HEADER VIRAL PROTEIN/IMMUNE SYSTEM 08-FEB-21 7E3B TITLE SARS-COV-2 SPIKE IN COMPLEX WITH THE AB5 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: HEAVY CHAIN OF AB5; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: LIGHT CHAIN OF AB5; 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 7E3B 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 : 353268 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 7E3B 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_1300020678. 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 AB5 FABS; SPIKE REMARK 245 PROTEIN S1; HEAVY CHAIN OF AB5; REMARK 245 LIGHT CHAIN OF AB5 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 ALA B 123 REMARK 465 SER B 124 REMARK 465 THR B 125 REMARK 465 LYS B 126 REMARK 465 GLY B 127 REMARK 465 PRO B 128 REMARK 465 SER B 129 REMARK 465 VAL B 130 REMARK 465 PHE B 131 REMARK 465 PRO B 132 REMARK 465 LEU B 133 REMARK 465 ALA B 134 REMARK 465 PRO B 135 REMARK 465 SER B 136 REMARK 465 SER B 137 REMARK 465 LYS B 138 REMARK 465 SER B 139 REMARK 465 THR B 140 REMARK 465 SER B 141 REMARK 465 GLY B 142 REMARK 465 GLY B 143 REMARK 465 THR B 144 REMARK 465 ALA B 145 REMARK 465 ALA B 146 REMARK 465 LEU B 147 REMARK 465 GLY B 148 REMARK 465 CYS B 149 REMARK 465 LEU B 150 REMARK 465 VAL B 151 REMARK 465 LYS B 152 REMARK 465 ASP B 153 REMARK 465 TYR B 154 REMARK 465 PHE B 155 REMARK 465 PRO B 156 REMARK 465 GLU B 157 REMARK 465 PRO B 158 REMARK 465 VAL B 159 REMARK 465 THR B 160 REMARK 465 VAL B 161 REMARK 465 SER B 162 REMARK 465 TRP B 163 REMARK 465 ASN B 164 REMARK 465 SER B 165 REMARK 465 GLY B 166 REMARK 465 ALA B 167 REMARK 465 LEU B 168 REMARK 465 THR B 169 REMARK 465 SER B 170 REMARK 465 GLY B 171 REMARK 465 VAL B 172 REMARK 465 HIS B 173 REMARK 465 THR B 174 REMARK 465 PHE B 175 REMARK 465 PRO B 176 REMARK 465 ALA B 177 REMARK 465 VAL B 178 REMARK 465 LEU B 179 REMARK 465 GLN B 180 REMARK 465 SER B 181 REMARK 465 SER B 182 REMARK 465 GLY B 183 REMARK 465 LEU B 184 REMARK 465 TYR B 185 REMARK 465 SER B 186 REMARK 465 LEU B 187 REMARK 465 SER B 188 REMARK 465 SER B 189 REMARK 465 VAL B 190 REMARK 465 VAL B 191 REMARK 465 THR B 192 REMARK 465 VAL B 193 REMARK 465 PRO B 194 REMARK 465 SER B 195 REMARK 465 SER B 196 REMARK 465 SER B 197 REMARK 465 LEU B 198 REMARK 465 GLY B 199 REMARK 465 THR B 200 REMARK 465 GLN B 201 REMARK 465 THR B 202 REMARK 465 TYR B 203 REMARK 465 ILE B 204 REMARK 465 CYS B 205 REMARK 465 ASN B 206 REMARK 465 VAL B 207 REMARK 465 ASN B 208 REMARK 465 HIS B 209 REMARK 465 LYS B 210 REMARK 465 PRO B 211 REMARK 465 SER B 212 REMARK 465 ASN B 213 REMARK 465 THR B 214 REMARK 465 LYS B 215 REMARK 465 VAL B 216 REMARK 465 ASP B 217 REMARK 465 LYS B 218 REMARK 465 