.61 REMARK 500 ALA B 51 -6.29 67.07 REMARK 500 SER B 65 140.28 -170.02 REMARK 500 GLU B 68 -13.37 69.41 REMARK 500 PRO B 95 78.98 -66.31 REMARK 500 PHE C 29 1.74 -69.49 REMARK 500 ASP C 54 51.32 -91.30 REMARK 500 SER C 63 31.99 -97.66 REMARK 500 SER C 102 -61.97 -93.09 REMARK 500 MET C 105 65.45 60.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30977 RELATED DB: EMDB REMARK 900 SARS-COV-2 SPIKE IN COMPLEX WITH THE AB4 NEUTRALIZING ANTIBODY REMARK 900 (STATE 3) DBREF 7E39 A 333 526 UNP P0DTC2 SPIKE_SARS2 333 526 DBREF 7E39 B 1 214 PDB 7E39 7E39 1 214 DBREF 7E39 C 1 448 PDB 7E39 7E39 1 448 SEQRES 1 A 194 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 A 194 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 A 194 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 A 194 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 A 194 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 A 194 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 A 194 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 A 194 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 A 194 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 A 194 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 A 194 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 A 194 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 A 194 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 A 194 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 A 194 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 1 B 214 ASN ILE GLN MET THR GLN SER PRO SER ALA MET SER ALA SEQRES 2 B 214 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA ARG SEQRES 3 B 214 GLN GLY ILE SER ASN TYR LEU ALA TRP PHE GLN GLN LYS SEQRES 4 B 214 PRO GLY LYS VAL PRO LYS HIS LEU ILE TYR ALA ALA SER SEQRES 5 B 214 SER LEU LEU SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 B 214 GLY SER GLU THR GLU PHE THR LEU THR ILE SER SER LEU SEQRES 7 B 214 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS LEU GLN HIS SEQRES 8 B 214 ASN SER TYR PRO TYR THR PHE GLY GLN GLY THR LYS LEU SEQRES 9 B 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 B 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 B 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 B 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 B 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 B 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 B 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 B 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 B 214 PHE ASN ARG GLY GLU CYS SEQRES 1 C 448 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY VAL VAL GLN SEQRES 2 C 448 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 448 PHE ILE PHE SER SER TYR GLY MET HIS TRP VAL ARG GLN SEQRES 4 C 448 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA VAL ILE TRP SEQRES 5 C 448 PHE ASP GLY SER ASN LYS TYR TYR ALA ASP SER VAL LYS SEQRES 6 C 448 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 C 448 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 C 448 ALA VAL TYR TYR CYS ALA ARG GLU THR VAL SER TYR GLY SEQRES 9 C 448 MET ASP VAL TRP GLY GLN GLY THR THR VAL THR VAL SER SEQRES 10 C 448 SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA SEQRES 11 C 448 PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU SEQRES 12 C 448 GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR SEQRES 13 C 448 VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS SEQRES 14 C 448 THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER