HEADER VIRAL PROTEIN/IMMUNE SYSTEM 08-FEB-21 7E3C TITLE SARS-COV-2 SPIKE IN COMPLEX WITH THE AB1 NEUTRALIZING ANTIBODY TITLE 2 (FOCUSED REFINEMENT ON FAB-RBD) 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 AB1; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HEAVY CHAIN OF AB1; COMPND 11 CHAIN: B; 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 7E3C 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. 4.20 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) : 4.200 REMARK 3 NUMBER OF PARTICLES : 136287 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 7E3C 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_1300020677. 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 AB1 ANTIBODIES; REMARK 245 SPIKE PROTEIN S1; LIGHT CHAIN REMARK 245 OF AB1; HEAVY CHAIN OF AB1 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, C, B 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 ASP C 1 REMARK 465 ILE C 2 REMARK 465 THR C 74 REMARK 465 ILE C 75 REMARK 465 SER C 76 REMARK 465 SER C 77 REMARK 465 ARG C 109 REMARK 465 THR C 110 REMARK 465 VAL C 111 REMARK 465 ALA C 112 REMARK 465 ALA C 113 REMARK 465 PRO C 114 REMARK 465 SER C 115 REMARK 465 VAL C 116 REMARK 465 PHE C 117 REMARK 465 ILE C 118 REMARK 465 PHE C 119 REMARK 465 PRO C 120 REMARK 465 PRO C 121 REMARK 465 SER C 122 REMARK 465 ASP C 123 REMARK 465 GLU C 124 REMARK 465 GLN C 125 REMARK 465 LEU C 126 REMARK 465 LYS C 127 REMARK 465 SER C 128 REMARK 465 GLY C 129 REMARK 465 THR C 130 REMARK 465 ALA C 131 REMARK 465 SER C 132 REMARK 465 VAL C 133 REMARK 465 VAL C 134 REMARK 465 CYS C 135 REMARK 465 LEU C 136 REMARK 465 LEU C 137 REMARK 465 ASN C 138 REMARK 465 ASN C 139 REMARK 465 PHE C 140 REMARK 465 TYR C 141 REMARK 465 PRO C 142 REMARK 465 ARG C 143 REMARK 465 GLU C 144 REMARK 465 ALA C 145 REMARK 465 LYS C 146 REMARK 465 VAL C 147 REMARK 465 GLN C 148 REMARK 465 TRP C 149 REMARK 465 LYS C 150 REMARK 465 VAL C 151 REMARK 465 ASP C 152 REMARK 465 ASN C 153 REMARK 465 ALA C 154 REMARK 465 LEU C 155 REMARK 465 GLN C 156 REMARK 465 SER C 157 REMARK 465 GLY C 158 REMARK 465 ASN C 159 REMARK 465 SER C 160 REMARK 465 GLN C 161 REMARK 465 GLU C 162 REMARK 465 SER C 163 REMARK 465 VAL C 164 REMARK 465 THR C 165 REMARK 465 GLU C 166 REMARK 465 GLN C 167 REMARK 465 ASP C 168 REMARK 465 SER C 169 REMARK 465 LYS C 170 REMARK 465 ASP C 171 REMARK 465 SER C 172 REMARK 465 THR C 173 REMARK 465 TYR C 174 REMARK 465 SER C 175 REMARK 465 LEU C 176 REMARK 465 SER C 177 REMARK 465 SER C 178 REMARK 465 THR C 179 REMARK 465 LEU C 180 REMARK 465 THR C 181 REMARK 465 LEU C 182 REMARK 465 SER C 183 REMARK 465 LYS C 184 REMARK 465 ALA C 185 REMARK 465 ASP C 186 REMARK 465 TYR C 187 REMARK 465 GLU C 188 REMARK 465 LYS C 189 REMARK 465 HIS C 190 REMARK 465 LYS C 191 REMARK 465 VAL C 192 REMARK 465 TYR C 193 REMARK 