HEADER VIRAL PROTEIN/IMMUNE SYSTEM 14-APR-25 9UHH TITLE WT RBD IN COMPLEX WITH ANTIBODY BA5-12-GR COMPND MOL_ID: 1; COMPND 2 MOLECULE: BA5_12_H; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BA5_12_L; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: C; COMPND 12 FRAGMENT: RECEPTOR-BINDING DOMAIN (RBD); COMPND 13 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 2; SOURCE 14 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 15 ORGANISM_TAXID: 2697049; SOURCE 16 STRAIN: OMICRON/JN.1; SOURCE 17 GENE: S, 2; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, COMPLEX, VIRAL PROTEIN, ANTIBODY, VIRAL PROTEIN/IMMUNE KEYWDS 2 SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR C.YUE,X.MAO REVDAT 1 22-JUL-26 9UHH 0 JRNL AUTH C.YUE,X.MAO JRNL TITL WT RBD IN COMPLEX WITH ANTIBODY BA5-12-GR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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 : 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) : 4.050 REMARK 3 NUMBER OF PARTICLES : 2850 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9UHH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 23-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300056542. 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 : SEVERE ACUTE RESPIRATORY REMARK 245 SYNDROME CORONAVIRUS 2 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 : 7.40 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 : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 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 : 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 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 31 47.62 -95.50 REMARK 500 VAL A 48 -58.04 -120.10 REMARK 500 VAL A 100 48.97 33.94 REMARK 500 MET A 106 -13.97 -140.29 REMARK 500 ASN B 30 -128.31 58.08 REMARK 500 ALA C 352 58.00 -96.46 REMARK 500 SER C 477 -117.77 44.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-64164 RELATED DB: EMDB REMARK 900 WT RBD IN COMPLEX WITH ANTIBODY BA5-12-GR DBREF 9UHH A 1 119 PDB 9UHH 9UHH 1 119 DBREF 9UHH B 1 107 PDB 9UHH 9UHH 1 107 DBREF 9UHH C 334 528 UNP P0DTC2 SPIKE_SARS2 334 528 SEQRES 1 A 119 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 A 119 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 119 PHE THR VAL SER SER ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 A 119 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER VAL ILE TYR SEQRES 5 A 119 SER GLY GLY SER THR TYR TYR ALA ASP SER VAL LYS GLY SEQRES 6 A 119 ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 A 119 TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA SEQRES 8 A 119 VAL TYR TYR CYS ALA ARG ASP MET VAL GLY ALA ARG ALA SEQRES 9 A 119 GLY MET GLU VAL TRP GLY GLN GLY THR THR VAL THR VAL SEQRES 10 A 119 SER SER SEQRES 1 B 107 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 B 107 SER VAL GLY ASP ARG VAL THR PHE THR CYS GLN ALA SER SEQRES 3 B 107 GLN ASP ILE ASN ILE TYR LEU ASN TRP TYR GLN GLN LYS SEQRES 4 B 107 THR GLY LYS ALA PRO LYS LEU LEU ILE TYR ASP ALA SER SEQRES 5 B 107 ASN LEU GLU THR GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 B 107 GLY SER GLY THR GLU PHE THR PHE THR ILE SER SER LEU SEQRES 7 B 107 GLN PRO GLU ASP ILE ALA THR TYR TYR CYS LEU GLN TYR SEQRES 8 B 107 ASP ASN LEU PRO ARG ALA PHE GLY GLN GLY THR LYS VAL SEQRES 9 B 107 GLU ILE LYS SEQRES 1 C 195 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 