HEADER VIRAL PROTEIN/IMMUNE SYSTEM 11-DEC-23 8XE9 TITLE XBB.1.5 RBD IN COMPLEX WITH BD55-1205 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BD55-1205 HEAVY CHAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BD55-1205 LIGHT CHAIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S2'; COMPND 11 CHAIN: C; COMPND 12 FRAGMENT: RECEPTOR BINDING DOMAIN; 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 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 VARIANT: XBB.1.5; SOURCE 18 GENE: S, 2; SOURCE 19 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 21 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS SARS-COV-2, XBB.1.5, RBD, VIRAL PROTEIN, VIRAL PROTEIN-PROTEIN KEYWDS 2 BINDING COMPLEX, ANTIBODY, BD55-1205, VIRAL PROTEIN-IMMUNE SYSTEM KEYWDS 3 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR L.L.FENG REVDAT 2 24-APR-24 8XE9 1 COMPND REMARK SEQADV SEQRES REVDAT 2 2 1 HELIX SHEET SSBOND ATOM REVDAT 1 06-MAR-24 8XE9 0 JRNL AUTH L.L.FENG JRNL TITL XBB.1.5 RBD IN COMPLEX WITH BD55-1205 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 266321 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 8XE9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300043241. 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 : XBB.1.5 RBD IN COMPLEX WITH REMARK 245 BD55-1205; BD55-1205; XBB.1.5 REMARK 245 RBD 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 5200.00 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 ALA A 91 -169.11 -170.28 REMARK 500 LEU A 99 47.66 37.10 REMARK 500 ALA B 51 -6.26 71.58 REMARK 500 SER B 52 -3.18 -140.71 REMARK 500 SER B 77 112.70 -160.42 REMARK 500 SER B 80 -3.11 63.28 REMARK 500 TYR B 91 50.97 -94.79 REMARK 500 PRO B 95 31.08 -84.64 REMARK 500 ARG C 357 125.44 -39.82 REMARK 500 ALA C 363 123.21 -37.44 REMARK 500 ASN C 370 32.37 -94.65 REMARK 500 ALA C 372 154.99 67.94 REMARK 500 ALA C 484 59.15 -95.67 REMARK 500 PRO C 499 45.43 -78.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-38283 RELATED DB: EMDB REMARK 900 XBB.1.5 RBD IN COMPLEX WITH BD55-1205 DBREF 8XE9 A 1 117 PDB 8XE9 8XE9 1 117 DBREF 8XE9 B 1 107 PDB 8XE9 8XE9 1 107 DBREF 8XE9 C 334 529 UNP P0DTC2 SPIKE_SARS2 334 529 SEQADV 8XE9 HIS C 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 8XE9 THR C 346 UNP P0DTC2 ARG 346 VARIANT SEQADV 8XE9 ILE C 368 UNP P0DTC2 LEU 368 VARIANT SEQADV 8XE9 PHE C 371 UNP P0DTC2 SER 371 VARIANT SEQADV 8XE9 PRO C 373 UNP P0DTC2 SER 373 VARIANT SEQADV 8XE9 PHE C 375 UNP P0DTC2 SER 375 VARIANT SEQADV 8XE9 ALA C 376 UNP P0DTC2 THR 376 VARIANT SEQADV 8XE9 ASN C 405 UNP P0DTC2 ASP 405 VARIANT SEQADV 8XE9 SER C 408 UNP P0DTC2 ARG 408 VARIANT SEQADV 8XE9 ASN C 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 8XE9 LYS C 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 8XE9 PRO C 445 UNP P0DTC2 VAL 445 VARIANT SEQADV 8XE9 SER C 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 8XE9 LYS C 460 UNP P0DTC2 ASN 460 VARIANT SEQADV 8XE9 ASN C 477 UNP P0DTC2 SER 477 VARIANT SEQADV 8XE9 LYS C 478 UNP P0DTC2 THR 478 VARIANT SEQADV 8XE9 ALA C 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 8XE9 PRO C 486 UNP P0DTC2 PHE 486 VARIANT SEQADV 8XE9 SER C 490 UNP P0DTC2 PHE 490 VARIANT SEQADV 8XE9 ARG C 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 8XE9 TYR C 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 8XE9 HIS C 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 A 117 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 117 PRO GLY GLY SER LEU ARG LEU SER CYS ALA VAL SER GLY SEQRES 3 A 117 PHE THR VAL SER ARG ASN TYR MET THR TRP ALA ARG GLN SEQRES 4 A 117 ALA PRO GLY LYS GLY PRO GLU TRP VAL SER VAL ILE TYR SEQRES 5 A 117 PRO GLY GLY SER THR PHE TYR ALA ASP SER VAL LYS GLY SEQRES 6 A 117 ARG PHE THR ILE SER ARG ASP SER SER LYS ASN ILE LEU SEQRES 7 A 117 TYR LEU GLN MET ASN SER LEU ARG VAL ASP ASP THR ALA SEQRES 8 A 117 VAL TYR TYR CYS ALA ARG ASP LEU THR ILE ARG GLY GLU SEQRES 9 A 117 ALA SER TRP GLY GLN GLY THR LEU VAL THR VAL SER SER SEQRES 1 B 