465 ALA C 194 REMARK 465 CYS C 195 REMARK 465 GLU C 196 REMARK 465 VAL C 197 REMARK 465 THR C 198 REMARK 465 HIS C 199 REMARK 465 GLN C 200 REMARK 465 GLY C 201 REMARK 465 LEU C 202 REMARK 465 SER C 203 REMARK 465 SER C 204 REMARK 465 PRO C 205 REMARK 465 VAL C 206 REMARK 465 THR C 207 REMARK 465 LYS C 208 REMARK 465 SER C 209 REMARK 465 PHE C 210 REMARK 465 ASN C 211 REMARK 465 ARG C 212 REMARK 465 GLY C 213 REMARK 465 GLU C 214 REMARK 465 CYS C 215 REMARK 465 GLU B 1 REMARK 465 VAL B 2 REMARK 465 LEU B 3 REMARK 465 ASN B 73 REMARK 465 SER B 74 REMARK 465 LYS B 75 REMARK 465 SER B 116 REMARK 465 SER B 117 REMARK 465 ALA B 118 REMARK 465 SER B 119 REMARK 465 THR B 120 REMARK 465 LYS B 121 REMARK 465 GLY B 122 REMARK 465 PRO B 123 REMARK 465 SER B 124 REMARK 465 VAL B 125 REMARK 465 PHE B 126 REMARK 465 PRO B 127 REMARK 465 LEU B 128 REMARK 465 ALA B 129 REMARK 465 PRO B 130 REMARK 465 SER B 131 REMARK 465 SER B 132 REMARK 465 LYS B 133 REMARK 465 SER B 134 REMARK 465 THR B 135 REMARK 465 SER B 136 REMARK 465 GLY B 137 REMARK 465 GLY B 138 REMARK 465 THR B 139 REMARK 465 ALA B 140 REMARK 465 ALA B 141 REMARK 465 LEU B 142 REMARK 465 GLY B 143 REMARK 465 CYS B 144 REMARK 465 LEU B 145 REMARK 465 VAL B 146 REMARK 465 LYS B 147 REMARK 465 ASP B 148 REMARK 465 TYR B 149 REMARK 465 PHE B 150 REMARK 465 PRO B 151 REMARK 465 GLU B 152 REMARK 465 PRO B 153 REMARK 465 VAL B 154 REMARK 465 THR B 155 REMARK 465 VAL B 156 REMARK 465 SER B 157 REMARK 465 TRP B 158 REMARK 465 ASN B 159 REMARK 465 SER B 160 REMARK 465 GLY B 161 REMARK 465 ALA B 162 REMARK 465 LEU B 163 REMARK 465 THR B 164 REMARK 465 SER B 165 REMARK 465 GLY B 166 REMARK 465 VAL B 167 REMARK 465 HIS B 168 REMARK 465 THR B 169 REMARK 465 PHE B 170 REMARK 465 PRO B 171 REMARK 465 ALA B 172 REMARK 465 VAL B 173 REMARK 465 LEU B 174 REMARK 465 GLN B 175 REMARK 465 SER B 176 REMARK 465 SER B 177 REMARK 465 GLY B 178 REMARK 465 LEU B 179 REMARK 465 TYR B 180 REMARK 465 SER B 181 REMARK 465 LEU B 182 REMARK 465 SER B 183 REMARK 465 SER B 184 REMARK 465 VAL B 185 REMARK 465 VAL B 186 REMARK 465 THR B 187 REMARK 465 VAL B 188 REMARK 465 PRO B 189 REMARK 465 SER B 190 REMARK 465 SER B 191 REMARK 465 SER B 192 REMARK 465 LEU B 193 REMARK 465 GLY B 194 REMARK 465 THR B 195 REMARK 465 GLN B 196 REMARK 465 THR B 197 REMARK 465 TYR B 198 REMARK 465 ILE B 199 REMARK 465 CYS B 200 REMARK 465 ASN B 201 REMARK 465 VAL B 202 REMARK 465 ASN B 203 REMARK 465 HIS B 204 REMARK 465 LYS B 205 REMARK 465 PRO B 206 REMARK 465 SER B 207 REMARK 465 ASN B 208 REMARK 465 THR B 209 REMARK 465 LYS B 210 REMARK 465 VAL B 211 REMARK 465 ASP B 212 REMARK 465 LYS B 213 REMARK 465 LYS B 214 REMARK 465 VAL B 215 REMARK 465 GLU B 216 REMARK 465 PRO B 217 REMARK 465 LYS B 218 REMARK 465 SER B 219 REMARK 465 CYS B 220 REMARK 465 ASP B 221 REMARK 465 LYS B 222 