HEADER VIRAL PROTEIN/IMMUNE SYSTEM 05-SEP-22 8GS9 TITLE SARS-COV-2 BA.2 SPIKE RBD IN COMPLEX BOUND WITH VACBB-551 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HEAVY CHAIN OF VACBB-551; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: LIGHT CHAIN OF VACBB-551; COMPND 12 CHAIN: K; COMPND 13 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 ANTIBODY, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR C.C.LIU,B.JU,S.L.SHEN,Z.ZHANG REVDAT 2 22-NOV-23 8GS9 1 JRNL REMARK REVDAT 1 03-MAY-23 8GS9 0 JRNL AUTH B.JU,Q.FAN,C.LIU,S.SHEN,M.WANG,H.GUO,B.ZHOU,X.GE,Z.ZHANG JRNL TITL OMICRON BQ.1.1 AND XBB.1 UNPRECEDENTEDLY ESCAPE BROADLY JRNL TITL 2 NEUTRALIZING ANTIBODIES ELICITED BY PROTOTYPE VACCINATION. JRNL REF CELL REP V. 42 12532 2023 JRNL REFN ESSN 2211-1247 JRNL PMID 37219999 JRNL DOI 10.1016/J.CELREP.2023.112532 REMARK 2 REMARK 2 RESOLUTION. 2.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, GCTF, UCSF CHIMERA, REMARK 3 PHENIX, CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7XB0 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : 53.800 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) : 2.660 REMARK 3 NUMBER OF PARTICLES : 506671 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 8GS9 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_1300032029. 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 SPIKE RBD REMARK 245 AND VACBB-551; SARS-COV-2 SPIKE REMARK 245 RBD; VACBB-551 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.20 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FOR 5S, WAIT FOR 2S, BLOT REMARK 245 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 : 6153 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K 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 : 105000 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 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 ASN A 360 13.56 97.06 REMARK 500 PHE A 371 51.22 -92.93 REMARK 500 TYR A 451 78.59 143.53 REMARK 500 LEU A 455 -60.19 -92.78 REMARK 500 GLU H 26 -5.93 77.44 REMARK 500 VAL H 48 -61.68 -107.64 REMARK 500 ASP H 65 -1.28 70.43 REMARK 500 SER K 10 141.42 -170.35 REMARK 500 ALA K 51 -8.40 75.28 REMARK 500 SER K 67 -173.78 -171.13 REMARK 500 ALA K 84 -168.64 -163.43 REMARK 500 GLU K 91 -114.59 54.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34226 RELATED DB: EMDB REMARK 900 SARS-COV-2 BA.2 SPIKE RBD IN COMPLEX BOUND WITH VACBB-551 DBREF 8GS9 A 337 517 UNP P0DTC2 SPIKE_SARS2 337 517 DBREF 8GS9 H 2 114 PDB 8GS9 8GS9 2 114 DBREF 8GS9 K 1 102 PDB 8GS9 8GS9 1 102 SEQADV 8GS9 ASP A 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 8GS9 PHE A 371 UNP P0DTC2 SER 371 VARIANT SEQADV 8GS9 PRO A 373 UNP P0DTC2 SER 373 VARIANT SEQADV 8GS9 PHE A 375 UNP P0DTC2 SER 375 VARIANT SEQADV 8GS9 ALA A 376 UNP P0DTC2 THR 376 VARIANT SEQADV 8GS9 ASN A 405 UNP P0DTC2 ASP 405 VARIANT SEQADV 8GS9 SER A 408 UNP P0DTC2 ARG 408 VARIANT SEQADV 8GS9 ASN A 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 8GS9 LYS A 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 8GS9 ASN A 477 UNP P0DTC2 SER 477 VARIANT SEQADV 8GS9 LYS A 478 UNP P0DTC2 THR 478 VARIANT SEQADV 8GS9 ALA A 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 8GS9 ARG A 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 8GS9 ARG A 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 8GS9 TYR A 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 8GS9 HIS A 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 A 181 PRO PHE ASP GLU VAL PHE ASN ALA THR ARG PHE ALA SER SEQRES 2 A 181 VAL TYR ALA TRP ASN ARG LYS ARG ILE SER ASN CYS VAL SEQRES 3 A 181 ALA ASP TYR SER VAL LEU TYR ASN PHE ALA PRO PHE PHE SEQRES 4 A 181 ALA PHE LYS CYS TYR GLY VAL SER PRO THR LYS LEU ASN SEQRES 5 A 181 ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SER PHE VAL SEQRES 6 A 181 ILE ARG GLY ASN GLU VAL SER GLN ILE ALA PRO GLY GLN SEQRES 7 A 181 THR GLY ASN ILE ALA ASP TYR ASN TYR LYS LEU PRO ASP SEQRES 8 A 181 ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SER