107 GLU ILE VAL MET THR GLN SER PRO ALA THR LEU ALA VAL SEQRES 2 B 107 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 B 107 GLU SER PHE ASN SER ASN LEU ALA TRP TYR GLN GLN LYS SEQRES 4 B 107 PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR GLY ALA SER SEQRES 5 B 107 THR ARG ALA SER ASP VAL PRO ALA ARG PHE SER GLY SER SEQRES 6 B 107 GLY SER GLY THR GLU PHE THR LEU THR ILE SER SER VAL SEQRES 7 B 107 GLN SER GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN TYR SEQRES 8 B 107 GLY ASP TRP PRO LEU TRP THR PHE GLY GLN GLY THR LYS SEQRES 9 B 107 VAL GLU ILE SEQRES 1 C 196 ASN LEU CYS PRO PHE HIS GLU VAL PHE ASN ALA THR THR SEQRES 2 C 196 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 C 196 ASN CYS VAL ALA ASP TYR SER VAL ILE TYR ASN PHE ALA SEQRES 4 C 196 PRO PHE PHE ALA PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 C 196 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 C 196 SER PHE VAL ILE ARG GLY ASN GLU VAL SER GLN ILE ALA SEQRES 7 C 196 PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN TYR LYS SEQRES 8 C 196 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 C 196 SER ASN LYS LEU ASP SER LYS PRO SER GLY ASN TYR ASN SEQRES 10 C 196 TYR LEU TYR ARG LEU PHE ARG LYS SER LYS LEU LYS PRO SEQRES 11 C 196 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 C 196 ASN LYS PRO CYS ASN GLY VAL ALA GLY PRO ASN CYS TYR SEQRES 13 C 196 SER PRO LEU GLN SER TYR GLY PHE ARG PRO THR TYR GLY SEQRES 14 C 196 VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 C 196 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO LYS SEQRES 16 C 196 LYS HELIX 1 AA1 ASP A 61 LYS A 64 5 4 HELIX 2 AA2 ARG A 86 THR A 90 5 5 HELIX 3 AA3 PHE C 338 ASN C 343 1 6 HELIX 4 AA4 SER C 349 TRP C 353 5 5 HELIX 5 AA5 SER C 383 LEU C 387 5 5 HELIX 6 AA6 ARG C 403 ILE C 410 5 8 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 25 N GLN A 3 SHEET 3 AA1 4 ILE A 77 MET A 82 -1 O LEU A 80 N LEU A 20 SHEET 4 AA1 4 PHE A 67 ASP A 72 -1 N THR A 68 O GLN A 81 SHEET 1 AA2 6 GLY A 10 VAL A 12 0 SHEET 2 AA2 6 THR A 111 VAL A 115 1 O THR A 114 N GLY A 10 SHEET 3 AA2 6 ALA A 91 ARG A 97 -1 N ALA A 91 O VAL 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 PRO A 45 ILE A 51 -1 O GLU A 46 N ARG A 38 SHEET 6 AA2 6 THR A 57 TYR A 59 -1 O PHE A 58 N VAL A 50 SHEET 1 AA3 4 GLY A 10 VAL A 12 0 SHEET 2 AA3 4 THR A 111 VAL A 115 1 O THR A 114 N GLY A 10 SHEET 3 AA3 4 ALA A 91 ARG A 97 -1 N ALA A 91 O VAL A 113 SHEET 4 AA3 4 SER A 106 TRP A 107 -1 O SER A 106 N ARG A 97 SHEET 1 AA4 4 MET B 4 GLN B 6 0 SHEET 2 AA4 4 CYS B 23 ALA B 25 -1 O ARG B 24 N THR B 5 SHEET 3 AA4 4 GLU B 70 ILE B 75 -1 O PHE B 71 N CYS B 23 SHEET 4 AA4 4 ALA B 19 THR B 20 -1 N ALA B 19 O ILE B 75 SHEET 1 AA5 4 MET B 4 GLN B 6 0 SHEET 2 AA5 4 CYS B 23 ALA B 25 -1 O ARG B 24 N THR B 5 SHEET 3 AA5 4 GLU B 70 ILE B 75 -1 O PHE B 71 N CYS B 23 SHEET 4 AA5 4 PHE B 62 SER B 65 -1 N SER B 63 O THR B 74 SHEET 1 AA6 2 LEU B 11 ALA B 12 0 SHEET 2 AA6 2 VAL B 105 GLU B 106 1 O GLU B 106 N LEU B 11 SHEET 1 AA7 5 THR B 53 ARG B 54 0 SHEET 2 AA7 5 ARG B 45 TYR B 49 -1 N TYR B 49 O THR B 53 SHEET 3 AA7 5 LEU B 33 GLN B 38 -1 N GLN B 37 O ARG B 45 SHEET 4 AA7 5 VAL B 85 ASP B 93 -1 O GLN B 89 N ALA B 34 SHEET 5 AA7 5 LEU B 96 THR B 98 -1 O LEU B 96 N ASP B 93 SHEET 1 AA8 4 CYS C 379 TYR C 380 0 SHEET 2 AA8 4 GLY C 431 CYS C 432 -1 O GLY C 431 N TYR C 380 SHEET 3 AA8 4 LEU C 513 GLU C 516 -1 O LEU C 513 N CYS C 432 SHEET 4 AA8 4 ASN C 394 ALA C 397 -1 N ASN C 394 O GLU C 516 SHEET 1 AA9 2 PHE C 400 ILE C 402 0 SHEET 2 AA9 2 TYR C 508 VAL C 510 -1 O TYR C 508 N ILE C 402 SHEET 1 AB1 2 LEU C 452 ARG C 454 0 SHEET 2 AB1 2 LEU C 492 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 2.03 SSBOND 3 CYS C 336 CYS C 361 1555 1555 2.03 SSBOND 4 CYS C 379 CYS C 432 1555 1555 2.03 SSBOND 5 CYS C 391 CYS C 525 1555 1555 2.03 SSBOND 6 CYS C 480 CYS C 488 1555 1555 2.03 CISPEP 1 SER B 7 PRO B 8 0 -0.79 CISPEP 2 TRP B 94 PRO B 95 0 3.64 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