LYS B 219 REMARK 465 VAL B 220 REMARK 465 GLU B 221 REMARK 465 PRO B 222 REMARK 465 LYS B 223 REMARK 465 SER B 224 REMARK 465 CYS B 225 REMARK 465 ASP B 226 REMARK 465 LYS B 227 REMARK 465 THR B 228 REMARK 465 HIS B 229 REMARK 465 THR B 230 REMARK 465 CYS B 231 REMARK 465 PRO B 232 REMARK 465 PRO B 233 REMARK 465 CYS B 234 REMARK 465 PRO B 235 REMARK 465 ALA B 236 REMARK 465 PRO B 237 REMARK 465 GLU B 238 REMARK 465 ALA B 239 REMARK 465 ALA B 240 REMARK 465 GLY B 241 REMARK 465 GLY B 242 REMARK 465 PRO B 243 REMARK 465 SER B 244 REMARK 465 VAL B 245 REMARK 465 PHE B 246 REMARK 465 LEU B 247 REMARK 465 PHE B 248 REMARK 465 PRO B 249 REMARK 465 PRO B 250 REMARK 465 LYS B 251 REMARK 465 PRO B 252 REMARK 465 LYS B 253 REMARK 465 ASP B 254 REMARK 465 THR B 255 REMARK 465 LEU B 256 REMARK 465 MET B 257 REMARK 465 ILE B 258 REMARK 465 SER B 259 REMARK 465 ARG B 260 REMARK 465 THR B 261 REMARK 465 PRO B 262 REMARK 465 GLU B 263 REMARK 465 VAL B 264 REMARK 465 THR B 265 REMARK 465 CYS B 266 REMARK 465 VAL B 267 REMARK 465 VAL B 268 REMARK 465 VAL B 269 REMARK 465 ASP B 270 REMARK 465 VAL B 271 REMARK 465 SER B 272 REMARK 465 HIS B 273 REMARK 465 GLU B 274 REMARK 465 ASP B 275 REMARK 465 PRO B 276 REMARK 465 GLU B 277 REMARK 465 VAL B 278 REMARK 465 LYS B 279 REMARK 465 PHE B 280 REMARK 465 ASN B 281 REMARK 465 TRP B 282 REMARK 465 TYR B 283 REMARK 465 VAL B 284 REMARK 465 ASP B 285 REMARK 465 GLY B 286 REMARK 465 VAL B 287 REMARK 465 GLU B 288 REMARK 465 VAL B 289 REMARK 465 HIS B 290 REMARK 465 ASN B 291 REMARK 465 ALA B 292 REMARK 465 LYS B 293 REMARK 465 THR B 294 REMARK 465 LYS B 295 REMARK 465 PRO B 296 REMARK 465 ARG B 297 REMARK 465 GLU B 298 REMARK 465 GLU B 299 REMARK 465 GLN B 300 REMARK 465 TYR B 301 REMARK 465 ASN B 302 REMARK 465 SER B 303 REMARK 465 THR B 304 REMARK 465 TYR B 305 REMARK 465 ARG B 306 REMARK 465 VAL B 307 REMARK 465 VAL B 308 REMARK 465 SER B 309 REMARK 465 VAL B 310 REMARK 465 LEU B 311 REMARK 465 THR B 312 REMARK 465 VAL B 313 REMARK 465 LEU B 314 REMARK 465 HIS B 315 REMARK 465 GLN B 316 REMARK 465 ASP B 317 REMARK 465 TRP B 318 REMARK 465 LEU B 319 REMARK 465 ASN B 320 REMARK 465 GLY B 321 REMARK 465 LYS B 322 REMARK 465 GLU B 323 REMARK 465 TYR B 324 REMARK 465 LYS B 325 REMARK 465 CYS B 326 REMARK 465 LYS B 327 REMARK 465 VAL B 328 REMARK 465 SER B 329 REMARK 465 ASN B 330 REMARK 465 LYS B 331 REMARK 465 ALA B 332 REMARK 465 LEU B 333 REMARK 465 PRO B 334 REMARK 465 ALA B 335 REMARK 465 PRO B 336 REMARK 465 ILE B 337 REMARK 465 GLU B 338 REMARK 465 LYS B 339 REMARK 465 THR B 340 REMARK 465 ILE B 341 REMARK 465 SER B 342 REMARK 465 LYS B 343 REMARK 465 ALA B 344 REMARK 465 LYS B 345 REMARK 465 GLY B 346 REMARK 465 GLN B 347 REMARK 