REMARK 465 THR B 223 REMARK 465 HIS B 224 REMARK 465 THR B 225 REMARK 465 CYS B 226 REMARK 465 PRO B 227 REMARK 465 PRO B 228 REMARK 465 CYS B 229 REMARK 465 PRO B 230 REMARK 465 ALA B 231 REMARK 465 PRO B 232 REMARK 465 GLU B 233 REMARK 465 ALA B 234 REMARK 465 ALA B 235 REMARK 465 GLY B 236 REMARK 465 GLY B 237 REMARK 465 PRO B 238 REMARK 465 SER B 239 REMARK 465 VAL B 240 REMARK 465 PHE B 241 REMARK 465 LEU B 242 REMARK 465 PHE B 243 REMARK 465 PRO B 244 REMARK 465 PRO B 245 REMARK 465 LYS B 246 REMARK 465 PRO B 247 REMARK 465 LYS B 248 REMARK 465 ASP B 249 REMARK 465 THR B 250 REMARK 465 LEU B 251 REMARK 465 MET B 252 REMARK 465 ILE B 253 REMARK 465 SER B 254 REMARK 465 ARG B 255 REMARK 465 THR B 256 REMARK 465 PRO B 257 REMARK 465 GLU B 258 REMARK 465 VAL B 259 REMARK 465 THR B 260 REMARK 465 CYS B 261 REMARK 465 VAL B 262 REMARK 465 VAL B 263 REMARK 465 VAL B 264 REMARK 465 ASP B 265 REMARK 465 VAL B 266 REMARK 465 SER B 267 REMARK 465 HIS B 268 REMARK 465 GLU B 269 REMARK 465 ASP B 270 REMARK 465 PRO B 271 REMARK 465 GLU B 272 REMARK 465 VAL B 273 REMARK 465 LYS B 274 REMARK 465 PHE B 275 REMARK 465 ASN B 276 REMARK 465 TRP B 277 REMARK 465 TYR B 278 REMARK 465 VAL B 279 REMARK 465 ASP B 280 REMARK 465 GLY B 281 REMARK 465 VAL B 282 REMARK 465 GLU B 283 REMARK 465 VAL B 284 REMARK 465 HIS B 285 REMARK 465 ASN B 286 REMARK 465 ALA B 287 REMARK 465 LYS B 288 REMARK 465 THR B 289 REMARK 465 LYS B 290 REMARK 465 PRO B 291 REMARK 465 ARG B 292 REMARK 465 GLU B 293 REMARK 465 GLU B 294 REMARK 465 GLN B 295 REMARK 465 TYR B 296 REMARK 465 ASN B 297 REMARK 465 SER B 298 REMARK 465 THR B 299 REMARK 465 TYR B 300 REMARK 465 ARG B 301 REMARK 465 VAL B 302 REMARK 465 VAL B 303 REMARK 465 SER B 304 REMARK 465 VAL B 305 REMARK 465 LEU B 306 REMARK 465 THR B 307 REMARK 465 VAL B 308 REMARK 465 LEU B 309 REMARK 465 HIS B 310 REMARK 465 GLN B 311 REMARK 465 ASP B 312 REMARK 465 TRP B 313 REMARK 465 LEU B 314 REMARK 465 ASN B 315 REMARK 465 GLY B 316 REMARK 465 LYS B 317 REMARK 465 GLU B 318 REMARK 465 TYR B 319 REMARK 465 LYS B 320 REMARK 465 CYS B 321 REMARK 465 LYS B 322 REMARK 465 VAL B 323 REMARK 465 SER B 324 REMARK 465 ASN B 325 REMARK 465 LYS B 326 REMARK 465 ALA B 327 REMARK 465 LEU B 328 REMARK 465 PRO B 329 REMARK 465 ALA B 330 REMARK 465 PRO B 331 REMARK 465 ILE B 332 REMARK 465 GLU B 333 REMARK 465 LYS B 334 REMARK 465 THR B 335 REMARK 465 ILE B 336 REMARK 465 SER B 337 REMARK 465 LYS B 338 REMARK 465 ALA B 339 REMARK 465 LYS B 340 REMARK 465 GLY B 341 REMARK 465 GLN B 342 REMARK 465 PRO B 343 REMARK 465 ARG B 344 REMARK 465 GLU B 345 REMARK 465 PRO B 346 REMARK 465 GLN B 347 REMARK 465 VAL B 348 REMARK 465 TYR B 349 REMARK 465 THR B 350 REMARK 465 LEU B 351 REMARK 465 PRO B 352 REMARK 465 PRO B 353 REMARK 465 SER B 354 REMARK 465 ARG B 355 REMARK 465 GLU B 356 REMARK 