SEQRES 15 C 448 LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY SEQRES 16 C 448 THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER SEQRES 17 C 448 ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER CYS SEQRES 18 C 448 ASP LYS THR HIS THR CYS PRO PRO CYS PRO ALA PRO GLU SEQRES 19 C 448 ALA ALA GLY GLY PRO SER VAL PHE LEU PHE PRO PRO LYS SEQRES 20 C 448 PRO LYS ASP THR LEU MET ILE SER ARG THR PRO GLU VAL SEQRES 21 C 448 THR CYS VAL VAL VAL ASP VAL SER HIS GLU ASP PRO GLU SEQRES 22 C 448 VAL LYS PHE ASN TRP TYR VAL ASP GLY VAL GLU VAL HIS SEQRES 23 C 448 ASN ALA LYS THR LYS PRO ARG GLU GLU GLN TYR ASN SER SEQRES 24 C 448 THR TYR ARG VAL VAL SER VAL LEU THR VAL LEU HIS GLN SEQRES 25 C 448 ASP TRP LEU ASN GLY LYS GLU TYR LYS CYS LYS VAL SER SEQRES 26 C 448 ASN LYS ALA LEU PRO ALA PRO ILE GLU LYS THR ILE SER SEQRES 27 C 448 LYS ALA LYS GLY GLN PRO ARG GLU PRO GLN VAL TYR THR SEQRES 28 C 448 LEU PRO PRO SER ARG GLU GLU MET THR LYS ASN GLN VAL SEQRES 29 C 448 SER LEU THR CYS LEU VAL LYS GLY PHE TYR PRO SER ASP SEQRES 30 C 448 ILE ALA VAL GLU TRP GLU SER ASN GLY GLN PRO GLU ASN SEQRES 31 C 448 ASN TYR LYS THR THR PRO PRO VAL LEU ASP SER ASP GLY SEQRES 32 C 448 SER PHE PHE LEU TYR SER LYS LEU THR VAL ASP LYS SER SEQRES 33 C 448 ARG TRP GLN GLN GLY ASN VAL PHE SER CYS SER VAL MET SEQRES 34 C 448 HIS GLU ALA LEU HIS ASN HIS TYR THR GLN LYS SER LEU SEQRES 35 C 448 SER LEU SER PRO GLY LYS HET NAG A 601 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 NAG C8 H15 N O6 HELIX 1 AA1 PHE A 338 ASN A 343 1 6 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 VAL A 367 ALA A 372 1 6 HELIX 4 AA4 SER A 383 ASN A 388 1 6 HELIX 5 AA5 ASP A 405 ILE A 410 5 6 HELIX 6 AA6 GLY A 416 ASN A 422 1 7 HELIX 7 AA7 SER A 438 SER A 443 1 6 HELIX 8 AA8 GLN B 79 PHE B 83 5 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O SER A 399 N ASN A 354 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O TYR A 508 N ILE A 402 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 THR A 376 CYS A 379 -1 N LYS A 378 O VAL A 433 SHEET 1 AA2 2 TYR A 453 ARG A 454 0 SHEET 2 AA2 2 LEU A 492 GLN A 493 -1 O GLN A 493 N TYR A 453 SHEET 1 AA3 2 TYR A 473 GLN A 474 0 SHEET 2 AA3 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA4 4 MET B 4 GLN B 6 0 SHEET 2 AA4 4 VAL B 19 ILE B 29 -1 O ARG B 24 N THR B 5 SHEET 3 AA4 4 GLU B 68 ILE B 75 -1 O PHE B 71 N CYS B 23 SHEET 4 AA4 4 PHE B 62 GLY B 66 -1 N SER B 63 O THR B 74 SHEET 1 AA5 2 ALA B 10 SER B 12 0 SHEET 2 AA5 2 THR B 102 LEU B 104 1 O LEU B 104 N MET B 11 SHEET 1 AA6 4 SER B 53 LEU B 54 0 SHEET 2 AA6 4 LYS B 45 TYR B 49 -1 N TYR B 49 O SER B 53 SHEET 3 AA6 4 LEU B 33 GLN B 38 -1 N GLN B 37 O LYS B 45 SHEET 4 AA6 4 THR B 85 GLN B 90 -1 O THR B 85 N GLN B 38 SHEET 1 AA7 4 GLN C 3 GLU C 6 0 SHEET 2 AA7 4 SER C 17 SER C 25 -1 O ALA C 23 N VAL C 5 SHEET 3 AA7 4 ASN C 77 MET C 83 -1 O GLN C 82 N LEU C 18 SHEET 4 AA7 4 ARG C 67 ARG C 72 -1 N ARG C 72 O ASN C 77 SHEET 1 AA8 6 VAL C 11 VAL C 12 0 SHEET 2 AA8 6 THR C 112 VAL C 116 1 O THR C 115 N VAL C 12 SHEET 3 AA8 6 ALA C 92 ARG C 98 -1 N TYR C 94 O THR C 112 SHEET 4 AA8 6 MET C 34 GLN C 39 -1 N VAL C 37 O TYR C 95 SHEET 5 AA8 6 LEU C 45 ILE C 51 -1 O ALA C 49 N TRP C 36 SHEET 6 AA8 6 ASN C 57 TYR C 59 -1 O LYS C 58 N VAL C 50 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.04 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 5 CYS B 23 CYS B 88 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG A 601 1555 1555 1.44 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000