HEADER VIRAL PROTEIN/IMMUNE SYSTEM 28-JUN-23 8JVA TITLE CRYO-EM STRUCTURE OF THE N-TERMINAL DOMAIN OF OMICRON BA.1 IN COMPLEX TITLE 2 WITH NANOBODY N235 AND S2L20 FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY N235; COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: S2L20 LIGHT CHAIN; COMPND 7 CHAIN: A; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: S2L20 HEAVY CHAIN; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: SPIKE PROTEIN S2'; COMPND 15 CHAIN: F; COMPND 16 FRAGMENT: N-TERMINAL; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 3 ORGANISM_TAXID: 30538; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 21 MOL_ID: 4; SOURCE 22 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 23 2; SOURCE 24 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 25 ORGANISM_TAXID: 2697049; SOURCE 26 STRAIN: OMICRON/BA.1; SOURCE 27 GENE: S, 2; SOURCE 28 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 29 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 30 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS COMPLEX, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM KEYWDS 2 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR B.LIU,H.H.LIU,P.HAN,J.X.QI REVDAT 1 22-MAY-24 8JVA 0 JRNL AUTH B.LIU,H.LIU,P.HAN,X.WANG,C.WANG,X.YAN,W.LEI,K.XU,J.ZHOU, JRNL AUTH 2 J.QI,R.FAN,G.WU,W.X.TIAN,G.F.GAO,Q.WANG JRNL TITL ENHANCED POTENCY OF AN IGM-LIKE NANOBODY TARGETING CONSERVED JRNL TITL 2 EPITOPE IN SARS-COV-2 SPIKE N-TERMINAL DOMAIN. JRNL REF SIGNAL TRANSDUCT TARGET THER V. 9 131 2024 JRNL REFN ESSN 2059-3635 JRNL PMID 38740785 JRNL DOI 10.1038/S41392-024-01847-8 REMARK 2 REMARK 2 RESOLUTION. 2.81 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) : 2.810 REMARK 3 NUMBER OF PARTICLES : 139757 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8JVA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 06-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039002. 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 : THE N-TERMINAL DOMAIN OF REMARK 245 OMICRON BA.1 IN COMPLEX WITH REMARK 245 NANOBODY N235 AND S2L20 FAB 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) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 6000.00 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, A, B, F 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 HIS D 121 REMARK 465 HIS D 122 REMARK 465 HIS D 123 REMARK 465 HIS D 124 REMARK 465 HIS D 125 REMARK 465 HIS D 126 REMARK 465 MET A -20 REMARK 465 GLU A -19 REMARK 465 THR A -18 REMARK 465 ASP A -17 REMARK 465 THR A -16 REMARK 465 LEU A -15 REMARK 465 LEU A -14 REMARK 465 LEU A -13 REMARK 465 TRP A -12 REMARK 465 VAL A -11 REMARK 465 LEU A -10 REMARK 465 LEU A -9 REMARK 465 LEU A -8 REMARK 465 TRP