465 GLU B 357 REMARK 465 MET B 358 REMARK 465 THR B 359 REMARK 465 LYS B 360 REMARK 465 ASN B 361 REMARK 465 GLN B 362 REMARK 465 VAL B 363 REMARK 465 SER B 364 REMARK 465 LEU B 365 REMARK 465 THR B 366 REMARK 465 CYS B 367 REMARK 465 LEU B 368 REMARK 465 VAL B 369 REMARK 465 LYS B 370 REMARK 465 GLY B 371 REMARK 465 PHE B 372 REMARK 465 TYR B 373 REMARK 465 PRO B 374 REMARK 465 SER B 375 REMARK 465 ASP B 376 REMARK 465 ILE B 377 REMARK 465 ALA B 378 REMARK 465 VAL B 379 REMARK 465 GLU B 380 REMARK 465 TRP B 381 REMARK 465 GLU B 382 REMARK 465 SER B 383 REMARK 465 ASN B 384 REMARK 465 GLY B 385 REMARK 465 GLN B 386 REMARK 465 PRO B 387 REMARK 465 GLU B 388 REMARK 465 ASN B 389 REMARK 465 ASN B 390 REMARK 465 TYR B 391 REMARK 465 LYS B 392 REMARK 465 THR B 393 REMARK 465 THR B 394 REMARK 465 PRO B 395 REMARK 465 PRO B 396 REMARK 465 VAL B 397 REMARK 465 LEU B 398 REMARK 465 ASP B 399 REMARK 465 SER B 400 REMARK 465 ASP B 401 REMARK 465 GLY B 402 REMARK 465 SER B 403 REMARK 465 PHE B 404 REMARK 465 PHE B 405 REMARK 465 LEU B 406 REMARK 465 TYR B 407 REMARK 465 SER B 408 REMARK 465 LYS B 409 REMARK 465 LEU B 410 REMARK 465 THR B 411 REMARK 465 VAL B 412 REMARK 465 ASP B 413 REMARK 465 LYS B 414 REMARK 465 SER B 415 REMARK 465 ARG B 416 REMARK 465 TRP B 417 REMARK 465 GLN B 418 REMARK 465 GLN B 419 REMARK 465 GLY B 420 REMARK 465 ASN B 421 REMARK 465 VAL B 422 REMARK 465 PHE B 423 REMARK 465 SER B 424 REMARK 465 CYS B 425 REMARK 465 SER B 426 REMARK 465 VAL B 427 REMARK 465 MET B 428 REMARK 465 HIS B 429 REMARK 465 GLU B 430 REMARK 465 ALA B 431 REMARK 465 LEU B 432 REMARK 465 HIS B 433 REMARK 465 ASN B 434 REMARK 465 HIS B 435 REMARK 465 TYR B 436 REMARK 465 THR B 437 REMARK 465 GLN B 438 REMARK 465 LYS B 439 REMARK 465 SER B 440 REMARK 465 LEU B 441 REMARK 465 SER B 442 REMARK 465 LEU B 443 REMARK 465 SER B 444 REMARK 465 PRO B 445 REMARK 465 GLY B 446 REMARK 465 LYS B 447 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 3 CG CD OE1 NE2 REMARK 470 LEU C 4 CG CD1 CD2 REMARK 470 THR C 5 OG1 CG2 REMARK 470 GLN C 6 CG CD OE1 NE2 REMARK 470 SER C 7 OG REMARK 470 PRO C 8 CG CD REMARK 470 SER C 9 OG REMARK 470 PHE C 10 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU C 11 CG CD1 CD2 REMARK 470 SER C 12 OG REMARK 470 SER C 14 OG REMARK 470 VAL C 15 CG1 CG2 REMARK 470 ASP C 17 CG OD1 OD2 REMARK 470 ARG C 18 CG CD NE CZ NH1 NH2 REMARK 470 VAL C 19 CG1 CG2 REMARK 470 THR C 20 OG1 CG2 REMARK 470 ILE C 21 CG1 CG2 CD1 REMARK 470 THR C 22 OG1 CG2 REMARK 470 ARG C 24 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 27 CG CD OE1 NE2 REMARK 470 LYS C 39 CG CD CE NZ REMARK 470 LYS C 42 CG CD CE NZ REMARK 470 LYS C 45 CG CD CE NZ REMARK 470 SER C 52 OG REMARK 470 THR C 53 OG1 CG2 REMARK 470 LEU C 54 CG CD1 CD2 REMARK 470 GLN C 55 CG CD OE1 NE2 REMARK 470 THR C 56 OG1 CG2 