2 C 195 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 C 195 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 C 195 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 C 195 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 C 195 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 C 195 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 8 C 195 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 C 195 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 C 195 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 C 195 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 C 195 SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 C 195 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 C 195 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 C 195 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO LYS HET NAG C1001 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 TYR C 365 ASN C 370 1 6 HELIX 4 AA4 ASP C 405 ILE C 410 5 6 HELIX 5 AA5 GLY C 416 ASN C 422 1 7 HELIX 6 AA6 GLY C 502 TYR C 505 5 4 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 SER A 17 SER A 25 -1 O ALA A 23 N VAL A 5 SHEET 3 AA1 4 THR A 77 ASN A 83 -1 O LEU A 80 N LEU A 20 SHEET 4 AA1 4 THR A 68 ASP A 72 -1 N SER A 70 O TYR A 79 SHEET 1 AA2 6 GLY A 10 ILE A 12 0 SHEET 2 AA2 6 THR A 113 VAL A 117 1 O THR A 116 N GLY A 10 SHEET 3 AA2 6 ALA A 91 ALA A 96 -1 N TYR A 93 O THR A 113 SHEET 4 AA2 6 MET A 34 GLN A 39 -1 N GLN A 39 O VAL A 92 SHEET 5 AA2 6 GLU A 46 ILE A 51 -1 O VAL A 48 N TRP A 36 SHEET 6 AA2 6 THR A 57 TYR A 59 -1 O TYR A 58 N VAL A 50 SHEET 1 AA3 2 THR B 5 GLN B 6 0 SHEET 2 AA3 2 CYS B 23 GLN B 24 -1 O GLN B 24 N THR B 5 SHEET 1 AA4 5 SER B 10 ALA B 13 0 SHEET 2 AA4 5 THR B 102 ILE B 106 1 O LYS B 103 N LEU B 11 SHEET 3 AA4 5 THR B 85 LEU B 89 -1 N TYR B 86 O THR B 102 SHEET 4 AA4 5 ASN B 34 GLN B 38 -1 N ASN B 34 O LEU B 89 SHEET 5 AA4 5 LYS B 45 TYR B 49 -1 O LEU B 47 N TRP B 35 SHEET 1 AA5 3 VAL B 19 PHE B 21 0 SHEET 2 AA5 3 THR B 72 ILE B 75 -1 O PHE B 73 N PHE B 21 SHEET 3 AA5 3 PHE B 62 SER B 65 -1 N SER B 65 O THR B 72 SHEET 1 AA6 5 ASN C 354 ILE C 358 0 SHEET 2 AA6 5 ASN C 394 ARG C 403 -1 O VAL C 395 N ILE C 358 SHEET 3 AA6 5 PRO C 507 GLU C 516 -1 O VAL C 510 N PHE C 400 SHEET 4 AA6 5 GLY C 431 ILE C 434 -1 N ILE C 434 O VAL C 511 SHEET 5 AA6 5 LYS C 378 TYR C 380 -1 N LYS C 378 O VAL C 433 SHEET 1 AA7 2 LEU C 452 TYR C 453 0 SHEET 2 AA7 2 GLN C 493 SER C 494 -1 O GLN C 493 N TYR C 453 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 C 336 CYS C 361 1555 1555 2.03 SSBOND 4 CYS C 379 CYS C 432 1555 1555 2.04 SSBOND 5 CYS C 391 CYS C 525 1555 1555 2.03 SSBOND 6 CYS C 480 CYS C 488 1555 1555 2.03 LINK ND2 ASN C 343 C1 NAG C1001 1555 1555 1.44 CISPEP 1 LEU B 94 PRO B 95 0 1.67 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 152 723 CONECT 723 152 CONECT 1062 1571 CONECT 1571 1062 CONECT 1748 1955 CONECT 1805 3273 CONECT 1955 1748 CONECT 2095 2508 CONECT 2185 3251 CONECT 2508 2095 CONECT 2899 2956 CONECT 2956 2899 CONECT 3251 2185 CONECT 3273 1805 3274 3284 CONECT 3274 3273 3275 3281 CONECT 3275 3274 3276 3282 CONECT 3276 3275 3277 3283 CONECT 3277 3276 3278 3284 CONECT 3278 3277 3285 CONECT 3279 3280 3281 3286 CONECT 3280 3279 CONECT 3281 3274 3279 CONECT 3282 3275 CONECT 3283 3276 CONECT 3284 3273 3277 CONECT 3285 3278 CONECT 3286 3279 MASTER 121 0 1 6 27 0 0 6 3283 3 27 34 END