ASN LYS SEQRES 9 A 181 LEU ASP SER LYS VAL GLY GLY ASN TYR ASN TYR LEU TYR SEQRES 10 A 181 ARG LEU PHE ARG LYS SER ASN LEU LYS PRO PHE GLU ARG SEQRES 11 A 181 ASP ILE SER THR GLU ILE TYR GLN ALA GLY ASN LYS PRO SEQRES 12 A 181 CYS ASN GLY VAL ALA GLY PHE ASN CYS TYR PHE PRO LEU SEQRES 13 A 181 ARG SER TYR GLY PHE ARG PRO THR TYR GLY VAL GLY HIS SEQRES 14 A 181 GLN PRO TYR ARG VAL VAL VAL LEU SER PHE GLU LEU SEQRES 1 H 113 VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN PRO SEQRES 2 H 113 GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLU ILE SEQRES 3 H 113 ILE VAL SER ARG ASN TYR MET ASN TRP VAL ARG GLN ALA SEQRES 4 H 113 PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE TYR ALA SEQRES 5 H 113 GLY GLY SER THR PHE TYR ALA ASP SER VAL LYS ASP ARG SEQRES 6 H 113 PHE THR ILE SER ARG ASP ASN SER LYS ASN THR LEU TYR SEQRES 7 H 113 LEU GLN MET ASN ARG LEU ARG ALA GLU ASP THR ALA VAL SEQRES 8 H 113 TYR TYR CYS ALA ARG SER LEU GLY ASP ARG PHE ASP PHE SEQRES 9 H 113 TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 1 K 102 ASP ILE GLN LEU THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 K 102 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 K 102 GLN GLY ILE PRO SER TYR LEU ALA TRP TYR GLN GLN ASN SEQRES 4 K 102 PRO GLY ARG ALA PRO LYS LEU LEU ILE TYR ALA ALA SER SEQRES 5 K 102 THR LEU GLN ASN GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 K 102 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 K 102 GLN SER GLU ASP PHE ALA THR TYR TYR CYS GLN HIS GLU SEQRES 8 K 102 ASP THR PHE GLY GLN GLY THR LYS LEU GLU ILE 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 TYR A 365 PHE A 371 1 7 HELIX 4 AA4 SER A 383 LEU A 390 5 8 HELIX 5 AA5 ASN A 405 ILE A 410 5 6 HELIX 6 AA6 GLY A 416 ASN A 422 1 7 HELIX 7 AA7 GLY A 502 HIS A 505 5 4 HELIX 8 AA8 ARG H 86 THR H 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 VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O VAL A 510 N PHE A 400 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 ALA A 376 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 1 AA2 2 LEU A 452 ARG A 454 0 SHEET 2 AA2 2 LEU A 492 SER A 494 -1 O ARG 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 H 3 SER H 7 0 SHEET 2 AA4 4 LEU H 18 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 AA4 4 THR H 77 MET H 82 -1 O MET H 82 N LEU H 18 SHEET 4 AA4 4 PHE H 67 ASP H 72 -1 N THR H 68 O GLN H 81 SHEET 1 AA5 5 THR H 57 TYR H 59 0 SHEET 2 AA5 5 LEU H 45 ILE H 51 -1 N VAL H 50 O PHE H 58 SHEET 3 AA5 5 TYR H 33 GLN H 39 -1 N ARG H 38 O GLU H 46 SHEET 4 AA5 5 ALA H 91 SER H 98 -1 O ALA H 96 N ASN H 35 SHEET 5 AA5 5 PHE H 103 TRP H 106 -1 O PHE H 105 N ARG H 97 SHEET 1 AA6 5 THR H 57 TYR H 59 0 SHEET 2 AA6 5 LEU H 45 ILE H 51 -1 N VAL H 50 O PHE H 58 SHEET 3 AA6 5 TYR H 33 GLN H 39 -1 N ARG H 38 O GLU H 46 SHEET 4 AA6 5 ALA H 91 SER H 98 -1 O ALA H 96 N ASN H 35 SHEET 5 AA6 5 THR H 110 VAL H 112 -1 O THR H 110 N TYR H 93 SHEET 1 AA7 4 LEU K 4 SER K 7 0 SHEET 2 AA7 4 VAL K 19 ALA K 25 -1 O ARG K 24 N THR K 5 SHEET 3 AA7 4 ASP K 70 ILE K 75 -1 O PHE K 71 N CYS K 23 SHEET 4 AA7 4 PHE K 62 SER K 67 -1 N SER K 63 O THR K 74 SHEET 1 AA8 6 LEU K 11 SER K 12 0 SHEET 2 AA8 6 THR K 98 GLU K 101 1 O LYS K 99 N LEU K 11 SHEET 3 AA8 6 THR K 85 HIS K 90 -1 N TYR K 86 O THR K 98 SHEET 4 AA8 6 ALA K 34 GLN K 38 -1 N GLN K 38 O THR K 85 SHEET 5 AA8 6 LYS K 45 TYR K 49 -1 O LYS K 45 N GLN K 37 SHEET 6 AA8 6 THR K 53 LEU K 54 -1 O THR K 53 N TYR K 49 SHEET 1 AA9 4 LEU K 11 SER K 12 0 SHEET 2 AA9 4 THR K 98 GLU K 101 1 O LYS K 99 N LEU K 11 SHEET 3 AA9 4 THR K 85 HIS K 90 -1 N TYR K 86 O THR K 98 SHEET 4 AA9 4 THR K 93 PHE K 94 -1 O THR K 93 N HIS K 90 SSBOND 1 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 2 CYS A 480 CYS A 488 1555 1555 2.04 SSBOND 3 CYS H 22 CYS H 95 1555 1555 2.04 SSBOND 4 CYS K 23 CYS K 88 1555 1555 2.04 CISPEP 1 ALA A 372 PRO A 373 0 -3.27 CISPEP 2 SER K 7 PRO K 8 0 -3.50 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