REMARK 470 VAL C 58 CG1 CG2 REMARK 470 PRO C 59 CG CD REMARK 470 SER C 60 OG REMARK 470 ARG C 61 CG CD NE CZ NH1 NH2 REMARK 470 PHE C 62 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER C 63 OG REMARK 470 SER C 65 OG REMARK 470 SER C 67 OG REMARK 470 THR C 69 OG1 CG2 REMARK 470 GLU C 70 CG CD OE1 OE2 REMARK 470 PHE C 71 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR C 72 OG1 CG2 REMARK 470 LEU C 73 CG CD1 CD2 REMARK 470 LYS C 108 CG CD CE NZ REMARK 470 LEU B 4 CG CD1 CD2 REMARK 470 VAL B 5 CG1 CG2 REMARK 470 GLU B 6 CG CD OE1 OE2 REMARK 470 SER B 7 OG REMARK 470 LEU B 11 CG CD1 CD2 REMARK 470 VAL B 12 CG1 CG2 REMARK 470 GLN B 13 CG CD OE1 NE2 REMARK 470 PRO B 14 CG CD REMARK 470 SER B 17 OG REMARK 470 LEU B 18 CG CD1 CD2 REMARK 470 ARG B 19 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 20 CG CD1 CD2 REMARK 470 SER B 21 OG REMARK 470 LYS B 43 CG CD CE NZ REMARK 470 ASP B 61 CG OD1 OD2 REMARK 470 SER B 62 OG REMARK 470 VAL B 63 CG1 CG2 REMARK 470 LYS B 64 CG CD CE NZ REMARK 470 ARG B 66 CG CD NE CZ NH1 NH2 REMARK 470 CYS B 67 SG REMARK 470 THR B 68 OG1 CG2 REMARK 470 ILE B 69 CG1 CG2 CD1 REMARK 470 SER B 70 OG REMARK 470 ARG B 71 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 72 CG ND1 CD2 CE1 NE2 REMARK 470 ASN B 83 CG OD1 ND2 REMARK 470 SER B 84 OG REMARK 470 LEU B 85 CG CD1 CD2 REMARK 470 ARG B 86 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 88 CG CD OE1 OE2 REMARK 470 ASP B 89 CG OD1 OD2 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 NH1 ARG A 457 O SER A 459 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 432 CA - CB - SG ANGL. DEV. = 11.8 DEGREES REMARK 500 PRO C 8 N - CA - CB ANGL. DEV. = 7.3 DEGREES REMARK 500 PRO B 14 N - CA - CB ANGL. DEV. = 7.3 DEGREES 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 -61.62 -120.27 REMARK 500 ALA A 372 -5.17 66.04 REMARK 500 ARG A 408 1.28 -65.40 REMARK 500 ALA A 411 149.55 -174.18 REMARK 500 TYR A 423 100.12 -160.00 REMARK 500 ASN A 487 14.09 59.44 REMARK 500 LEU A 518 -169.88 -129.89 REMARK 500 ILE C 29 -60.12 -133.01 REMARK 500 SER C 30 -15.40 73.03 REMARK 500 ASN C 31 -8.02 -149.41 REMARK 500 TYR C 32 65.10 -102.11 REMARK 500 TYR C 49 -157.36 -75.78 REMARK 500 ALA C 51 -31.06 -133.24 REMARK 500 GLN C 55 -32.57 -136.53 REMARK 500 PHE C 62 145.20 -171.70 REMARK 500 SER C 67 -6.15 66.51 REMARK 500 ARG B 71 -136.93 -161.52 REMARK 500 ARG B 86 -166.02 -77.63 REMARK 500 ALA B 91 -176.24 -171.52 REMARK 500 ALA B 96 142.20 -170.59 REMARK 500 ASP B 105 -160.62 -79.75 REMARK 500 VAL B 106 137.53 -39.