HEADER VIRAL PROTEIN/IMMUNE SYSTEM 19-JAN-26 22PD TITLE CRYO EM STRUCTURE OF SARS-COV-2 (BA.4) RBD IN COMPLEX WITH THZ937 FAB TITLE 2 (LOCAL REFINE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: THZ937 FAB HEAVY CHAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: THZ937 FAB LIGHT CHAIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SARS-COV-2 BA.4 SPIKE RBD; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS; SOURCE 13 ORGANISM_TAXID: 2901879; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2;ANTIBODY;, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN- KEYWDS 2 IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR X.WANG,F.GUO REVDAT 1 16-SEP-26 22PD 0 JRNL AUTH Q.ZHANG,P.CHEN,F.GUO,R.ZHOU,R.GUO,X.GE,Q.YANG,X.XIE,W.XIA, JRNL AUTH 2 J.FAN,Z.YANG,Y.XU,H.HUANG,J.LI,H.WANG,H.LIAO,X.SHI,N.LIU, JRNL AUTH 3 Y.CHEN,Z.CHEN,J.MA,X.WANG,T.ZHANG,L.ZHANG JRNL TITL TWENTY-YEAR PERSISTENCE OF SARS-COV-1 IMMUNE IMPRINTING JRNL TITL 2 SHAPES ANTIBODY RESPONSES TO SARS-COV-2 INFECTION. JRNL REF IMMUNITY 2026 JRNL REFN ISSN 1074-7613 JRNL PMID 42705227 JRNL DOI 10.1016/J.IMMUNI.2026.08.009 REMARK 2 REMARK 2 RESOLUTION. 2.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, CRYOSPARC 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) : 2.950 REMARK 3 NUMBER OF PARTICLES : 537361 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 22PD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 28-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1300068914. 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 : CRYO EM STRUCTURE OF SARS-COV-2 REMARK 245 (BA.4) RBD IN COMPLEX WITH REMARK 245 THZ937 FAB (LOCAL REFINE) 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 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) : 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 PRO C 527 REMARK 465 THR C 531 REMARK 465 ASN C 532 REMARK 465 LEU C 533 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG C 355 CG CD NE CZ NH1 NH2 REMARK 470 ILE C 358 CG1 CG2 CD1 REMARK 470 VAL C 362 CG1 CG2 REMARK 470 ASP C 364 CG OD1 OD2 REMARK 470 VAL C 367 CG1 CG2 REMARK 470 GLN C 414 CG CD OE1 NE2 REMARK 470 ILE C 418 CG1 CG2 CD1 REMARK 470 LYS C 458 CG CD CE NZ REMARK 470 ILE C 468 CG1 CG2 CD1 REMARK 470 TYR C 473 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS C 528 CG CD CE NZ REMARK 470 LYS C 529 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASP B 82 OH TYR B 86 2.18 REMARK 500 OH TYR A 33 O VAL C 503 2.18 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 VAL A 48 -60.44 -120.47 REMARK 500 ASP A 55 47.90 32.90 REMARK 500 PHE A 103 -173.30 -170.54 REMARK 500 THR B 31 25.43 -144.20 REMARK 500 ALA B 51 -7.08 72.94 REMARK 500 PRO B 80 -3.40 -56.50 REMARK 500 SER B 91 30.52 -143.06 REMARK 500 ARG B 108 -163.35 -167.71 REMARK 500 THR B 109 108.39 -46.03 REMARK 500 ALA C 352 60.82 -102.77 REMARK 500 ALA C 372 65.89 35.89 REMARK 500 ALA C 376 -61.82 -109.69 REMARK 500 PHE C 377 -0.44 59.46 REMARK 500 CYS C 379 -159.75 -99.80 REMARK 500 TYR C 380 -38.05 -145.35 REMARK 500 ASP C 389 31.18 -88.83 REMARK 500 ASN C 422 -164.84 -100.03 REMARK 500 ASN C 481 -163.72 -79.67 REMARK 500 PRO C 491 46.93 -88.64 REMARK 500 LYS C 529 16.84 52.