A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 THR A -2 REMARK 465 GLY A -1 REMARK 465 ASP A 0 REMARK 465 CYS A 214 REMARK 465 SER A 215 REMARK 465 MET B -20 REMARK 465 GLU B -19 REMARK 465 THR B -18 REMARK 465 ASP B -17 REMARK 465 THR B -16 REMARK 465 LEU B -15 REMARK 465 LEU B -14 REMARK 465 LEU B -13 REMARK 465 TRP B -12 REMARK 465 VAL B -11 REMARK 465 LEU B -10 REMARK 465 LEU B -9 REMARK 465 LEU B -8 REMARK 465 TRP B -7 REMARK 465 VAL B -6 REMARK 465 PRO B -5 REMARK 465 GLY B -4 REMARK 465 SER B -3 REMARK 465 THR B -2 REMARK 465 GLY B -1 REMARK 465 ASP B 0 REMARK 465 LYS B 139 REMARK 465 SER B 140 REMARK 465 THR B 141 REMARK 465 SER B 142 REMARK 465 GLY B 143 REMARK 465 GLY B 200 REMARK 465 THR B 201 REMARK 465 GLN B 202 REMARK 465 THR B 203 REMARK 465 TYR B 204 REMARK 465 ILE B 205 REMARK 465 CYS B 206 REMARK 465 ASN B 207 REMARK 465 VAL B 208 REMARK 465 ASN B 209 REMARK 465 HIS B 210 REMARK 465 LYS B 211 REMARK 465 PRO B 212 REMARK 465 SER B 213 REMARK 465 ASN B 214 REMARK 465 THR B 215 REMARK 465 LYS B 216 REMARK 465 VAL B 217 REMARK 465 ASP B 218 REMARK 465 LYS B 219 REMARK 465 ARG B 220 REMARK 465 VAL B 221 REMARK 465 GLU B 222 REMARK 465 PRO B 223 REMARK 465 LYS B 224 REMARK 465 SER B 225 REMARK 465 CYS B 226 REMARK 465 ASP B 227 REMARK 465 LYS B 228 REMARK 465 THR B 229 REMARK 465 HIS B 230 REMARK 465 THR B 231 REMARK 465 CYS B 232 REMARK 465 PRO B 233 REMARK 465 PRO B 234 REMARK 465 CYS B 235 REMARK 465 PRO B 236 REMARK 465 ALA B 237 REMARK 465 PRO B 238 REMARK 465 GLU B 239 REMARK 465 LEU B 240 REMARK 465 LEU B 241 REMARK 465 GLY B 242 REMARK 465 GLY B 243 REMARK 465 PRO B 244 REMARK 465 SER B 245 REMARK 465 VAL B 246 REMARK 465 PHE B 247 REMARK 465 LEU B 248 REMARK 465 PHE B 249 REMARK 465 PRO B 250 REMARK 465 PRO B 251 REMARK 465 LYS B 252 REMARK 465 PRO B 253 REMARK 465 LYS B 254 REMARK 465 ASP B 255 REMARK 465 THR B 256 REMARK 465 LEU B 257 REMARK 465 MET B 258 REMARK 465 ILE B 259 REMARK 465 SER B 260 REMARK 465 ARG B 261 REMARK 465 THR B 262 REMARK 465 PRO B 263 REMARK 465 GLU B 264 REMARK 465 VAL B 265 REMARK 465 THR B 266 REMARK 465 CYS B 267 REMARK 465 VAL B 268 REMARK 465 VAL B 269 REMARK 465 VAL B 270 REMARK 465 ASP B 271 REMARK 465 VAL B 272 REMARK 465 SER B 273 REMARK 465 HIS B 274 REMARK 465 GLU B 275 REMARK 465 ASP B 276 REMARK 465 PRO B 277 REMARK 465 GLU B 278 REMARK 465 VAL B 279 REMARK 465 LYS B 280 REMARK 465 PHE B 281 REMARK 465 ASN B 282 REMARK 465 TRP B 283 REMARK 465 TYR B 284 REMARK 465 VAL B 285 REMARK 465 ASP B 286 REMARK 465 GLY B 287 REMARK 465 VAL B 288 REMARK 465 GLU B 289 REMARK 465 VAL B 290 REMARK 465 HIS B 291 REMARK 465 ASN B 292 REMARK 465 ALA B 293 REMARK 465 LYS B 294 REMARK 465 THR B 295 REMARK 465 LYS B 296 REMARK 465 PRO B 297 REMARK 465 ARG B 