HEADER VIRAL PROTEIN/IMMUNE SYSTEM 14-APR-25 9UHF TITLE JN.1 RBD IN COMPLEX WITH ANTIBODY BA5-12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECEPTOR-BINDING DOMAIN (RBD); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BA5-12-H; COMPND 8 CHAIN: I; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: BA5-12-L; COMPND 12 CHAIN: M; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 STRAIN: OMICRON/JN.1; SOURCE 7 GENE: S, 2; SOURCE 8 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; 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 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 9UHF 0 JRNL AUTH C.YUE,X.MAO JRNL TITL JN.1 RBD IN COMPLEX WITH ANTIBODY BA5-12 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.18 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) : 4.180 REMARK 3 NUMBER OF PARTICLES : 73940 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 9UHF 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_1300056489. 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 : JN.1 RBD IN COMPLEX WITH REMARK 245 ANTIBODY BA5-12 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 K3 (6K 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 : DARK 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, I, M, B 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 ASN A 334 39.06 -96.83 REMARK 500 LEU A 335 134.84 -38.42 REMARK 500 PHE A 374 150.22 -49.15 REMARK 500 LYS A 386 58.39 -95.24 REMARK 500 SER A 446 19.79 57.96 REMARK 500 ASN A 487 -8.13 66.66 REMARK 500 GLU I 26 -1.67 67.97 REMARK 500 VAL I 48 -62.17 -97.88 REMARK 500 ALA I 91 -174.66 -171.72 REMARK 500 ASN M 30 -111.75 38.44 REMARK 500 TYR M 32 42.92 -143.94 REMARK 500 ALA M 51 -4.47 62.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-64162 RELATED DB: EMDB REMARK 900 JN.1 RBD IN COMPLEX WITH ANTIBODY BA5-12 DBREF 9UHF A 332 530 UNP P0DTC2 SPIKE_SARS2 332 530 DBREF 9UHF I 1 119 PDB 9UHF 9UHF 1 119 DBREF 9UHF M 1 107 PDB 9UHF 9UHF 1 107 SEQADV 9UHF VAL A 332 UNP P0DTC2 ILE 332 CONFLICT SEQADV 9UHF HIS A 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 9UHF THR A 356 UNP P0DTC2 LYS 356 CONFLICT SEQADV 9UHF PHE A 371 UNP P0DTC2 SER 371 VARIANT SEQADV 9UHF PRO A 373 UNP P0DTC2 SER 373 VARIANT SEQADV 9UHF PHE A 375 UNP P0DTC2 SER 375 VARIANT SEQADV 9UHF ALA A 376 UNP P0DTC2 THR 376 VARIANT SEQADV 9UHF LYS A 403 UNP P0DTC2 ARG 403 CONFLICT SEQADV 9UHF ASN A 405 UNP P0DTC2 ASP 405 VARIANT SEQADV 9UHF SER A 408 UNP P0DTC2 ARG 408 VARIANT SEQADV 9UHF ASN A 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 9UHF LYS A 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 9UHF HIS A 445 UNP P0DTC2 VAL 445 CONFLICT SEQADV 9UHF SER A 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 9UHF ASP A 450 UNP P0DTC2 ASN 450 CONFLICT SEQADV 9UHF TRP A 452 UNP P0DTC2 LEU 452 CONFLICT SEQADV 9UHF SER A 455 UNP P0DTC2 LEU 455 CONFLICT SEQADV 9UHF LYS A 460 UNP P0DTC2 ASN 460 VARIANT SEQADV 9UHF ASN A 477 UNP P0DTC2 SER 477 VARIANT SEQADV 9UHF LYS A 478 UNP P0DTC2 THR 478 VARIANT SEQADV 9UHF LYS A 481 UNP