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-68583 RELATED DB: EMDB REMARK 900 CRYO EM STRUCTURE OF SARS-COV-2 (BA.4) RBD IN COMPLEX WITH THZ937 REMARK 900 FAB (LOCAL REFINE) DBREF 22PD A 1 128 PDB 22PD 22PD 1 128 DBREF 22PD B 1 112 PDB 22PD 22PD 1 112 DBREF 22PD C 334 533 PDB 22PD 22PD 334 533 SEQRES 1 A 128 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 A 128 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 128 PHE SER VAL SER THR ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 A 128 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE TYR SEQRES 5 A 128 GLY GLY ASP THR THR TYR TYR ALA ASP SER VAL ARG GLY SEQRES 6 A 128 ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 A 128 TYR LEU GLU MET ASN SER LEU ARG THR ASP ASP THR ALA SEQRES 8 A 128 VAL TYR TYR CYS ALA ARG ASP GLU GLY ARG TYR PHE ASP SEQRES 9 A 128 ILE TRP THR GLY HIS VAL GLY PRO ASN CYS PHE ASP TYR SEQRES 10 A 128 TRP GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 1 B 112 ASP ILE GLN LEU THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 B 112 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 B 112 GLN SER ILE SER THR TYR LEU ASN TRP TYR GLN GLN LYS SEQRES 4 B 112 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR GLY ALA SER SEQRES 5 B 112 ASN LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 B 112 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 B 112 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SER SEQRES 8 B 112 TYR ILE THR LEU VAL THR PHE GLY GLN GLY THR ARG LEU SEQRES 9 B 112 GLU ILE LYS ARG THR VAL ALA ALA SEQRES 1 C 200 ASN LEU CYS PRO PHE ASP GLU VAL PHE ASN ALA THR ARG SEQRES 2 C 200 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 C 200 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN PHE ALA SEQRES 4 C 200 PRO PHE PHE ALA PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 C 200 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 C 200 SER PHE VAL ILE ARG GLY ASN GLU VAL SER GLN ILE ALA SEQRES 7 C 200 PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN TYR LYS SEQRES 8 C 200 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 C 200 SER ASN LYS LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 C 200 TYR ARG TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 C 200 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 C 200 ASN LYS PRO CYS ASN GLY VAL ALA GLY VAL ASN CYS TYR SEQRES 13 C 200 PHE PRO LEU GLN SER TYR GLY PHE ARG PRO THR TYR GLY SEQRES 14 C 200 VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 C 200 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO LYS SEQRES 16 C 200 LYS SER THR ASN LEU HET NAG