298 REMARK 465 GLU B 299 REMARK 465 GLU B 300 REMARK 465 GLN B 301 REMARK 465 TYR B 302 REMARK 465 ASN B 303 REMARK 465 SER B 304 REMARK 465 THR B 305 REMARK 465 TYR B 306 REMARK 465 ARG B 307 REMARK 465 VAL B 308 REMARK 465 VAL B 309 REMARK 465 SER B 310 REMARK 465 VAL B 311 REMARK 465 LEU B 312 REMARK 465 THR B 313 REMARK 465 VAL B 314 REMARK 465 LEU B 315 REMARK 465 HIS B 316 REMARK 465 GLN B 317 REMARK 465 ASP B 318 REMARK 465 TRP B 319 REMARK 465 LEU B 320 REMARK 465 ASN B 321 REMARK 465 GLY B 322 REMARK 465 LYS B 323 REMARK 465 GLU B 324 REMARK 465 TYR B 325 REMARK 465 LYS B 326 REMARK 465 CYS B 327 REMARK 465 LYS B 328 REMARK 465 VAL B 329 REMARK 465 SER B 330 REMARK 465 ASN B 331 REMARK 465 LYS B 332 REMARK 465 ALA B 333 REMARK 465 LEU B 334 REMARK 465 PRO B 335 REMARK 465 ALA B 336 REMARK 465 PRO B 337 REMARK 465 ILE B 338 REMARK 465 GLU B 339 REMARK 465 LYS B 340 REMARK 465 THR B 341 REMARK 465 ILE B 342 REMARK 465 SER B 343 REMARK 465 LYS B 344 REMARK 465 ALA B 345 REMARK 465 LYS B 346 REMARK 465 GLY B 347 REMARK 465 GLN B 348 REMARK 465 PRO B 349 REMARK 465 ARG B 350 REMARK 465 GLU B 351 REMARK 465 PRO B 352 REMARK 465 GLN B 353 REMARK 465 VAL B 354 REMARK 465 TYR B 355 REMARK 465 THR B 356 REMARK 465 LEU B 357 REMARK 465 PRO B 358 REMARK 465 PRO B 359 REMARK 465 SER B 360 REMARK 465 ARG B 361 REMARK 465 ASP B 362 REMARK 465 GLU B 363 REMARK 465 LEU B 364 REMARK 465 THR B 365 REMARK 465 LYS B 366 REMARK 465 ASN B 367 REMARK 465 GLN B 368 REMARK 465 VAL B 369 REMARK 465 SER B 370 REMARK 465 LEU B 371 REMARK 465 THR B 372 REMARK 465 CYS B 373 REMARK 465 LEU B 374 REMARK 465 VAL B 375 REMARK 465 LYS B 376 REMARK 465 GLY B 377 REMARK 465 PHE B 378 REMARK 465 TYR B 379 REMARK 465 PRO B 380 REMARK 465 SER B 381 REMARK 465 ASP B 382 REMARK 465 ILE B 383 REMARK 465 ALA B 384 REMARK 465 VAL B 385 REMARK 465 GLU B 386 REMARK 465 TRP B 387 REMARK 465 GLU B 388 REMARK 465 SER B 389 REMARK 465 ASN B 390 REMARK 465 GLY B 391 REMARK 465 GLN B 392 REMARK 465 PRO B 393 REMARK 465 GLU B 394 REMARK 465 ASN B 395 REMARK 465 ASN B 396 REMARK 465 TYR B 397 REMARK 465 LYS B 398 REMARK 465 THR B 399 REMARK 465 THR B 400 REMARK 465 PRO B 401 REMARK 465 PRO B 402 REMARK 465 VAL B 403 REMARK 465 LEU B 404 REMARK 465 ASP B 405 REMARK 465 SER B 406 REMARK 465 ASP B 407 REMARK 465 GLY B 408 REMARK 465 SER B 409 REMARK 465 PHE B 410 REMARK 465 PHE B 411 REMARK 465 LEU B 412 REMARK 465 TYR B 413 REMARK 465 SER B 414 REMARK 465 LYS B 415 REMARK 465 LEU B 416 REMARK 465 THR B 417 REMARK 465 VAL B 418 REMARK 465 ASP B 419 REMARK 465 LYS B 420 REMARK 465 SER B 421 REMARK 465 ARG B 422 REMARK 465 TRP B 423 REMARK 465 GLN B 424 REMARK 465 GLN B 425 REMARK 465 GLY B 426 REMARK 465 ASN B 427 REMARK 465 VAL B 428 REMARK 