HEADER VIRAL PROTEIN 19-DEC-22 8C0Y TITLE SARS-COV2 OMICRON BA.1 RBD IN COMPLEX WITH CAB-A17 ANTIBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S2'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CAB-A17 ANTIBODY (VARIABLE); COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: CAB-A17 ANTIBODY (VARIABLE); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: S, 2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS ANTIBODY, SPIKE, COMPLEX, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.DAS,B.M.HALLBERG REVDAT 2 03-JUL-24 8C0Y 1 JRNL REVDAT 1 19-JUN-24 8C0Y 0 JRNL AUTH D.J.SHEWARD,P.PUSHPARAJ,H.DAS,A.J.GREANEY,C.KIM,S.KIM, JRNL AUTH 2 L.HANKE,E.HYLLNER,R.DYRDAK,J.LEE,X.C.DOPICO,P.DOSENOVIC, JRNL AUTH 3 T.P.PEACOCK,G.M.MCINERNEY,J.ALBERT,M.CORCORAN,J.D.BLOOM, JRNL AUTH 4 B.MURRELL,G.B.KARLSSON HEDESTAM,B.M.HALLBERG JRNL TITL STRUCTURAL BASIS OF BROAD SARS-COV-2 CROSS-NEUTRALIZATION BY JRNL TITL 2 AFFINITY-MATURED PUBLIC ANTIBODIES. JRNL REF CELL REP MED V. 5 01577 2024 JRNL REFN ESSN 2666-3791 JRNL PMID 38761799 JRNL DOI 10.1016/J.XCRM.2024.101577 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.S.BOSE,R.H.SARMA REMARK 1 TITL DELINEATION OF THE INTIMATE DETAILS OF THE BACKBONE REMARK 1 TITL 2 CONFORMATION OF PYRIDINE NUCLEOTIDE COENZYMES IN AQUEOUS REMARK 1 TITL 3 SOLUTION. REMARK 1 REF BIOCHEM BIOPHYS RES COMMUN V. 66 1173 1975 REMARK 1 REFN ESSN 1090-2104 REMARK 1 DOI 10.1016/0006-291X(75)90482-9 REMARK 2 REMARK 2 RESOLUTION. 2.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, WARP, COOT, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7KSG REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 142.000 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) : 2.680 REMARK 3 NUMBER OF PARTICLES : 199751 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 8C0Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1292127474. 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-COV2 OMICRON BA.1 SPIKE IN REMARK 245 COMPLEX WITH CAB-A17 ANTIBODY; REMARK 245 SARS-COV-2 OMICRON RBD; CAB-A17 REMARK 245 ANTIBODY (FAB) REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.50 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 : 25652 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5460.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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, D, 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 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 ASN A 370 REMARK 465 SER A 371 REMARK 465 ALA A 372 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER A 359 OD1 ASN A 394 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 343 32.82 -96.58 REMARK 500 ASN A 481 18.22 56.44 REMARK 500 THR A 523 33.22 -141.04 REMARK 500 ARG D 18 148.12 -176.91 REMARK 500 ALA D 19 148.06 -174.07 REMARK 500 ALA D 51 -8.93 72.29 REMARK 500 GLU B 26 12.99 57.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG D 96 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-16375 RELATED DB: EMDB REMARK 900 SARS-COV2 OMICRON BA.1 RBD IN COMPLEX WITH CAB-A17 ANTIBODY DBREF 8C0Y A 334 526 UNP P0DTC2 SPIKE_SARS2 334 526 DBREF 8C0Y D 1 106 PDB 8C0Y 8C0Y 1 106 DBREF 8C0Y B 1 116 PDB 8C0Y 8C0Y 1 116 SEQADV 8C0Y ASP A 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 8C0Y PRO A 373 UNP P0DTC2 SER 373 VARIANT SEQADV 8C0Y PHE A 375 UNP P0DTC2 SER 375 VARIANT SEQADV 8C0Y ASN A 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 8C0Y LYS A 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 8C0Y SER A 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 8C0Y ASN A 477 UNP P0DTC2 SER 477 VARIANT SEQADV 8C0Y LYS A 478 UNP P0DTC2 THR 478 VARIANT SEQADV 8C0Y ALA A 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 8C0Y ARG A 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 8C0Y SER A 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 8C0Y ARG A 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 