HEADER PROTEIN BINDING 08-JAN-24 8XRQ TITLE SARS-COV-2 BA.1 SPIKE RBD IN COMPLEX BOUND WITH VACBB-639 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 639 FAB; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: LIGHT CHAIN OF VACBB 639 FAB; 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_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, PROTEIN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR C.C.LIU,B.JU,Z.ZHANG REVDAT 3 26-MAR-25 8XRQ 1 JRNL REVDAT 2 19-MAR-25 8XRQ 1 JRNL REVDAT 1 18-DEC-24 8XRQ 0 JRNL AUTH M.WANG,C.LIU,Q.FAN,Y.SUN,S.TANG,H.GUO,B.ZHOU,H.WANG,X.GE, JRNL AUTH 2 Z.ZHANG,B.JU JRNL TITL RAPID CLONAL EXPANSION AND SOMATIC HYPERMUTATION CONTRIBUTE JRNL TITL 2 TO THE FATE OF SARS-COV-2 BROADLY NEUTRALIZING ANTIBODIES. JRNL REF J IMMUNOL. V. 214 278 2025 JRNL REFN ESSN 1550-6606 JRNL PMID 40073246 JRNL DOI 10.1093/JIMMUN/VKAE056 REMARK 2 REMARK 2 RESOLUTION. 4.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : GAUTOMATCH, EPU, CTFFIND, 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 : NULL 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) : 4.190 REMARK 3 NUMBER OF PARTICLES : 104464 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 8XRQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300044038. 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-639; SARS-COV-2 SPIKE REMARK 245 RBD; VACBB-639 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 : 4899 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA 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 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 LEU A 517 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 465 ALA B 122 REMARK 465 LYS C 107 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 B 28 136.39 72.79 REMARK 500 SER B 30 -124.61 59.62 REMARK 500 PRO B 41 174.70 -56.67 REMARK 500 ILE B 48 -60.81 -90.88 REMARK 500 SER B 54 -168.36 -125.45 REMARK 500 ARG B 64 -51.00 -121.19 REMARK 500 SER B 103 -168.95 -113.96 REMARK 500 ASP B 107 -31.01 -131.70 REMARK 500 PRO C 8 -157.59 -87.81 REMARK 500 ARG C 18 176.41 -57.50 REMARK 500 GLN C 27 -67.45 -103.40 REMARK 500 SER C 28 116.64 -167.44 REMARK 500 PHE C 30 -100.32 54.27 REMARK 500 SER C 31 44.08 -141.85 REMARK 500 PRO C 44 -179.17 -68.55 REMARK 500 ALA C 51 -6.01 75.75 REMARK 500 PRO C 59 -174.99 -67.76 REMARK 500 SER C 67 46.90 -142.90 REMARK 500 GLU C 68 -20.66 67.11 REMARK 500 THR C 69 -17.40 -143.06 REMARK 500 PRO C 80 -12.96 -47.75 REMARK 500 GLU C 81 -166.53 -121.73 REMARK 500 SER C 92 -35.81 -149.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38610 RELATED DB: EMDB REMARK 900 SARS-COV-2 BA.1 SPIKE RBD IN COMPLEX BOUND WITH VACBB-639 DBREF 8XRQ A 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 DBREF 8XRQ B 1 122 PDB 8XRQ 8XRQ 1 122 DBREF 8XRQ C 1 107 PDB 8XRQ 8XRQ 1 107 SEQADV 8XRQ ASP A 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 8XRQ LEU A 371 UNP P0DTC2 SER 371 VARIANT SEQADV 8XRQ PRO A 373 UNP P0DTC2 SER 373 VARIANT SEQADV 8XRQ PHE A 375 UNP P0DTC2 SER 375 VARIANT SEQADV 8XRQ ASN A 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 8XRQ LYS A 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 8XRQ SER A 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 8XRQ ASN A 477 UNP P0DTC2 SER 477 VARIANT SEQADV 8XRQ LYS A 478 UNP P0DTC2 THR 478 VARIANT SEQADV 8XRQ ALA A 