465 PHE B 429 REMARK 465 SER B 430 REMARK 465 CYS B 431 REMARK 465 SER B 432 REMARK 465 VAL B 433 REMARK 465 MET B 434 REMARK 465 HIS B 435 REMARK 465 GLU B 436 REMARK 465 ALA B 437 REMARK 465 LEU B 438 REMARK 465 HIS B 439 REMARK 465 ASN B 440 REMARK 465 HIS B 441 REMARK 465 TYR B 442 REMARK 465 THR B 443 REMARK 465 GLN B 444 REMARK 465 LYS B 445 REMARK 465 SER B 446 REMARK 465 LEU B 447 REMARK 465 SER B 448 REMARK 465 LEU B 449 REMARK 465 SER B 450 REMARK 465 PRO B 451 REMARK 465 GLY B 452 REMARK 465 LYS B 453 REMARK 465 MET F 1 REMARK 465 PHE F 2 REMARK 465 VAL F 3 REMARK 465 PHE F 4 REMARK 465 LEU F 5 REMARK 465 VAL F 6 REMARK 465 LEU F 7 REMARK 465 LEU F 8 REMARK 465 PRO F 9 REMARK 465 LEU F 10 REMARK 465 VAL F 11 REMARK 465 SER F 12 REMARK 465 SER F 13 REMARK 465 GLN F 14 REMARK 465 CYS F 15 REMARK 465 VAL F 16 REMARK 465 ASN F 17 REMARK 465 LEU F 18 REMARK 465 THR F 19 REMARK 465 THR F 20 REMARK 465 ARG F 21 REMARK 465 THR F 22 REMARK 465 GLY F 72 REMARK 465 THR F 73 REMARK 465 ASN F 74 REMARK 465 GLY F 75 REMARK 465 ARG F 102 REMARK 465 LYS F 147 REMARK 465 ASN F 148 REMARK 465 ASN F 149 REMARK 465 LYS F 150 REMARK 465 SER F 151 REMARK 465 TRP F 152 REMARK 465 MET F 153 REMARK 465 GLU F 154 REMARK 465 SER F 155 REMARK 465 MET F 177 REMARK 465 ASP F 178 REMARK 465 LEU F 179 REMARK 465 GLU F 180 REMARK 465 GLY F 181 REMARK 465 LYS F 182 REMARK 465 GLN F 183 REMARK 465 GLY F 184 REMARK 465 ASN F 185 REMARK 465 ILE F 210A REMARK 465 VAL F 210B REMARK 465 LEU F 249 REMARK 465 THR F 250 REMARK 465 PRO F 251 REMARK 465 GLY F 252 REMARK 465 ASP F 253 REMARK 465 SER F 254 REMARK 465 SER F 255 REMARK 465 SER F 256 REMARK 465 GLY F 257 REMARK 465 TRP F 258 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 GLU D 44 -127.12 60.82 REMARK 500 PRO D 54 161.85 -47.37 REMARK 500 ARG A 30 -127.09 58.92 REMARK 500 TYR A 32 77.29 -100.15 REMARK 500 ALA A 51 -10.63 71.75 REMARK 500 VAL B 48 -62.43 -104.90 REMARK 500 TYR B 103 -116.19 62.44 REMARK 500 ASP B 154 63.92 63.38 REMARK 500 SER B 163 119.11 -162.16 REMARK 500 SER B 189 -169.25 -160.73 REMARK 500 VAL B 192 -60.84 -102.77 REMARK 500 PHE F 32 -149.77 61.40 REMARK 500 ASN F 87 -134.42 60.08 REMARK 500 PRO F 230 59.33 -90.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-36672 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE N-TERMINAL DOMAIN OF OMICRON BA.1 IN REMARK 900 COMPLEX WITH NANOBODY N235 AND S2L20 FAB DBREF 8JVA D 1 126 PDB 8JVA 8JVA 1 126 DBREF 8JVA A -20 215 PDB 8JVA 8JVA -20 215 DBREF 8JVA B -20 453 PDB 8JVA 8JVA -20 453 DBREF 8JVA F 1 303 UNP P0DTC2 SPIKE_SARS2 1 303 SEQADV 8JVA VAL F 67 UNP P0DTC2 ALA 67 VARIANT SEQADV 8JVA F UNP P0DTC2 HIS 69 DELETION SEQADV 8JVA F UNP P0DTC2 VAL 70 DELETION SEQADV 8JVA ILE F 95 UNP