465 PRO B 348 REMARK 465 ARG B 349 REMARK 465 GLU B 350 REMARK 465 PRO B 351 REMARK 465 GLN B 352 REMARK 465 VAL B 353 REMARK 465 TYR B 354 REMARK 465 THR B 355 REMARK 465 LEU B 356 REMARK 465 PRO B 357 REMARK 465 PRO B 358 REMARK 465 SER B 359 REMARK 465 ARG B 360 REMARK 465 GLU B 361 REMARK 465 GLU B 362 REMARK 465 MET B 363 REMARK 465 THR B 364 REMARK 465 LYS B 365 REMARK 465 ASN B 366 REMARK 465 GLN B 367 REMARK 465 VAL B 368 REMARK 465 SER B 369 REMARK 465 LEU B 370 REMARK 465 THR B 371 REMARK 465 CYS B 372 REMARK 465 LEU B 373 REMARK 465 VAL B 374 REMARK 465 LYS B 375 REMARK 465 GLY B 376 REMARK 465 PHE B 377 REMARK 465 TYR B 378 REMARK 465 PRO B 379 REMARK 465 SER B 380 REMARK 465 ASP B 381 REMARK 465 ILE B 382 REMARK 465 ALA B 383 REMARK 465 VAL B 384 REMARK 465 GLU B 385 REMARK 465 TRP B 386 REMARK 465 GLU B 387 REMARK 465 SER B 388 REMARK 465 ASN B 389 REMARK 465 GLY B 390 REMARK 465 GLN B 391 REMARK 465 PRO B 392 REMARK 465 GLU B 393 REMARK 465 ASN B 394 REMARK 465 ASN B 395 REMARK 465 TYR B 396 REMARK 465 LYS B 397 REMARK 465 THR B 398 REMARK 465 THR B 399 REMARK 465 PRO B 400 REMARK 465 PRO B 401 REMARK 465 VAL B 402 REMARK 465 LEU B 403 REMARK 465 ASP B 404 REMARK 465 SER B 405 REMARK 465 ASP B 406 REMARK 465 GLY B 407 REMARK 465 SER B 408 REMARK 465 PHE B 409 REMARK 465 PHE B 410 REMARK 465 LEU B 411 REMARK 465 TYR B 412 REMARK 465 SER B 413 REMARK 465 LYS B 414 REMARK 465 LEU B 415 REMARK 465 THR B 416 REMARK 465 VAL B 417 REMARK 465 ASP B 418 REMARK 465 LYS B 419 REMARK 465 SER B 420 REMARK 465 ARG B 421 REMARK 465 TRP B 422 REMARK 465 GLN B 423 REMARK 465 GLN B 424 REMARK 465 GLY B 425 REMARK 465 ASN B 426 REMARK 465 VAL B 427 REMARK 465 PHE B 428 REMARK 465 SER B 429 REMARK 465 CYS B 430 REMARK 465 SER B 431 REMARK 465 VAL B 432 REMARK 465 MET B 433 REMARK 465 HIS B 434 REMARK 465 GLU B 435 REMARK 465 ALA B 436 REMARK 465 LEU B 437 REMARK 465 HIS B 438 REMARK 465 ASN B 439 REMARK 465 HIS B 440 REMARK 465 TYR B 441 REMARK 465 THR B 442 REMARK 465 GLN B 443 REMARK 465 LYS B 444 REMARK 465 SER B 445 REMARK 465 LEU B 446 REMARK 465 SER B 447 REMARK 465 LEU B 448 REMARK 465 SER B 449 REMARK 465 PRO B 450 REMARK 465 GLY B 451 REMARK 465 LYS B 452 REMARK 465 ILE C 106 REMARK 465 LYS C 107 REMARK 465 ARG C 108 REMARK 465 THR C 109 REMARK 465 VAL C 110 REMARK 465 ALA C 111 REMARK 465 ALA C 112 REMARK 465 PRO C 113 REMARK 465 SER C 114 REMARK 465 VAL C 115 REMARK 465 PHE C 116 REMARK 465 ILE C 117 REMARK 465 PHE C 118 REMARK 465 PRO C 119 REMARK 465 PRO C 120 REMARK 465 SER C 121 REMARK 465 ASP C 122 REMARK 465 GLU C 123 REMARK 465 GLN C 124 REMARK 465 LEU C 125 REMARK 465 LYS C 126 REMARK 465 SER C 127 REMARK 465 GLY C 128 REMARK 465 THR C 129 REMARK 