P0DTC2 ASN 481 CONFLICT SEQADV 9UHF A UNP P0DTC2 VAL 483 DELETION SEQADV 9UHF LYS A 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 9UHF PRO A 486 UNP P0DTC2 PHE 486 VARIANT SEQADV 9UHF ARG A 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 9UHF TYR A 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 9UHF HIS A 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 A 198 VAL THR ASN LEU CYS PRO PHE HIS GLU VAL PHE ASN ALA SEQRES 2 A 198 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG THR ARG SEQRES 3 A 198 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 4 A 198 PHE ALA PRO PHE PHE ALA PHE LYS CYS TYR GLY VAL SER SEQRES 5 A 198 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 6 A 198 ALA ASP SER PHE VAL ILE LYS GLY ASN GLU VAL SER GLN SEQRES 7 A 198 ILE ALA PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN SEQRES 8 A 198 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 9 A 198 TRP ASN SER ASN LYS LEU ASP SER LYS HIS SER GLY ASN SEQRES 10 A 198 TYR ASP TYR TRP TYR ARG SER PHE ARG LYS SER LYS LEU SEQRES 11 A 198 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 12 A 198 ALA GLY ASN LYS PRO CYS LYS GLY LYS GLY PRO ASN CYS SEQRES 13 A 198 TYR PHE PRO LEU GLN SER TYR GLY PHE ARG PRO THR TYR SEQRES 14 A 198 GLY VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 A 198 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 16 A 198 LYS LYS SER SEQRES 1 I 119 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 I 119 PRO GLY GLY SER VAL ARG LEU SER CYS THR VAL SER GLU SEQRES 3 I 119 LEU ILE VAL SER ARG ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 I 119 SER PRO GLY ARG GLY LEU GLU TRP VAL SER LEU ILE TYR SEQRES 5 I 119 PRO GLY GLY SER SER TYR TYR ALA ASP SER VAL LYS GLY SEQRES 6 I 119 ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR LEU SEQRES 7 I 119 TYR LEU GLN MET ASN SER LEU ARG GLY GLU ASP THR ALA SEQRES 8 I 119 VAL TYR TYR CYS VAL ARG ASP MET VAL GLY ALA ARG ALA SEQRES 9 I 119 GLY MET GLU VAL TRP GLY GLN GLY THR THR VAL THR VAL SEQRES 10 I 119 SER SER SEQRES 1 M 107 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 M 107 SER VAL GLY ASP ARG VAL THR PHE THR CYS GLN ALA SER SEQRES 3 M 107 GLN ASP ILE ASN ILE TYR LEU ASN TRP TYR GLN GLN LYS SEQRES 4 M 107 THR GLY LYS ALA PRO LYS LEU LEU ILE TYR ASP ALA SER SEQRES 5 M 107 ASN LEU GLU THR GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 M 107 GLY SER GLY THR GLU PHE THR PHE THR ILE SER SER LEU SEQRES 7 M 107 GLN PRO GLU ASP ILE ALA THR TYR TYR CYS LEU GLN TYR SEQRES 8 M 107 ASP ASN LEU PRO ARG ALA PHE GLY GLN GLY THR LYS VAL SEQRES 9 M 107 GLU ILE LYS HET NAG B 1 14 HET NAG B 2 14 HET NAG A 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 3(C8 H15 N O6) HELIX 1 AA1 PRO A 337 ASN A 343 1 7 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 TYR A 365 ALA A 372 1 8 HELIX 4 AA4 PRO A 384 ASN A 388 5 5 HELIX 5 AA5 LYS A 403 ILE A 410 1 8 HELIX 6 AA6 ILE I 28 ASN I 32 5 5 HELIX 7 AA7 ASP I 61 LYS I 64 5 4 HELIX 8 AA8 GLN M 79 ILE M 83 5 5 SHEET 1 AA1 4 ARG A 357 ILE A 358 0 