P0DTC2 THR 95 VARIANT SEQADV 8JVA F UNP P0DTC2 GLY 142 DELETION SEQADV 8JVA F UNP P0DTC2 VAL 143 DELETION SEQADV 8JVA F UNP P0DTC2 TYR 144 DELETION SEQADV 8JVA ASP F 145 UNP P0DTC2 TYR 145 VARIANT SEQADV 8JVA F UNP P0DTC2 ASN 211 DELETION SEQADV 8JVA ILE F 210A UNP P0DTC2 LEU 212 VARIANT SEQADV 8JVA GLU F 212 UNP P0DTC2 INSERTION SEQADV 8JVA PRO F 213 UNP P0DTC2 INSERTION SEQADV 8JVA GLU F 214 UNP P0DTC2 INSERTION SEQRES 1 D 126 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 126 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 D 126 LEU ILE ILE SER ARG TYR ASP MET SER TRP TYR ARG GLN SEQRES 4 D 126 ALA PRO GLY LYS GLU ARG GLU LEU VAL ALA THR THR PRO SEQRES 5 D 126 ILE PRO ALA ALA ARG PRO GLN TYR ALA ASP SER VAL LYS SEQRES 6 D 126 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 D 126 VAL SER LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 D 126 ALA VAL TYR TYR CYS ASN LEU GLY PRO GLU SER GLN ASP SEQRES 9 D 126 HIS ASN TYR ASN TYR TRP GLY GLN GLY THR GLN VAL THR SEQRES 10 D 126 VAL SER SER HIS HIS HIS HIS HIS HIS SEQRES 1 A 236 MET GLU THR ASP THR LEU LEU LEU TRP VAL LEU LEU LEU SEQRES 2 A 236 TRP VAL PRO GLY SER THR GLY ASP VAL ILE TRP MET THR SEQRES 3 A 236 GLN SER PRO SER SER LEU SER ALA SER VAL GLY ASP ARG SEQRES 4 A 236 VAL THR ILE THR CYS GLN ALA SER GLN ASP ILE ARG PHE SEQRES 5 A 236 TYR LEU ASN TRP TYR GLN GLN LYS PRO GLY LYS ALA PRO SEQRES 6 A 236 LYS LEU LEU ILE SER ASP ALA SER ASN MET GLU THR GLY SEQRES 7 A 236 VAL PRO SER ARG PHE SER GLY SER GLY SER GLY THR ASP SEQRES 8 A 236 PHE THR PHE THR ILE SER SER LEU GLN PRO GLU ASP ILE SEQRES 9 A 236 ALA THR TYR TYR CYS GLN GLN TYR ASP ASN LEU PRO PHE SEQRES 10 A 236 THR PHE GLY PRO GLY THR LYS VAL ASP PHE LYS ARG THR SEQRES 11 A 236 VAL ALA ALA PRO SER VAL PHE ILE PHE PRO PRO SER ASP SEQRES 12 A 236 GLU GLN LEU LYS SER GLY THR ALA SER VAL VAL CYS LEU SEQRES 13 A 236 LEU ASN ASN PHE TYR PRO ARG GLU ALA LYS VAL GLN TRP SEQRES 14 A 236 LYS VAL ASP ASN ALA LEU GLN SER GLY ASN SER GLN GLU SEQRES 15 A 236 SER VAL THR GLU GLN ASP SER LYS ASP SER THR TYR SER SEQRES 16 A 236 LEU SER SER THR LEU THR LEU SER LYS ALA ASP TYR GLU SEQRES 17 A 236 LYS HIS LYS VAL TYR ALA CYS GLU VAL THR HIS GLN GLY SEQRES 18 A 236 LEU SER SER PRO VAL THR LYS SER PHE ASN ARG GLY GLU SEQRES 19 A 236 CYS SER SEQRES 1 B 473 MET GLU THR ASP THR LEU LEU LEU TRP VAL LEU LEU LEU SEQRES 2 B 473 TRP VAL PRO GLY SER THR GLY ASP GLU VAL GLN LEU VAL SEQRES 3 B 473 GLU SER GLY GLY GLY VAL VAL GLN PRO GLY GLY SER LEU SEQRES 4 B 473 ARG LEU SER CYS ALA ALA SER GLY PHE THR PHE ASN SER SEQRES 5 B 473 TYR GLY MET HIS TRP VAL ARG GLN ALA PRO GLY LYS GLY SEQRES 6 B 473 LEU GLU TRP VAL ALA PHE ILE ARG TYR ASP GLY GLY ASN SEQRES 7 B 473 LYS TYR TYR ALA ASP SER VAL LYS GLY