465 ALA C 130 REMARK 465 SER C 131 REMARK 465 VAL C 132 REMARK 465 VAL C 133 REMARK 465 CYS C 134 REMARK 465 LEU C 135 REMARK 465 LEU C 136 REMARK 465 ASN C 137 REMARK 465 ASN C 138 REMARK 465 PHE C 139 REMARK 465 TYR C 140 REMARK 465 PRO C 141 REMARK 465 ARG C 142 REMARK 465 GLU C 143 REMARK 465 ALA C 144 REMARK 465 LYS C 145 REMARK 465 VAL C 146 REMARK 465 GLN C 147 REMARK 465 TRP C 148 REMARK 465 LYS C 149 REMARK 465 VAL C 150 REMARK 465 ASP C 151 REMARK 465 ASN C 152 REMARK 465 ALA C 153 REMARK 465 LEU C 154 REMARK 465 GLN C 155 REMARK 465 SER C 156 REMARK 465 GLY C 157 REMARK 465 ASN C 158 REMARK 465 SER C 159 REMARK 465 GLN C 160 REMARK 465 GLU C 161 REMARK 465 SER C 162 REMARK 465 VAL C 163 REMARK 465 THR C 164 REMARK 465 GLU C 165 REMARK 465 GLN C 166 REMARK 465 ASP C 167 REMARK 465 SER C 168 REMARK 465 LYS C 169 REMARK 465 ASP C 170 REMARK 465 SER C 171 REMARK 465 THR C 172 REMARK 465 TYR C 173 REMARK 465 SER C 174 REMARK 465 LEU C 175 REMARK 465 SER C 176 REMARK 465 SER C 177 REMARK 465 THR C 178 REMARK 465 LEU C 179 REMARK 465 THR C 180 REMARK 465 LEU C 181 REMARK 465 SER C 182 REMARK 465 LYS C 183 REMARK 465 ALA C 184 REMARK 465 ASP C 185 REMARK 465 TYR C 186 REMARK 465 GLU C 187 REMARK 465 LYS C 188 REMARK 465 HIS C 189 REMARK 465 LYS C 190 REMARK 465 VAL C 191 REMARK 465 TYR C 192 REMARK 465 ALA C 193 REMARK 465 CYS C 194 REMARK 465 GLU C 195 REMARK 465 VAL C 196 REMARK 465 THR C 197 REMARK 465 HIS C 198 REMARK 465 GLN C 199 REMARK 465 GLY C 200 REMARK 465 LEU C 201 REMARK 465 SER C 202 REMARK 465 SER C 203 REMARK 465 PRO C 204 REMARK 465 VAL C 205 REMARK 465 THR C 206 REMARK 465 LYS C 207 REMARK 465 SER C 208 REMARK 465 PHE C 209 REMARK 465 ASN C 210 REMARK 465 ARG C 211 REMARK 465 GLY C 212 REMARK 465 GLU C 213 REMARK 465 CYS C 214 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. = 10.6 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 SER A 438 32.43 -141.17 REMARK 500 CYS A 525 -169.00 -122.77 REMARK 500 SER B 15 -6.35 72.71 REMARK 500 SER B 31 -2.22 -142.08 REMARK 500 ASN B 76 58.32 37.06 REMARK 500 TYR B 101 118.13 -37.94 REMARK 500 SER B 102 -177.57 -172.72 REMARK 500 SER B 103 -54.73 -120.72 REMARK 500 ASP B 107 -169.50 -123.75 REMARK 500 SER B 121 -168.66 -162.75 REMARK 500 ALA C 51 -5.68 66.88 REMARK 500 SER C 67 -173.48 -172.