HEADER VIRAL PROTEIN/IMMUNE SYSTEM 31-OCT-25 9XGW TITLE CRYO-EM STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX TITLE 2 WITH CS-42 FAB (LOCAL REFINEMENT OF RBD AND FV) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAVY CHAIN OF CS-42 FAB; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LIGHT CHAIN OF CS-42 FAB; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: E; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: SAMPLE SEQUENCE STARTS FROM 333 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 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 15 2; SOURCE 16 ORGANISM_TAXID: 2697049; SOURCE 17 GENE: S, 2; SOURCE 18 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS VIRAL PROTEIN, ANTIBODY, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR U.J.KIM,D.M.WANG,G.Y.YOON,H.S.CHO REVDAT 1 09-SEP-26 9XGW 0 JRNL AUTH D.S.KIM,U.KIM,H.M.WOO,H.LEE,E.S.JO,M.J.NOH,S.Y.LEE,B.K.PARK, JRNL AUTH 2 J.S.YANG,K.C.KIM,J.Y.LEE,D.M.WANG,H.S.CHO,H.J.KIM JRNL TITL BROAD NEUTRALIZING ACTIVITY OF MONOCLONAL ANTIBODIES AGAINST JRNL TITL 2 THE OMICRON VARIANTS ISOLATED FROM PATIENTS WITH EARLY JRNL TITL 3 SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS-2. JRNL REF J MED VIROL V. 98 70969 2026 JRNL REFN ISSN 1096-9071 JRNL PMID 42126192 JRNL DOI 10.1002/JMV.70969 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, TOPAZ, UCSF CHIMERAX, REMARK 3 PHENIX, CRYOSPARC, 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 : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 37804 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 9XGW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-NOV-25. REMARK 100 THE DEPOSITION ID IS D_1300064988. 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 : SARS-COV-2 RECEPTOR BINDING REMARK 245 DOMAIN IN COMPLEX WITH CS-42 REMARK 245 FAB; SARS-COV-2 RECEPTOR REMARK 245 BINDING DOMAIN; CS-42FAB REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.05 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 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 : FEI FALCON IV (4K X 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 : 105000 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, E 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 GLU B 1 REMARK 465 ILE B 2 REMARK 465 THR E 333 REMARK 465 ASN E 334 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 A 52 -169.25 -78.32 REMARK 500 ASN A 54 47.61 -87.04 REMARK 500 SER A 55 23.77 49.02 REMARK 500 GLN B 27 174.91 65.06 REMARK 500 SER B 30 -156.40 59.71 REMARK 500 ALA B 52 -0.69 67.49 REMARK 500 LEU B 96 -139.31 39.51 REMARK 500 LEU B 97 -172.12 -172.66 REMARK 500 ALA E 352 63.07 -100.36 REMARK 500 SER E 438 33.34 -140.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-66860 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX REMARK 900 WITH CS-42 FAB (LOCAL REFINEMENT OF RBD AND FV) DBREF 9XGW A 1 127 PDB 9XGW 9XGW 1 127 DBREF 9XGW B 1 109 PDB 9XGW 9XGW 1 109 DBREF 9XGW E 333 516 UNP P0DTC2 SPIKE_SARS2 333 516 SEQRES 1 A 127 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 127 PRO GLY ARG SER LEU LYS LEU SER CYS ALA ALA SER GLY SEQRES 3 A 127 PHE THR PHE ASP ASN TYR ALA MET HIS TRP VAL ARG GLN SEQRES 4 A 127 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER GLY SER SER SEQRES 5 A 127 TRP ASN SER GLY THR ILE GLY TYR ALA ASP SER VAL LYS SEQRES 6 A 127 GLY ARG PHE ILE ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 A 127 LEU HIS LEU GLN MET ASN ARG LEU ARG VAL GLU ASP THR SEQRES 8 A 127 ALA LEU TYR TYR CYS ALA LYS ASP LEU SER GLY ASP GLU SEQRES 9 A 127 TYR ASP TYR ASP SER SER GLY LEU GLY PHE ASP TYR TRP SEQRES 10 A 127 GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 1 B 109 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 B 109 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 B 109 GLN SER VAL SER SER SER TYR LEU ALA TRP