ARG PHE THR ILE SEQRES 8 B 473 SER ARG ASP ASN SER LYS ASN THR LEU TYR LEU GLN MET SEQRES 9 B 473 LYS SER LEU ARG ALA GLU ASP THR ALA VAL TYR TYR CYS SEQRES 10 B 473 ALA ASN LEU LYS ASP SER ARG TYR SER GLY SER TYR TYR SEQRES 11 B 473 ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 12 B 473 ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SEQRES 13 B 473 SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY SEQRES 14 B 473 CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SEQRES 15 B 473 SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR SEQRES 16 B 473 PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SEQRES 17 B 473 SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR SEQRES 18 B 473 GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN SEQRES 19 B 473 THR LYS VAL ASP LYS ARG VAL GLU PRO LYS SER CYS ASP SEQRES 20 B 473 LYS THR HIS THR CYS PRO PRO CYS PRO ALA PRO GLU LEU SEQRES 21 B 473 LEU GLY GLY PRO SER VAL PHE LEU PHE PRO PRO LYS PRO SEQRES 22 B 473 LYS ASP THR LEU MET ILE SER ARG THR PRO GLU VAL THR SEQRES 23 B 473 CYS VAL VAL VAL ASP VAL SER HIS GLU ASP PRO GLU VAL SEQRES 24 B 473 LYS PHE ASN TRP TYR VAL ASP GLY VAL GLU VAL HIS ASN SEQRES 25 B 473 ALA LYS THR LYS PRO ARG GLU GLU GLN TYR ASN SER THR SEQRES 26 B 473 TYR ARG VAL VAL SER VAL LEU THR VAL LEU HIS GLN ASP SEQRES 27 B 473 TRP LEU ASN GLY LYS GLU TYR LYS CYS LYS VAL SER ASN SEQRES 28 B 473 LYS ALA LEU PRO ALA PRO ILE GLU LYS THR ILE SER LYS SEQRES 29 B 473 ALA LYS GLY GLN PRO ARG GLU PRO GLN VAL TYR THR LEU SEQRES 30 B 473 PRO PRO SER ARG ASP GLU LEU THR LYS ASN GLN VAL SER SEQRES 31 B 473 LEU THR CYS LEU VAL LYS GLY PHE TYR PRO SER ASP ILE SEQRES 32 B 473 ALA VAL GLU TRP GLU SER ASN GLY GLN PRO GLU ASN ASN SEQRES 33 B 473 TYR LYS THR THR PRO PRO VAL LEU ASP SER ASP GLY SER SEQRES 34 B 473 PHE PHE LEU TYR SER LYS LEU THR VAL ASP LYS SER ARG SEQRES 35 B 473 TRP GLN GLN GLY ASN VAL PHE SER CYS SER VAL MET HIS SEQRES 36 B 473 GLU ALA LEU HIS ASN HIS TYR THR GLN LYS SER LEU SER SEQRES 37 B 473 LEU SER PRO GLY LYS SEQRES 1 F 300 MET PHE VAL PHE LEU VAL LEU LEU PRO LEU VAL SER SER SEQRES 2 F 300 GLN CYS VAL ASN LEU THR THR ARG THR GLN LEU PRO PRO SEQRES 3 F 300 ALA TYR THR ASN SER PHE THR ARG GLY VAL TYR TYR PRO SEQRES 4 F 300 ASP LYS VAL PHE ARG SER SER VAL LEU HIS SER THR GLN SEQRES 5 F 300 ASP LEU PHE LEU PRO PHE PHE SER ASN VAL THR TRP PHE SEQRES 6 F 300 HIS VAL ILE SER GLY THR ASN GLY THR LYS ARG PHE ASP SEQRES 7 F 300 ASN PRO VAL LEU PRO PHE ASN ASP GLY VAL TYR PHE ALA SEQRES 8 F 300 SER ILE GLU LYS SER ASN ILE ILE ARG GLY TRP ILE PHE SEQRES 9 F 300 GLY THR THR LEU ASP SER LYS THR GLN SER LEU LEU ILE SEQRES 10 F 300 VAL ASN ASN ALA THR ASN VAL VAL ILE LYS VAL CYS GLU SEQRES 11 F 300 PHE GLN PHE