HEADER VIRAL PROTEIN/IMMUNE SYSTEM 31-OCT-25 9XGX TITLE CRYO-EM STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX TITLE 2 WITH SR-23 FAB (LOCAL REFINEMENT OF RBD AND FV) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAVY CHAIN OF SR-23 FAB; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LIGHT CHAIN OF SR-23 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 9XGX 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. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, TOPAZ, UCSF CHIMERAX, REMARK 3 CRYOSPARC, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE 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) : 2.800 REMARK 3 NUMBER OF PARTICLES : 115041 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 9XGX 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_1300064973. 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 SR-23 REMARK 245 FAB; SARS-COV-2 RECEPTOR REMARK 245 BINDING DOMAIN; SR-23 FAB 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 : GATAN K3 BIOCONTINUUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1700.00 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) : 6760.00 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 THR E 333 REMARK 465 ASN E 334 REMARK 465 LEU E 335 REMARK 465 PRO E 527 REMARK 465 LYS E 528 REMARK 465 LYS E 529 REMARK 465 SER E 530 REMARK 465 THR E 531 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 30 -157.33 51.92 REMARK 500 ALA B 51 -4.96 73.42 REMARK 500 TYR B 91 53.35 -96.74 REMARK 500 PRO E 337 31.83 -88.08 REMARK 500 CYS E 361 -175.21 -173.71 REMARK 500 PHE E 374 174.32 59.62 REMARK 500 SER E 438 46.50 -141.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-66861 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN IN COMPLEX REMARK 900 WITH SR-23 FAB (LOCAL REFINEMENT OF RBD AND FV) DBREF 9XGX A 1 117 PDB 9XGX 9XGX 1 117 DBREF 9XGX B 1 109 PDB 9XGX 9XGX 1 109 DBREF 9XGX E 333 531 UNP P0DTC2 SPIKE_SARS2 333 531 SEQRES 1 A 117 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 A 117 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 117 PHE THR VAL SER SER ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 A 117 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE PHE SEQRES 5 A 117 ALA GLY GLY SER THR PHE TYR ALA ASP SER VAL LYS GLY SEQRES 6 A 117 ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 A 117 PHE LEU GLN LEU ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 A 117 VAL TYR TYR CYS ALA ARG GLU ALA ILE LEU ARG GLY THR SEQRES 9 A 117 PHE ASP TRP GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 1 B 109 GLU ILE VAL LEU THR GLN SER PRO VAL THR LEU SER VAL 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 ASN LEU ALA TRP TYR GLN GLN LYS SEQRES 4 B 109 PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SER SEQRES 5 B 109 THR ARG ALA THR GLY ILE PRO ALA ARG PHE SER GLY SER SEQRES 6 B 109 GLY SER GLY THR GLU PHE THR LEU THR ILE SER SER LEU SEQRES 7 B 109 GLN SER GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN TYR SEQRES 8 B 109 ASN ASN TRP PRO PRO GLY TYR THR PHE GLY GLN GLY THR SEQRES 9 B 109 LYS LEU GLU ILE LYS SEQRES 1 E 199 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 E 199 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 E 199 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 E 199 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 E 199 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 E 199 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 E 199 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 E 199 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 E 199 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 E 199 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 