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30978 RELATED DB: EMDB REMARK 900 SARS-COV-2 SPIKE IN COMPLEX WITH THE AB5 NEUTRALIZING ANTIBODY REMARK 900 (FOCUSED REFINEMENT ON FAB-RBD) DBREF 7E3B A 333 526 UNP P0DTC2 SPIKE_SARS2 333 526 DBREF 7E3B B 1 452 PDB 7E3B 7E3B 1 452 DBREF 7E3B C 1 214 PDB 7E3B 7E3B 1 214 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 452 GLN VAL GLN LEU GLN GLU SER GLY PRO GLY LEU VAL LYS SEQRES 2 B 452 PRO SER GLU THR LEU SER LEU THR CYS THR VAL SER GLY SEQRES 3 B 452 GLY SER ILE SER SER TYR TYR TRP SER TRP ILE ARG GLN SEQRES 4 B 452 PRO PRO GLY LYS GLY LEU GLU TRP ILE GLY TYR ILE TYR SEQRES 5 B 452 TYR SER GLY SER THR ASN TYR ASN PRO SER LEU ARG SER SEQRES 6 B 452 ARG VAL THR ILE SER VAL ASP THR SER LYS ASN GLN PHE SEQRES 7 B 452 SER LEU LYS LEU SER SER VAL THR ALA ALA ASP THR ALA SEQRES 8 B 452 VAL TYR TYR CYS ALA ARG ASP ARG GLY TYR SER SER GLY SEQRES 9 B 452 TRP THR ASP GLY PHE ASP ILE TRP GLY GLN GLY THR MET SEQRES 10 B 452 VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER VAL SEQRES 11 B 452 PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY SEQRES 12 B 452 THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO SEQRES 13 B 452 GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SEQRES 14 B 452 SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER SEQRES 15 B 452 GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SER SEQRES 16 B 452 SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN SEQRES 17 B 452 HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU SEQRES 18 B 452 PRO LYS SER CYS ASP LYS THR HIS THR CYS PRO PRO CYS SEQRES 19 B 452 PRO ALA PRO GLU ALA ALA GLY GLY PRO SER VAL PHE LEU SEQRES 20 B 452 PHE PRO PRO LYS PRO LYS ASP THR LEU MET ILE SER ARG SEQRES 21 B 452 THR PRO GLU VAL THR CYS VAL VAL VAL ASP VAL SER HIS SEQRES 22 B 452 GLU ASP PRO GLU VAL LYS PHE ASN TRP TYR VAL ASP GLY SEQRES 23 B 452 VAL GLU VAL HIS ASN ALA LYS THR LYS PRO ARG GLU GLU SEQRES 24 B 452 GLN TYR ASN SER THR TYR ARG VAL VAL SER VAL LEU THR SEQRES 25 B 452 VAL LEU HIS GLN ASP TRP LEU ASN GLY LYS GLU TYR LYS SEQRES 26 B 452 CYS LYS VAL SER ASN LYS ALA LEU PRO ALA PRO ILE GLU SEQRES 27 B 452 LYS THR ILE SER LYS ALA LYS GLY GLN PRO ARG GLU PRO SEQRES 28 B 452 GLN VAL TYR THR LEU PRO PRO SER ARG GLU GLU MET THR SEQRES 29 B 452 LYS ASN GLN VAL SER LEU THR CYS LEU VAL LYS GLY PHE SEQRES 30 B 452 TYR PRO SER ASP ILE ALA VAL GLU TRP GLU SER ASN GLY SEQRES 31 B 452 GLN PRO GLU ASN ASN TYR LYS THR THR PRO PRO VAL LEU SEQRES 32 B 452 ASP SER ASP GLY SER PHE PHE LEU TYR SER LYS LEU THR SEQRES 33 B 452 VAL ASP LYS SER ARG TRP GLN GLN GLY ASN VAL PHE SER SEQRES 34 B 452 CYS SER VAL MET HIS GLU ALA LEU HIS ASN HIS TYR THR SEQRES 35 B 452 GLN LYS SER LEU SER LEU SER PRO GLY LYS SEQRES 1 C 214 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 C 214 SER VAL GLY ASP ARG VAL THR ILE THR CYS GLN ALA SER SEQRES 3 C 214 GLN ASP ILE THR ASN TYR LEU ASN TRP TYR GLN GLN LYS SEQRES 4 C 214 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ASP ALA SER SEQRES 5 C 214 ASN LEU GLU THR GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 