CYS ASN ASP PRO PHE LEU ASP HIS LYS ASN SEQRES 12 F 300 ASN LYS SER TRP MET GLU SER GLU PHE ARG VAL TYR SER SEQRES 13 F 300 SER ALA ASN ASN CYS THR PHE GLU TYR VAL SER GLN PRO SEQRES 14 F 300 PHE LEU MET ASP LEU GLU GLY LYS GLN GLY ASN PHE LYS SEQRES 15 F 300 ASN LEU ARG GLU PHE VAL PHE LYS ASN ILE ASP GLY TYR SEQRES 16 F 300 PHE LYS ILE TYR SER LYS HIS THR PRO ILE ILE VAL ARG SEQRES 17 F 300 GLU PRO GLU ASP LEU PRO GLN GLY PHE SER ALA LEU GLU SEQRES 18 F 300 PRO LEU VAL ASP LEU PRO ILE GLY ILE ASN ILE THR ARG SEQRES 19 F 300 PHE GLN THR LEU LEU ALA LEU HIS ARG SER TYR LEU THR SEQRES 20 F 300 PRO GLY ASP SER SER SER GLY TRP THR ALA GLY ALA ALA SEQRES 21 F 300 ALA TYR TYR VAL GLY TYR LEU GLN PRO ARG THR PHE LEU SEQRES 22 F 300 LEU LYS TYR ASN GLU ASN GLY THR ILE THR ASP ALA VAL SEQRES 23 F 300 ASP CYS ALA LEU ASP PRO LEU SER GLU THR LYS CYS THR SEQRES 24 F 300 LEU HET NAG F 401 14 HET NAG F 402 14 HET NAG F 403 14 HET NAG F 404 14 HET NAG F 405 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 5 NAG 5(C8 H15 N O6) HELIX 1 AA1 ILE D 28 TYR D 32 5 5 HELIX 2 AA2 ALA D 61 LYS D 65 5 5 HELIX 3 AA3 LYS D 87 THR D 91 5 5 HELIX 4 AA4 PRO D 100 GLN D 103 5 4 HELIX 5 AA5 SER A 121 LYS A 126 1 6 HELIX 6 AA6 THR B 28 TYR B 32 5 5 HELIX 7 AA7 ARG B 86 THR B 90 5 5 HELIX 8 AA8 ASP F 294 LEU F 303 1 10 SHEET 1 AA1 4 GLN D 3 SER D 7 0 SHEET 2 AA1 4 ARG D 19 SER D 25 -1 O ALA D 23 N GLN D 5 SHEET 3 AA1 4 THR D 78 MET D 83 -1 O LEU D 81 N LEU D 20 SHEET 4 AA1 4 PHE D 68 ASP D 73 -1 N ASP D 73 O THR D 78 SHEET 1 AA2 5 LEU D 11 VAL D 12 0 SHEET 2 AA2 5 THR D 114 VAL D 118 1 O THR D 117 N VAL D 12 SHEET 3 AA2 5 ALA D 92 LEU D 98 -1 N ALA D 92 O VAL D 116 SHEET 4 AA2 5 MET D 34 GLN D 39 -1 N SER D 35 O ASN D 97 SHEET 5 AA2 5 GLU D 46 THR D 51 -1 O THR D 51 N MET D 34 SHEET 1 AA3 4 MET A 4 SER A 7 0 SHEET 2 AA3 4 VAL A 19 ALA A 25 -1 O THR A 22 N SER A 7 SHEET 3 AA3 4 ASP A 70 ILE A 75 -1 O PHE A 73 N ILE A 21 SHEET 4 AA3 4 PHE A 62 SER A 67 -1 N SER A 63 O THR A 74 SHEET 1 AA4 3 SER A 10 ALA A 13 0 SHEET 2 AA4 3 THR A 102 PHE A 106 1 O LYS A 103 N LEU A 11 SHEET 3 AA4 3 THR A 85 TYR A 86 -1 N TYR A 86 O THR A 102 SHEET 1 AA5 3 LYS A 45 SER A 49 0 SHEET 2 AA5 3 LEU A 33 GLN A 37 -1 N TRP A 35 O LEU A 47 SHEET 3 AA5 3 CYS A 88 GLN A 90 -1 O GLN A 89 N ASN A 34 SHEET 1 AA6 4 SER A 114 PHE A 118 0 SHEET 2 AA6 4 ALA A 130 ASN A 137 -1 O LEU A 135 N PHE A 116 SHEET 3 AA6 4 SER A 174 LEU A 181 -1 O LEU A 179 N VAL A 132 SHEET 4 AA6 4 SER A 159 VAL A 163 -1 N GLN A 160 O THR A 178 SHEET 1 AA7 3 LYS A 145 VAL A 150 0 SHEET 2 AA7 3 TYR A 192 THR A 197 -1 O GLU A 195 N GLN A 147 SHEET 3 AA7 3 VAL A 205 PHE A 209 -1 O VAL A 205 N VAL A 196 SHEET 1 AA8 4 GLN B 3 SER B 7 0 SHEET 2 AA8 4 LEU B 18 SER B 25 -1 O ALA B 23 N VAL