TYR GLN GLN SEQRES 4 B 109 LYS PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SEQRES 5 B 109 SER SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY SEQRES 6 B 109 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG SEQRES 7 B 109 LEU GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN SEQRES 8 B 109 TYR GLY SER SER LEU LEU PHE THR PHE GLY PRO GLY THR SEQRES 9 B 109 LYS VAL GLU ILE LYS SEQRES 1 E 184 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 E 184 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 E 184 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 E 184 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 E 184 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 E 184 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 E 184 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 E 184 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 E 184 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 E 184 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 E 184 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 E 184 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 E 184 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 E 184 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 E 184 PHE GLU HET NAG E 601 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 ASP A 62 LYS A 65 5 4 HELIX 2 AA2 ARG A 87 THR A 91 5 5 HELIX 3 AA3 PRO E 337 ASN E 343 1 7 HELIX 4 AA4 TYR E 365 ALA E 372 1 8 HELIX 5 AA5 SER E 383 LEU E 387 5 5 HELIX 6 AA6 ASP E 405 ILE E 410 5 6 HELIX 7 AA7 GLY E 416 ASN E 422 1 7 HELIX 8 AA8 SER E 438 SER E 443 1 6 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O ALA A 23 N VAL A 5 SHEET 3 AA1 4 SER A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N ILE A 69 O GLN A 82 SHEET 1 AA2 6 GLY A 10 LEU A 11 0 SHEET 2 AA2 6 THR A 121 THR A 124 1 O THR A 124 N GLY A 10 SHEET 3 AA2 6 ALA A 92 LYS A 98 -1 N TYR A 94 O THR A 121 SHEET 4 AA2 6 MET A 34 GLN A 39 -1 N GLN A 39 O LEU A 93 SHEET 5 AA2 6 LEU A 45 SER A 51 -1 O GLU A 46 N ARG A 38 SHEET 6 AA2 6 THR A 57 TYR A 60 -1 O ILE A 58 N GLY A 50 SHEET 1 AA3 2 LEU B 4 GLN B 6 0 SHEET 2 AA3 2 CYS B 23 ALA B 25 -1 O ARG B 24 N THR B 5 SHEET 1 AA4 5 LEU B 11 SER B 12 0 SHEET 2 AA4 5 THR B 104 GLU B 107 1 O GLU B 107 N LEU B 11 SHEET 3 AA4 5 VAL B 86 GLN B 91 -1 N TYR B 87 O THR B 104 SHEET 4 AA4 5 LEU B 34 GLN B 39 -1 N GLN B 39 O VAL B 86 SHEET 5 AA4 5 ARG B 46 TYR B 50 -1 O ARG B 46 N GLN B 38 SHEET 1 AA5 3 ALA B 19 THR B 20 0 SHEET 2 AA5 3 THR B 73 ILE B 76 -1 O ILE B 76 N ALA B 19 SHEET 3 AA5 3 PHE B 63 SER B 66 -1 N SER B 66 O THR B 73 SHEET 1 AA6 5 ASN E 354 ILE E 358 0 SHEET 2 AA6 5 VAL E 395 ARG E 403 -1 O ALA E 397 N LYS E 356 SHEET 3 AA6 5 PRO E 507 LEU E 513 -1 O VAL E 510 N PHE E 400 SHEET 4 AA6 5 CYS E 432 ASN E 437 -1 N ILE E 434 O VAL E 511 SHEET 5 AA6 5 THR E 376 PHE E 377 -1 N THR E 376 O ALA E 435 SHEET 1 AA7 2 LEU E 452 ARG E 454 0 SHEET 2 AA7 2 LEU E 492 SER E 494 -1 O GLN E 493 N TYR E 453 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.03 SSBOND 2 CYS B 23 CYS B 89 1555 1555 2.03 SSBOND 3 CYS E 336 CYS E 361 1555 1555 2.03 SSBOND 4 CYS E 379 CYS E 432 1555 1555 2.03 SSBOND 5 CYS E 480 CYS E 488 1555 1555 2.03 LINK ND2 ASN E 343 C1 NAG E 601 1555 1555 1.44 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 CONECT 156 742 CONECT 742 156 CONECT 1125 1634 CONECT 1634 1125 CONECT 1805 2012 CONECT 1862 3247 CONECT 2012 1805 CONECT 2152 2565 CONECT 2565 2152 CONECT 2956 3013 CONECT 3013 2956 CONECT 3247 1862 3248 3258 CONECT 3248 3247 3249 3255 CONECT 3249 3248 3250 3256 CONECT 3250 3249 3251 3257 CONECT 3251 3250 3252 3258 CONECT 3252 3251 3259 CONECT 3253 3254 3255 3260 CONECT 3254 3253 CONECT 3255 3248 3253 CONECT 3256 3249 CONECT 3257 3250 CONECT 3258 3247 3251 CONECT 3259 3252 CONECT 3260 3253 MASTER 142 0 1 8 27 0 0 6 3257 3 25 34 END