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 8XRQ ARG A 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 8XRQ SER A 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 8XRQ ARG A 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 8XRQ TYR A 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 8XRQ 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 B 122 GLN VAL GLN LEU GLN GLU SER GLY PRO GLY LEU VAL LYS SEQRES 2 B 122 PRO SER GLU THR LEU SER LEU THR CYS THR VAL SER GLY SEQRES 3 B 122 GLY SER ILE SER SER TYR TYR TRP SER TRP ILE ARG GLN SEQRES 4 B 122 SER PRO GLY LYS GLY LEU GLU TRP ILE GLY TYR VAL TYR SEQRES 5 B 122 ASN SER GLY GLY THR ASN TYR ASN PRO SER LEU ARG SER SEQRES 6 B 122 ARG VAL THR ILE SER VAL ASP THR SER LYS ASN HIS PHE SEQRES 7 B 122 SER LEU LYS LEU ARG SER VAL THR THR ALA ASP THR GLY SEQRES 8 B 122 VAL TYR TYR CYS ALA ARG ASP LEU GLY TYR SER SER GLY SEQRES 9 B 122 TRP PRO ASP ALA PHE ASP ILE TRP GLY GLN GLY LYS MET SEQRES 10 B 122 VAL THR VAL SER ALA SEQRES 1 C 107 GLU ILE VAL LEU THR GLN SER PRO ALA THR LEU SER LEU SEQRES 2 C 107 SER PRO GLY GLU ARG ALA THR LEU SER CYS THR ALA SER SEQRES 3 C 107 GLN SER VAL PHE SER TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 C 107 PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA PHE SEQRES 5 C 107 ASN ARG ALA THR GLY ILE PRO ALA ARG PHE SER GLY SER SEQRES 6 C 107 GLY SER GLU THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 C 107 GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN HIS SEQRES 8 C 107 SER ASN TRP PRO GLY THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 C 107 GLU ILE LYS HELIX 1 AA1 TYR A 365 LEU A 371 1 7 HELIX 2 AA2 ASP A 405 ALA A 411 5 7 HELIX 3 AA3 GLY A 416 TYR A 421 1 6 SHEET 1 AA1 5 ARG A 357 ILE A 358 0 SHEET 2 AA1 5 VAL A 395 ALA A 397 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 PHE A 515 -1 O SER A 514 N TYR A 396 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 CYS A 379 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 1 AA2 4 ARG A 357 ILE A 358 0 SHEET 2 AA2 4 VAL A 395 ALA A 397 -1 O VAL A 395 N ILE A 358 SHEET 3 AA2 4 PRO A 507 PHE A 515 -1 O SER A 514 N TYR A 396 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 TYR A 453 0 SHEET 2 AA3 2 ARG A 493 SER A 494 -1 O ARG A 493 N TYR A 453 SHEET 1 AA4 2 TYR A 473 GLN A 474 0 SHEET 2 AA4 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA5 5 THR B 57 TYR B 59 0 SHEET 2 AA5 5 GLU B 46 VAL B 51 -1 N TYR B 50 O ASN B 58 SHEET 3 AA5 5 TRP B 34 GLN B 39 -1 N TRP B 34 O VAL B 51 SHEET 4 AA5 5 VAL B 92 ASP B 98 -1 O ALA B 96 N SER B 35 SHEET 5 AA5 5 PHE B 109 TRP B 112 -1 O ASP B 110 N ARG B 97 SHEET 1 AA6 2 THR B 68 ILE B 69 0 SHEET 2 AA6 2 LEU B 80 LYS B 81 -1 O LYS B 81 N THR B 68 SHEET 1 AA7 2 ALA C 19 LEU C 21 0 SHEET 2 AA7 2 LEU C 73 ILE C 75 -1 O LEU C 73 N LEU C 21 SHEET 1 AA8 5 ASN C 53 ARG C 54 0 SHEET 2 AA8 5 ARG C 45 TYR C 49 -1 N TYR C 49 O ASN C 53 SHEET 3 AA8 5 LEU C 33 GLN C 38 -1 N TRP C 35 O LEU C 47 SHEET 4 AA8 5 VAL C 85 GLN C 90 -1 O TYR C 87 N TYR C 36 SHEET 5 AA8 5 THR C 97 PHE C 98 -1 O THR C 97 N GLN C 90 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 B 22 CYS B 95 1555 1555 2.04 SSBOND 4 CYS C 23 CYS C 88 1555 1555 2.04 CISPEP 1 ALA A 372 PRO A 373 0 -2.66 CISPEP 2 SER C 7 PRO C 8 0 -1.49 CISPEP 3 TRP C 94 PRO C 95 0 -4.11 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