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30979 RELATED DB: EMDB REMARK 900 SARS-COV-2 SPIKE IN COMPLEX WITH THE AB1 NEUTRALIZING ANTIBODY REMARK 900 (FOCUSED REFINEMENT ON FAB-RBD) DBREF 7E3C A 333 526 UNP P0DTC2 SPIKE_SARS2 333 526 DBREF 7E3C C 1 215 PDB 7E3C 7E3C 1 215 DBREF 7E3C B 1 447 PDB 7E3C 7E3C 1 447 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 C 215 ASP ILE GLN LEU THR GLN SER PRO SER PHE LEU SER ALA SEQRES 2 C 215 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 C 215 GLN GLY ILE SER ASN TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 C 215 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SER SEQRES 5 C 215 THR LEU GLN THR GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 C 215 GLY SER GLY THR GLU PHE THR LEU THR ILE SER SER LEU SEQRES 7 C 215 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN LEU SEQRES 8 C 215 ASN SER TYR PRO PRO LEU THR PHE GLY GLY GLY SER ARG SEQRES 9 C 215 VAL GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE SEQRES 10 C 215 ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR SEQRES 11 C 215 ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG SEQRES 12 C 215 GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SEQRES 13 C 215 SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER SEQRES 14 C 215 LYS ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SEQRES 15 C 215 SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS SEQRES 16 C 215 GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SEQRES 17 C 215 SER PHE ASN ARG GLY GLU CYS SEQRES 1 B 447 GLU VAL LEU LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 447 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 447 LEU THR VAL SER SER ASN TYR MET THR TRP VAL ARG GLN SEQRES 4 B 447 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE TYR SEQRES 5 B 447 SER GLY GLY SER THR PHE TYR ALA ASP SER VAL LYS GLY SEQRES 6 B 447 ARG CYS THR ILE SER ARG HIS ASN SER LYS ASN THR LEU SEQRES 7 B 447 TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 B 447 VAL TYR TYR CYS ALA ARG ASP LEU ASP TYR TYR GLY MET SEQRES 9 B 447 ASP VAL TRP GLY GLN GLY THR THR VAL THR VAL SER SER SEQRES 10 B 447 ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SEQRES 11 B 447 SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY SEQRES 12 B 447 CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SEQRES 13 B 447 SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR SEQRES 14 B 447 PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SEQRES 15 B 447 SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR SEQRES 16 B 447 GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN SEQRES 17 B 447 THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER CYS ASP SEQRES 18 B 447 LYS THR HIS THR CYS PRO PRO CYS PRO ALA PRO GLU ALA SEQRES 19 B 447 ALA GLY GLY PRO SER VAL PHE LEU PHE PRO PRO LYS PRO SEQRES 20 B 447 LYS ASP THR LEU MET ILE SER ARG THR PRO GLU VAL THR SEQRES 21 B 447 CYS VAL VAL VAL ASP VAL SER HIS GLU ASP PRO GLU VAL SEQRES 22 B 447 LYS PHE ASN TRP TYR VAL ASP GLY VAL GLU VAL HIS ASN SEQRES 23 B 447 ALA LYS THR