E 199 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 E 199 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 E 199 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 E 199 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 E 199 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 16 E 199 LYS LYS SER THR HET NAG E 601 27 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 ILE A 100 GLY A 103 5 4 HELIX 3 AA3 GLN B 79 PHE B 83 5 5 HELIX 4 AA4 PRO E 337 ASN E 343 1 7 HELIX 5 AA5 SER E 349 TRP E 353 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 GLY A 16 SER A 25 -1 O ALA A 23 N VAL A 5 SHEET 3 AA1 4 THR A 77 LEU A 85 -1 O LEU A 80 N LEU A 20 SHEET 4 AA1 4 ILE A 69 ASP A 72 -1 N ASP A 72 O THR A 77 SHEET 1 AA2 5 THR A 57 TYR A 59 0 SHEET 2 AA2 5 LEU A 45 ILE A 51 -1 N VAL A 50 O PHE A 58 SHEET 3 AA2 5 MET A 34 GLN A 39 -1 N MET A 34 O ILE A 51 SHEET 4 AA2 5 ALA A 91 ALA A 99 -1 O ALA A 96 N SER A 35 SHEET 5 AA2 5 THR A 104 ASP A 106 -1 O THR A 104 N ALA A 99 SHEET 1 AA3 5 THR A 57 TYR A 59 0 SHEET 2 AA3 5 LEU A 45 ILE A 51 -1 N VAL A 50 O PHE A 58 SHEET 3 AA3 5 MET A 34 GLN A 39 -1 N MET A 34 O ILE A 51 SHEET 4 AA3 5 ALA A 91 ALA A 99 -1 O ALA A 96 N SER A 35 SHEET 5 AA3 5 THR A 111 VAL A 113 -1 O VAL A 113 N ALA A 91 SHEET 1 AA4 6 THR B 10 VAL B 13 0 SHEET 2 AA4 6 THR B 104 ILE B 108 1 O GLU B 107 N VAL B 13 SHEET 3 AA4 6 VAL B 85 GLN B 90 -1 N TYR B 86 O THR B 104 SHEET 4 AA4 6 ALA B 34 GLN B 38 -1 N GLN B 38 O VAL B 85 SHEET 5 AA4 6 ARG B 45 TYR B 49 -1 O ILE B 48 N TRP B 35 SHEET 6 AA4 6 THR B 53 ARG B 54 -1 O THR B 53 N TYR B 49 SHEET 1 AA5 4 THR B 10 VAL B 13 0 SHEET 2 AA5 4 THR B 104 ILE B 108 1 O GLU B 107 N VAL B 13 SHEET 3 AA5 4 VAL B 85 GLN B 90 -1 N TYR B 86 O THR B 104 SHEET 4 AA5 4 THR B 99 PHE B 100 -1 O THR B 99 N GLN B 90 SHEET 1 AA6 3 ARG B 18 ARG B 24 0 SHEET 2 AA6 3 GLU B 70 SER B 76 -1 O ILE B 75 N ALA B 19 SHEET 3 AA6 3 PHE B 62 SER B 67 -1 N SER B 65 O THR B 72 SHEET 1 AA7 5 ASN E 354 ILE E 358 0 SHEET 2 AA7 5 ASN E 394 ARG E 403 -1 O VAL E 395 N ILE E 358 SHEET 3 AA7 5 PRO E 507 GLU E 516 -1 O VAL E 510 N PHE E 400 SHEET 4 AA7 5 CYS E 432 ASN E 437 -1 N TRP E 436 O ARG E 509 SHEET 5 AA7 5 THR E 376 CYS E 379 -1 N THR E 376 O ALA E 435 SHEET 1 AA8 2 LEU E 452 ARG E 454 0 SHEET 2 AA8 2 LEU E 492 SER E 494 -1 O GLN E 493 N TYR E 453 SHEET 1 AA9 2 TYR E 473 GLN E 474 0 SHEET 2 AA9 2 CYS E 488 TYR E 489 -1 O TYR E 489 N TYR E 473 SSBOND 1 CYS A 22 CYS A 95 1555 1555 2.03 SSBOND 2 CYS B 23 CYS B 88 1555 1555 2.04 SSBOND 3 CYS E 336 CYS E 361 1555 1555 2.02 SSBOND 4 CYS E 379 CYS E 432 1555 1555 2.03 SSBOND 5 CYS E 391 CYS E 525 1555 1555 2.03 SSBOND 6 CYS E 480 CYS E 488 1555 1555 2.03 LINK ND2 ASN E 343 C1 NAG E 601 1555 1555 1.44 CISPEP 1 TRP B 94 PRO B 95 0 -3.52 CISPEP 2 PRO B 95 PRO B 96 0 2.49 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 305 1417 CONECT 1417 305 CONECT 2087 3053 CONECT 3053 2087 CONECT 3404 3806 CONECT 3507 6341 CONECT 3806 3404 CONECT 4075 4879 CONECT 4254 6328 CONECT 4879 4075 CONECT 5647 5750 CONECT 5750 5647 CONECT 6328 4254 CONECT 6341 3507 6342 6352 CONECT 6342 6341 6343 6349 6355 CONECT 6343 6342 6344 6350 6356 CONECT 6344 6343 6345 6351 6357 CONECT 6345 6344 6346 6352 6358 CONECT 6346 6345 6353 6359 6360 CONECT 6347 6348 6349 6354 CONECT 6348 6347 6361 6362 6363 CONECT 6349 6342 6347 6364 CONECT 6350 6343 6365 CONECT 6351 6344 6366 CONECT 6352 6341 6345 CONECT 6353 6346 6367 CONECT 6354 6347 CONECT 6355 6342 CONECT 6356 6343 CONECT 6357 6344 CONECT 6358 6345 CONECT 6359 6346 CONECT 6360 6346 CONECT 6361 6348 CONECT 6362 6348 CONECT 6363 6348 CONECT 6364 6349 CONECT 6365 6350 CONECT 6366 6351 CONECT 6367 6353 MASTER 144 0 1 8 36 0 0 6 3246 3 40 34 END