HEADER VIRAL PROTEIN/IMMUNE SYSTEM 05-SEP-22 8GSB TITLE SARS-COV-2 BA.1 SPIKE INCOMPLEX WITH VACBB-665 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 VACBB-665; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: LIGHT CHAIN OF VACBB-665; COMPND 11 CHAIN: K; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: S, 2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR C.C.LIU,B.JU,S.L.SHEN,Z.ZHANG REVDAT 1 06-SEP-23 8GSB 0 JRNL AUTH C.C.LIU,B.JU,S.L.SHEN,Z.ZHANG JRNL TITL COMPLEX OF SARS-COV-2 SPIKE BA.1 AND VACBB-665 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SERIALEM, GCTF, UCSF CHIMERA, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7T9L REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT 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) : 3.990 REMARK 3 NUMBER OF PARTICLES : 164748 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 8GSB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300032030. 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 SARS-COV-2 BA.1 REMARK 245 SPIKE RBD AND VACBB-665; SARS- REMARK 245 COV-2 BA.1 SPIKE RBD; VACBB-665 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.20 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FOR 5S, WAITING FOR 2.5S, REMARK 245 BLOT FORCE 0 REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 4354 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 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, H, K 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 ARG A 319 REMARK 465 VAL A 320 REMARK 465 GLN A 321 REMARK 465 PRO A 322 REMARK 465 THR A 323 REMARK 465 GLU A 324 REMARK 465 SER A 325 REMARK 465 ILE A 326 REMARK 465 VAL A 327 REMARK 465 ARG A 328 REMARK 465 PHE A 329 REMARK 465 PRO A 330 REMARK 465 ASN A 331 REMARK 465 ILE A 332 REMARK 465 THR A 333 REMARK 465 ASN A 334 REMARK 465 LEU A 335 REMARK 465 CYS A 336 REMARK 465 PRO A 337 REMARK 465 LEU A 367A REMARK 465 TYR A 367B REMARK 465 ASN A 367C REMARK 465 LEU A 367D REMARK 465 ALA A 367E REMARK 465 PRO A 367F REMARK 465 PHE A 367G REMARK 465 LEU A 518 REMARK 465 HIS A 519 REMARK 465 ALA A 520 REMARK 465 PRO A 521 REMARK 465 ALA A 522 REMARK 465 THR A 523 REMARK 465 VAL A 524 REMARK 465 CYS A 525 REMARK 465 GLY A 526 REMARK 465 PRO A 527 REMARK 465 LYS A 528 REMARK 465 LYS A 529 REMARK 465 SER A 530 REMARK 465 THR A 531 REMARK 465 ASN A 532 REMARK 465 LEU A 533 REMARK 465 VAL A 534 REMARK 465 LYS A 535 REMARK 465 ASN A 536 REMARK 465 LYS A 537 REMARK 465 CYS A 538 REMARK 465 VAL A 539 REMARK 465 ASN A 540 REMARK 465 PHE A 541 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 PHE A 342 -40.14 -152.26 REMARK 500 SER A 349 -168.83 -77.21 REMARK 500 TRP A 353 143.02 -173.56 REMARK 500 ARG A 355 -168.63 -118.62 REMARK 500 THR A 393 -13.75 78.45 REMARK 500 SER A 469 115.83 -160.74 REMARK 500 GLN A 474 131.12 79.95 REMARK 500 LYS A 478 69.09 -114.61 REMARK 500 CYS A 480 40.78 -103.19 REMARK 500 ASN A 487 -1.43 61.72 REMARK 500 PHE H 29 -4.92 73.89 REMARK 500 ILE H 48 -63.65 -125.03 REMARK 500 GLU H 66 -6.76 74.85 REMARK 500 THR H 91 107.27 -57.61 REMARK 500 THR H 104 -70.81 61.95 REMARK 500 ASN H 105 172.00 -56.25 REMARK 500 ALA K 52 -7.14 74.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34226 RELATED DB: EMDB REMARK 900 RELATED ID: 8GS9 RELATED DB: PDB REMARK 900 RELATED ID: EMD-34228 RELATED DB: EMDB REMARK 900 SARS-COV-2 BA.1 SPIKE INCOMPLEX WITH VACBB-665 DBREF 8GSB A 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 DBREF 8GSB H 2 121 PDB 8GSB 8GSB 2 121 DBREF 8GSB K 1 107 PDB 8GSB 8GSB 1 107 SEQADV 8GSB ASP A 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 8GSB LEU A 367D UNP P0DTC2 SER 371 VARIANT SEQADV 8GSB PRO A 367F UNP P0DTC2 SER 373 VARIANT SEQADV 8GSB PHE A 368 UNP P0DTC2 SER 375 VARIANT SEQADV 8GSB ASN A 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 8GSB LYS A 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 8GSB SER A 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 8GSB ASN A 477 UNP P0DTC2 SER 477 VARIANT SEQADV 8GSB LYS A 478 UNP P0DTC2 THR 478 VARIANT SEQADV 8GSB ALA A 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 8GSB ARG A 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 8GSB SER A 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 8GSB ARG A 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 8GSB TYR A 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 8GSB HIS A 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 A 223 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 A 223 