C1301 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 ARG A 86 THR A 90 5 5 HELIX 2 AA2 PHE C 338 ASN C 343 1 6 HELIX 3 AA3 ASP C 364 ALA C 372 1 9 HELIX 4 AA4 SER C 383 ASP C 389 1 7 HELIX 5 AA5 GLU C 406 ILE C 410 5 5 HELIX 6 AA6 GLY C 416 TYR C 421 1 6 HELIX 7 AA7 SER C 438 SER C 443 1 6 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 SER A 17 SER A 25 -1 O SER A 25 N GLN A 3 SHEET 3 AA1 4 THR A 77 ASN A 83 -1 O LEU A 80 N LEU A 20 SHEET 4 AA1 4 PHE A 67 ASP A 72 -1 N SER A 70 O TYR A 79 SHEET 1 AA2 2 LEU A 11 ILE A 12 0 SHEET 2 AA2 2 THR A 125 VAL A 126 1 O THR A 125 N ILE A 12 SHEET 1 AA3 5 THR A 56 TYR A 59 0 SHEET 2 AA3 5 GLU A 46 TYR A 52 -1 N VAL A 50 O TYR A 58 SHEET 3 AA3 5 TYR A 33 GLN A 39 -1 N TRP A 36 O SER A 49 SHEET 4 AA3 5 VAL A 92 ASP A 98 -1 O TYR A 94 N VAL A 37 SHEET 5 AA3 5 THR A 122 LEU A 123 -1 O THR A 122 N TYR A 93 SHEET 1 AA4 4 GLN B 6 SER B 7 0 SHEET 2 AA4 4 VAL B 19 ARG B 24 -1 O THR B 22 N SER B 7 SHEET 3 AA4 4 ASP B 70 ILE B 75 -1 O LEU B 73 N ILE B 21 SHEET 4 AA4 4 PHE B 62 SER B 67 -1 N SER B 63 O THR B 74 SHEET 1 AA5 6 SER B 10 ALA B 13 0 SHEET 2 AA5 6 THR B 102 ILE B 106 1 O GLU B 105 N ALA B 13 SHEET 3 AA5 6 THR B 85 GLN B 90 -1 N TYR B 86 O THR B 102 SHEET 4 AA5 6 LEU B 33 GLN B 38 -1 N GLN B 38 O THR B 85 SHEET 5 AA5 6 LYS B 45 TYR B 49 -1 O LEU B 47 N TRP B 35 SHEET 6 AA5 6 ASN B 53 LEU B 54 -1 O ASN B 53 N TYR B 49 SHEET 1 AA6 4 SER B 10 ALA B 13 0 SHEET 2 AA6 4 THR B 102 ILE B 106 1 O GLU B 105 N ALA B 13 SHEET 3 AA6 4 THR B 85 GLN B 90 -1 N TYR B 86 O THR B 102 SHEET 4 AA6 4 THR B 97 PHE B 98 -1 O THR B 97 N GLN B 90 SHEET 1 AA7 4 ASN C 354 ILE C 358 0 SHEET 2 AA7 4 ASN C 394 ARG C 403 -1 O VAL C 395 N ILE C 358 SHEET 3 AA7 4 PRO C 507 GLU C 516 -1 O VAL C 510 N PHE C 400 SHEET 4 AA7 4 CYS C 432 ALA C 435 -1 N CYS C 432 O LEU C 513 SHEET 1 AA8 2 TYR C 473 GLN C 474 0 SHEET 2 AA8 2 CYS C 488 TYR C 489 -1 O TYR C 489 N TYR C 473 SSBOND 1 CYS A 22 CYS A 95 1555 1555 2.04 SSBOND 2 CYS B 23 CYS B 88 1555 1555 2.04 SSBOND 3 CYS C 336 CYS C 361 1555 1555 2.03 SSBOND 4 CYS C 379 CYS C 432 1555 1555 2.07 SSBOND 5 CYS C 391 CYS C 525 1555 1555 2.03 SSBOND 6 CYS C 480 CYS C 488 1555 1555 2.04 LINK ND2 ASN C 343 C1 NAG C1301 1555 1555 1.44 CISPEP 1 GLY A 111 PRO A 112 0 -3.45 CISPEP 2 SER B 7 PRO B 8 0 -7.45 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 CONECT 152 729 CONECT 729 152 CONECT 1158 1658 CONECT 1658 1158 CONECT 1869 2071 CONECT 1930 3368 CONECT 2071 1869 CONECT 2213 2613 CONECT 2303 3346 CONECT 2613 2213 CONECT 2998 3047 CONECT 3047 2998 CONECT 3346 2303 CONECT 3368 1930 3369 3379 CONECT 3369 3368 3370 3376 CONECT 3370 3369 3371 3377 CONECT 3371 3370 3372 3378 CONECT 3372 3371 3373 3379 CONECT 3373 3372 3380 CONECT 3374 3375 3376 3381 CONECT 3375 3374 CONECT 3376 3369 3374 CONECT 3377 3370 CONECT 3378 3371 CONECT 3379 3368 3372 CONECT 3380 3373 CONECT 3381 3374 MASTER 176 0 1 7 31 0 0 6 3378 3 27 35 END