SHEET 2 AA1 4 VAL A 395 PHE A 400 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 4 TYR A 508 PHE A 515 -1 O VAL A 512 N ASP A 398 SHEET 4 AA1 4 VAL A 433 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 1 AA2 2 CYS A 361 VAL A 362 0 SHEET 2 AA2 2 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 1 AA3 2 TRP A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA4 4 LEU I 4 SER I 7 0 SHEET 2 AA4 4 SER I 17 VAL I 24 -1 O THR I 23 N VAL I 5 SHEET 3 AA4 4 THR I 77 ASN I 83 -1 O LEU I 80 N LEU I 20 SHEET 4 AA4 4 ILE I 69 ASP I 72 -1 N SER I 70 O TYR I 79 SHEET 1 AA5 6 LEU I 11 ILE I 12 0 SHEET 2 AA5 6 THR I 113 VAL I 117 1 N THR I 116 O ILE I 12 SHEET 3 AA5 6 ALA I 91 ARG I 97 -1 N ALA I 91 O VAL I 115 SHEET 4 AA5 6 MET I 34 GLN I 39 -1 N GLN I 39 O VAL I 92 SHEET 5 AA5 6 LEU I 45 ILE I 51 -1 O GLU I 46 N ARG I 38 SHEET 6 AA5 6 SER I 57 TYR I 59 -1 O TYR I 58 N LEU I 50 SHEET 1 AA6 4 THR M 5 SER M 7 0 SHEET 2 AA6 4 VAL M 19 GLN M 24 -1 O GLN M 24 N THR M 5 SHEET 3 AA6 4 GLU M 70 ILE M 75 -1 O ILE M 75 N VAL M 19 SHEET 4 AA6 4 PHE M 62 SER M 67 -1 N SER M 63 O THR M 74 SHEET 1 AA7 6 SER M 10 ALA M 13 0 SHEET 2 AA7 6 THR M 102 ILE M 106 1 O GLU M 105 N LEU M 11 SHEET 3 AA7 6 ALA M 84 GLN M 90 -1 N TYR M 86 O THR M 102 SHEET 4 AA7 6 LEU M 33 GLN M 38 -1 N ASN M 34 O LEU M 89 SHEET 5 AA7 6 LYS M 45 TYR M 49 -1 O LYS M 45 N GLN M 37 SHEET 6 AA7 6 ASN M 53 LEU M 54 -1 O ASN M 53 N TYR M 49 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.04 SSBOND 3 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 4 CYS I 22 CYS I 95 1555 1555 2.03 SSBOND 5 CYS M 23 CYS M 88 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG B 1 1555 1555 1.44 LINK ND2 ASN A 354 C1 NAG A 601 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 CISPEP 1 SER M 7 PRO M 8 0 -2.97 CISPEP 2 LEU M 94 PRO M 95 0 -2.80 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 36 247 CONECT 99 3330 CONECT 190 3358 CONECT 247 36 CONECT 396 801 CONECT 801 396 CONECT 1207 1254 CONECT 1254 1207 CONECT 1740 2326 CONECT 2326 1740 CONECT 2666 3175 CONECT 3175 2666 CONECT 3330 99 3331 3341 CONECT 3331 3330 3332 3338 CONECT 3332 3331 3333 3339 CONECT 3333 3332 3334 3340 CONECT 3334 3333 3335 3341 CONECT 3335 3334 3342 CONECT 3336 3337 3338 3343 CONECT 3337 3336 CONECT 3338 3331 3336 CONECT 3339 3332 CONECT 3340 3333 3344 CONECT 3341 3330 3334 CONECT 3342 3335 CONECT 3343 3336 CONECT 3344 3340 3345 3355 CONECT 3345 3344 3346 3352 CONECT 3346 3345 3347 3353 CONECT 3347 3346 3348 3354 CONECT 3348 3347 3349 3355 CONECT 3349 3348 3356 CONECT 3350 3351 3352 3357 CONECT 3351 3350 CONECT 3352 3345 3350 CONECT 3353 3346 CONECT 3354 3347 CONECT 3355 3344 3348 CONECT 3356 3349 CONECT 3357 3350 CONECT 3358 190 3359 3369 CONECT 3359 3358 3360 3366 CONECT 3360 3359 3361 3367 CONECT 3361 3360 3362 3368 CONECT 3362 3361 3363 3369 CONECT 3363 3362 3370 CONECT 3364 3365 3366 3371 CONECT 3365 3364 CONECT 3366 3359 3364 CONECT 3367 3360 CONECT 3368 3361 CONECT 3369 3358 3362 CONECT 3370 3363 CONECT 3371 3364 MASTER 126 0 3 8 28 0 0 6 3368 3 54 35 END