ILE THR ASN LEU CYS PRO PHE ASP GLU VAL PHE ASN ALA SEQRES 3 A 223 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 A 223 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 A 223 LEU ALA PRO PHE PHE THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 A 223 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 A 223 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 A 223 ILE ALA PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN SEQRES 9 A 223 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 A 223 TRP ASN SER ASN LYS LEU ASP SER LYS VAL SER GLY ASN SEQRES 11 A 223 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 A 223 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 A 223 ALA GLY ASN LYS PRO CYS ASN GLY VAL ALA GLY PHE ASN SEQRES 14 A 223 CYS TYR PHE PRO LEU ARG SER TYR SER PHE ARG PRO THR SEQRES 15 A 223 TYR GLY VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 A 223 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 A 223 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL SEQRES 18 A 223 ASN PHE SEQRES 1 H 120 MET GLN LEU VAL GLN SER GLY PRO GLU VAL LYS LYS PRO SEQRES 2 H 120 GLY SER SER VAL ARG VAL SER CYS LYS ALA SER GLY PHE SEQRES 3 H 120 THR PHE THR PRO SER ALA VAL GLN TRP VAL ARG GLN ALA SEQRES 4 H 120 ARG GLY GLN ARG LEU GLU TRP ILE GLY TRP ILE VAL VAL SEQRES 5 H 120 GLY SER GLY ASN THR ASN TYR ALA GLN LYS PHE GLN GLU SEQRES 6 H 120 ARG VAL THR ILE THR ARG ASP MET SER THR GLY THR VAL SEQRES 7 H 120 TYR MET ASP LEU SER SER LEU ARG SER GLU ASP THR ALA SEQRES 8 H 120 CYS TYR TYR CYS ALA ALA PRO HIS CYS ASN ARG THR ASN SEQRES 9 H 120 CYS TYR ASP GLY PHE ASP LEU TRP GLY GLN GLY THR VAL SEQRES 10 H 120 VAL THR VAL SEQRES 1 K 107 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 K 107 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 K 107 GLN SER VAL SER SER SER TYR LEU ALA TRP TYR GLN GLN SEQRES 4 K 107 LYS PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SEQRES 5 K 107 SER SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY SEQRES 6 K 107 THR GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG SEQRES 7 K 107 LEU GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN SEQRES 8 K 107 TYR GLY ARG SER PRO TRP THR PHE GLY GLN GLY THR LYS SEQRES 9 K 107 VAL GLU ILE HELIX 1 AA1 ASP A 405 ALA A 411 5 7 HELIX 2 AA2 ARG H 87 THR H 91 5 5 HELIX 3 AA3 GLU K 80 PHE K 84 5 5 SHEET 1 AA1 4 LYS A 378 CYS A 379 0 SHEET 2 AA1 4 GLY A 431 ASN A 437 -1 O VAL A 433 N LYS A 378 SHEET 3 AA1 4 PRO A 507 GLU A 516 -1 O VAL A 511 N ILE A 434 SHEET 4 AA1 4 ASN A 394 ALA A 397 -1 N TYR A 396 O SER A 514 SHEET 1 AA2 4 LYS A 378 CYS A 379 0 SHEET 2 AA2 4 GLY A 431 ASN A 437 -1 O VAL A 433 N LYS A 378 SHEET 3 AA2 4 PRO A 507 GLU A 516 -1 O VAL A 511 N ILE A 434 SHEET 4 AA2 4 PHE A 400 ARG A 403 -1 N ILE A 402 O TYR A 508 SHEET 1 AA3 2 LEU A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O ARG A 493 N TYR A 453 SHEET 1 AA4 4 VAL H 5 GLN H 6 0 SHEET 2 AA4 4 SER H 17 LYS H 23 -1 O LYS H 23 N VAL H 5 SHEET 3 AA4 4 THR H 78 SER H 84 -1 O LEU H 83 N VAL H 18 SHEET 4 AA4 4 VAL H 68 ASP H 73 -1 N THR H 71 O TYR H 80 SHEET 1 AA5 6 GLU H 10 VAL H 11 0 SHEET 2 AA5 6 THR H 117 THR H 120 1 O VAL H 118 N GLU H 10 SHEET 3 AA5 6 ALA H 92 ALA H 98 -1 N TYR H 94 O THR H 117 SHEET 4 AA5 6 ALA H 33 GLN H 39 -1 N GLN H 39 O CYS H 93 SHEET 5 AA5 6 GLU H 46 VAL H 52 -1 O GLU H 46 N ARG H 38 SHEET 6 AA5 6 THR H 58 TYR H 60 -1 O ASN H 59 N TRP H 50 SHEET 1 AA6 4 GLU H 10 VAL H 11 0 SHEET 2 AA6 4 THR H 117 THR H 120 1 O VAL H 118 N GLU H 10 SHEET 3 AA6 4 ALA H 92 ALA H 98 -1 N TYR H 94 O THR H 117 SHEET 4 AA6 4 LEU H 112 TRP H 113 -1 O LEU H 112 N ALA H 98 SHEET 1 AA7 4 THR K 5 SER K 7 0 SHEET 2 AA7 4 ALA K 19 ARG K 24 -1 O ARG K 24 N THR K 5 SHEET 3 AA7 4 ASP K 71 ILE K 76 -1 O PHE K 72 N CYS K 23 SHEET 4 AA7 4 PHE K 63 SER K 68 -1 N SER K 64 O THR K 75 SHEET 1 AA8 2 THR K 10 SER K 12 0 SHEET 2 AA8 2 LYS K 104 GLU K 106 1 O LYS K 104 N LEU K 11 SHEET 1 AA9 4 SER K 54 ARG K 55 0 SHEET 2 AA9 4 ARG K 46 TYR K 50 -1 N TYR K 50 O SER K 54 SHEET 3 AA9 4 LEU K 34 GLN K 39 -1 N TRP K 36 O LEU K 48 SHEET 4 AA9 4 VAL K 86 GLN K 91 -1 O GLN K 90 N ALA K 35 SSBOND 1 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 2 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 3 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 4 CYS H 101 CYS H 106 1555 1555 2.03 SSBOND 5 CYS K 23 CYS K 89 1555 1555 2.03 CISPEP 1 SER K 7 PRO K 8 0 -5.34 CISPEP 2 SER K 95 PRO K 96 0 0.70 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