C 214 GLY SER GLY THR ASP PHE THR PHE THR ILE SER SER LEU SEQRES 7 C 214 GLN PRO GLU ASP ILE ALA THR TYR TYR CYS GLN GLN TYR SEQRES 8 C 214 ASP ASN ILE PRO PHE THR PHE GLY LEU GLY THR LYS VAL SEQRES 9 C 214 ASP ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 C 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 C 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 C 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 C 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 C 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 C 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 C 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 C 214 PHE ASN ARG GLY GLU CYS 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 ASP A 364 ASN A 370 1 7 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 LYS A 417 ASN A 422 1 6 HELIX 7 AA7 GLY A 502 TYR A 505 5 4 HELIX 8 AA8 PRO B 61 ARG B 64 5 4 HELIX 9 AA9 THR 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 TYR A 508 N ILE A 402 SHEET 4 AA1 5 GLY A 431 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 LEU A 452 ARG A 454 0 SHEET 2 AA2 2 LEU A 492 SER A 494 -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 GLN B 3 SER B 7 0 SHEET 2 AA4 4 LEU B 18 SER B 25 -1 O THR B 23 N GLN B 5 SHEET 3 AA4 4 GLN B 77 LEU B 82 -1 O LEU B 80 N LEU B 20 SHEET 4 AA4 4 VAL B 67 ASP B 72 -1 N THR B 68 O LYS B 81 SHEET 1 AA5 6 LEU B 11 VAL B 12 0 SHEET 2 AA5 6 THR B 116 VAL B 120 1 O THR B 119 N VAL B 12 SHEET 3 AA5 6 ALA B 91 ARG B 97 -1 N TYR B 93 O THR B 116 SHEET 4 AA5 6 TRP B 34 GLN B 39 -1 N ILE B 37 O TYR B 94 SHEET 5 AA5 6 GLU B 46 ILE B 51 -1 O ILE B 51 N TRP B 34 SHEET 6 AA5 6 THR B 57 TYR B 59 -1 O ASN B 58 N TYR B 50 SHEET 1 AA6 4 THR C 5 GLN C 6 0 SHEET 2 AA6 4 VAL C 19 GLN C 24 -1 O GLN C 24 N THR C 5 SHEET 3 AA6 4 ASP C 70 ILE C 75 -1 O PHE C 71 N CYS C 23 SHEET 4 AA6 4 PHE C 62 SER C 67 -1 N SER C 67 O ASP C 70 SHEET 1 AA7 4 SER C 10 LEU C 11 0 SHEET 2 AA7 4 THR C 102 VAL C 104 1 O LYS C 103 N LEU C 11 SHEET 3 AA7 4 ALA C 84 GLN C 90 -1 N TYR C 86 O THR C 102 SHEET 4 AA7 4 LEU C 33 GLN C 38 -1 N TYR C 36 O TYR C 87 SHEET 1 AA8 4 SER C 10 LEU C 11 0 SHEET 2 AA8 4 THR C 102 VAL C 104 1 O LYS C 103 N LEU C 11 SHEET 3 AA8 4 ALA C 84 GLN C 90 -1 N TYR C 86 O THR C 102 SHEET 4 AA8 4 THR C 97 PHE C 98 -1 O THR C 97 N GLN C 90 SHEET 1 AA9 2 ILE C 48 TYR C 49 0 SHEET 2 AA9 2 ASN C 53 LEU C 54 -1 O ASN C 53 N TYR C 49 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 2.04 SSBOND 5 CYS B 22 CYS B 95 1555 1555 2.03 SSBOND 6 CYS C 23 CYS C 88 1555 1555 2.04 LINK ND2 ASN A 343 C1 NAG A 601 1555 1555 1.44 CISPEP 1 ILE C 94 PRO C 95 0 -3.52 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