LYS PRO ARG GLU GLU GLN TYR ASN SER THR SEQRES 24 B 447 TYR ARG VAL VAL SER VAL LEU THR VAL LEU HIS GLN ASP SEQRES 25 B 447 TRP LEU ASN GLY LYS GLU TYR LYS CYS LYS VAL SER ASN SEQRES 26 B 447 LYS ALA LEU PRO ALA PRO ILE GLU LYS THR ILE SER LYS SEQRES 27 B 447 ALA LYS GLY GLN PRO ARG GLU PRO GLN VAL TYR THR LEU SEQRES 28 B 447 PRO PRO SER ARG GLU GLU MET THR LYS ASN GLN VAL SER SEQRES 29 B 447 LEU THR CYS LEU VAL LYS GLY PHE TYR PRO SER ASP ILE SEQRES 30 B 447 ALA VAL GLU TRP GLU SER ASN GLY GLN PRO GLU ASN ASN SEQRES 31 B 447 TYR LYS THR THR PRO PRO VAL LEU ASP SER ASP GLY SER SEQRES 32 B 447 PHE PHE LEU TYR SER LYS LEU THR VAL ASP LYS SER ARG SEQRES 33 B 447 TRP GLN GLN GLY ASN VAL PHE SER CYS SER VAL MET HIS SEQRES 34 B 447 GLU ALA LEU HIS ASN HIS TYR THR GLN LYS SER LEU SER SEQRES 35 B 447 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 SER A 349 TRP A 353 5 5 HELIX 2 AA2 ASP A 364 ASN A 370 1 7 HELIX 3 AA3 GLY A 404 ARG A 408 1 5 HELIX 4 AA4 GLY A 416 ASN A 422 1 7 HELIX 5 AA5 SER A 438 SER A 443 1 6 HELIX 6 AA6 GLY C 57 ARG C 61 5 5 HELIX 7 AA7 ARG B 86 THR B 90 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 ALA A 397 N LYS A 356 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O SER A 514 N TYR A 396 SHEET 4 AA1 5 CYS A 432 ASN A 437 -1 N CYS A 432 O LEU A 513 SHEET 5 AA1 5 THR A 376 CYS A 379 -1 N THR A 376 O ALA A 435 SHEET 1 AA2 2 CYS A 361 VAL A 362 0 SHEET 2 AA2 2 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 1 AA3 2 LEU A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA4 3 THR C 5 GLN C 6 0 SHEET 2 AA4 3 VAL C 19 ALA C 25 -1 O ARG C 24 N GLN C 6 SHEET 3 AA4 3 GLY C 68 LEU C 73 -1 O THR C 69 N CYS C 23 SHEET 1 AA5 2 LEU C 11 ALA C 13 0 SHEET 2 AA5 2 VAL C 105 ILE C 107 1 O GLU C 106 N ALA C 13 SHEET 1 AA6 3 LYS C 45 ILE C 48 0 SHEET 2 AA6 3 LEU C 33 GLN C 38 -1 N GLN C 37 O LYS C 45 SHEET 3 AA6 3 THR C 85 GLN C 90 -1 O THR C 85 N GLN C 38 SHEET 1 AA7 3 LEU B 18 ALA B 23 0 SHEET 2 AA7 3 THR B 77 MET B 82 -1 O LEU B 80 N LEU B 20 SHEET 3 AA7 3 CYS B 67 ILE B 69 -1 N CYS B 67 O GLN B 81 SHEET 1 AA8 5 THR B 57 TYR B 59 0 SHEET 2 AA8 5 SER B 49 ILE B 51 -1 N VAL B 50 O PHE B 58 SHEET 3 AA8 5 TYR B 33 GLN B 39 -1 N MET B 34 O ILE B 51 SHEET 4 AA8 5 ALA B 96 LEU B 99 -1 O ASP B 98 N TYR B 33 SHEET 5 AA8 5 GLY B 103 TRP B 107 -1 N GLY B 103 O LEU B 99 SHEET 1 AA9 5 THR B 57 TYR B 59 0 SHEET 2 AA9 5 SER B 49 ILE B 51 -1 N VAL B 50 O PHE B 58 SHEET 3 AA9 5 TYR B 33 GLN B 39 -1 N MET B 34 O ILE B 51 SHEET 4 AA9 5 ALA B 91 TYR B 94 -1 O VAL B 92 N GLN B 39 SHEET 5 AA9 5 THR B 111 VAL B 113 -1 O VAL B 113 N ALA B 91 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.05 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 22 CYS B 95 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 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