B 5 SHEET 3 AA8 4 THR B 77 MET B 82 -1 O MET B 82 N LEU B 18 SHEET 4 AA8 4 PHE B 67 ASP B 72 -1 N SER B 70 O TYR B 79 SHEET 1 AA9 6 GLY B 10 VAL B 12 0 SHEET 2 AA9 6 THR B 115 VAL B 119 1 O THR B 118 N GLY B 10 SHEET 3 AA9 6 ALA B 91 ASN B 97 -1 N TYR B 93 O THR B 115 SHEET 4 AA9 6 MET B 34 GLN B 39 -1 N VAL B 37 O TYR B 94 SHEET 5 AA9 6 LEU B 45 ARG B 52 -1 O VAL B 48 N TRP B 36 SHEET 6 AA9 6 GLY B 54 TYR B 59 -1 O TYR B 58 N PHE B 50 SHEET 1 AB1 4 GLY B 10 VAL B 12 0 SHEET 2 AB1 4 THR B 115 VAL B 119 1 O THR B 118 N GLY B 10 SHEET 3 AB1 4 ALA B 91 ASN B 97 -1 N TYR B 93 O THR B 115 SHEET 4 AB1 4 TYR B 110 TRP B 111 -1 O TYR B 110 N ASN B 97 SHEET 1 AB2 3 SER B 128 VAL B 129 0 SHEET 2 AB2 3 VAL B 152 LYS B 153 -1 O LYS B 153 N SER B 128 SHEET 3 AB2 3 SER B 187 LEU B 188 -1 O LEU B 188 N VAL B 152 SHEET 1 AB3 7 ALA F 27 ASN F 30 0 SHEET 2 AB3 7 ASN F 61 PHE F 65 -1 O VAL F 62 N THR F 29 SHEET 3 AB3 7 TYR F 265 TYR F 269 -1 O TYR F 265 N PHE F 65 SHEET 4 AB3 7 VAL F 90 SER F 94 -1 N TYR F 91 O GLY F 268 SHEET 5 AB3 7 ASN F 188 ILE F 197 -1 O PHE F 192 N PHE F 92 SHEET 6 AB3 7 TYR F 200 PRO F 209 -1 O LYS F 206 N GLU F 191 SHEET 7 AB3 7 GLU F 224 LEU F 229 -1 O LEU F 229 N PHE F 201 SHEET 1 AB4 3 VAL F 47 PHE F 55 0 SHEET 2 AB4 3 GLN F 271 TYR F 279 -1 O ARG F 273 N ASP F 53 SHEET 3 AB4 3 ILE F 285 ASP F 290 -1 O ASP F 287 N LYS F 278 SHEET 1 AB5 6 LEU F 84 PRO F 85 0 SHEET 2 AB5 6 ARG F 237 THR F 240 -1 O PHE F 238 N LEU F 84 SHEET 3 AB5 6 TRP F 104 GLY F 107 -1 N GLY F 107 O ARG F 237 SHEET 4 AB5 6 SER F 116 ASN F 121 -1 O LEU F 117 N PHE F 106 SHEET 5 AB5 6 VAL F 126 PHE F 135 -1 O LYS F 129 N LEU F 118 SHEET 6 AB5 6 TYR F 160 ASN F 164 -1 O ASN F 164 N GLU F 132 SHEET 1 AB6 6 LEU F 84 PRO F 85 0 SHEET 2 AB6 6 ARG F 237 THR F 240 -1 O PHE F 238 N LEU F 84 SHEET 3 AB6 6 TRP F 104 GLY F 107 -1 N GLY F 107 O ARG F 237 SHEET 4 AB6 6 SER F 116 ASN F 121 -1 O LEU F 117 N PHE F 106 SHEET 5 AB6 6 VAL F 126 PHE F 135 -1 O LYS F 129 N LEU F 118 SHEET 6 AB6 6 GLU F 169 SER F 172 -1 O SER F 172 N VAL F 126 SHEET 1 AB7 2 LEU F 141 ASP F 145 0 SHEET 2 AB7 2 ALA F 243 LEU F 244 1 O LEU F 244 N LEU F 141 SSBOND 1 CYS D 22 CYS D 96 1555 1555 2.03 SSBOND 2 CYS A 23 CYS A 88 1555 1555 2.04 SSBOND 3 CYS A 134 CYS A 194 1555 1555 2.03 SSBOND 4 CYS B 22 CYS B 95 1555 1555 2.03 SSBOND 5 CYS F 131 CYS F 166 1555 1555 2.03 SSBOND 6 CYS F 291 CYS F 301 1555 1555 2.03 LINK ND2 ASN F 61 C1 NAG F 405 1555 1555 1.44 LINK ND2 ASN F 122 C1 NAG F 401 1555 1555 1.44 LINK ND2 ASN F 165 C1 NAG F 402 1555 1555 1.45 LINK ND2 ASN F 234 C1 NAG F 404 1555 1555 1.44 LINK ND2 ASN F 282 C1 NAG F 403 1555 1555 1.44 CISPEP 1 SER A 7 PRO A 8 0 -3.62 CISPEP 2 LEU A 94 PRO A 95 0 1.96 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