8C0Y TYR A 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 8C0Y HIS A 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 A 193 ASN LEU CYS PRO PHE ASP GLU VAL PHE ASN ALA THR ARG SEQRES 2 A 193 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 A 193 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 A 193 PRO PHE PHE THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 A 193 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 A 193 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 A 193 PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN TYR LYS SEQRES 8 A 193 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 A 193 SER ASN LYS LEU ASP SER LYS VAL SER GLY ASN TYR ASN SEQRES 10 A 193 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 A 193 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 A 193 ASN LYS PRO CYS ASN GLY VAL ALA GLY PHE ASN CYS TYR SEQRES 13 A 193 PHE PRO LEU ARG SER TYR SER PHE ARG PRO THR TYR GLY SEQRES 14 A 193 VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 A 193 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 1 D 106 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 D 106 SER PRO GLY GLU ARG ALA SER LEU SER CYS ARG ALA SER SEQRES 3 D 106 GLN SER LEU SER THR TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 D 106 PRO GLY GLN ALA PRO ARG LEU LEU ILE PHE GLY ALA SER SEQRES 5 D 106 SER ARG ALA SER GLY ILE PRO ASP ARG PHE SER GLY GLY SEQRES 6 D 106 GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG LEU SEQRES 7 D 106 GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN TYR SEQRES 8 D 106 GLY SER SER PRO ARG THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 D 106 GLU ILE SEQRES 1 B 116 ASP VAL HIS LEU VAL GLU SER GLY GLY GLY LEU ILE GLN SEQRES 2 B 116 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLU SEQRES 3 B 116 PHE ILE VAL SER ALA ASN TYR MET SER TRP VAL ARG GLN SEQRES 4 B 116 ALA PRO GLY GLU GLY LEU GLN TRP VAL SER VAL ILE TYR SEQRES 5 B 116 PRO GLY GLY SER THR PHE TYR ALA GLU SER VAL LYS GLY SEQRES 6 B 116 ARG PHE THR ILE SER ARG ASP ASN SER ARG ASN THR LEU SEQRES 7 B 116 TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR GLY SEQRES 8 B 116 VAL TYR TYR CYS ALA ARG ASP TYR GLY ASP PHE TYR PHE SEQRES 9 B 116 ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER 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 ASP A 364 LEU A 368 5 5 HELIX 4 AA4 SER A 383 LEU A 387 5 5 HELIX 5 AA5 ASP A 405 ILE A 410 5 6 HELIX 6 AA6 GLY A 416 ASN A 422 1 7 HELIX 7 AA7 GLU D 79 PHE D 83 5 5 HELIX 8 AA8 ILE B 28 ASN B 32 5 5 HELIX 9 AA9 ARG B 86 THR B 90 5 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O ALA A 397 N LYS A 356 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O TYR A 508 N ILE A 402 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 PHE A 375 TYR A 380 -1 N LYS A 378 O VAL A 433 SHEET 1 AA2 2 CYS A 391 PHE A 392 0 SHEET 2 AA2 2 VAL A 524 CYS A 525 -1 O VAL A 524 N PHE A 392 SHEET 1 AA3 2 LEU A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O ARG A 493 N TYR A 453 SHEET 1 AA4 2 TYR A 473 GLN A 474 0 SHEET 2 AA4 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA5 4 LEU D 4 GLN D 6 0 SHEET 2 AA5 4 SER D 20 ALA D 25 -1 O ARG D 24 N THR D 5 SHEET 3 AA5 4 ASP D 70 ILE D 75 -1 O PHE D 71 N CYS D 23 SHEET 4 AA5 4 PHE D 62 SER D 67 -1 N SER D 63 O THR D 74 SHEET 1 AA6 6 THR D 10 SER D 12 0 SHEET 2 AA6 6 THR D 102 GLU D 105 1 O GLU D 105 N LEU D 11 SHEET 3 AA6 6 VAL D 85 GLN D 90 -1 N TYR D 86 O THR D 102 SHEET 4 AA6 6 LEU D 33 GLN D 38 -1 N GLN D 38 O VAL D 85 SHEET 5 AA6 6 ARG D 45 PHE D 49 -1 O ARG D 45 N GLN D 37 SHEET 6 AA6 6 SER D 53 ARG D 54 -1 O SER D 53 N PHE D 49 SHEET 1 AA7 4 LEU B 4 SER B 7 0 SHEET 2 AA7 4 LEU B 18 ALA B 24 -1 O SER B 21 N SER B 7 SHEET 3 AA7 4 THR B 77 MET B 82 -1 O LEU B 80 N LEU B 20 SHEET 4 AA7 4 PHE B 67 ASP B 72 -1 N THR B 68 O GLN B 81 SHEET 1 AA8 6 LEU B 11 ILE B 12 0 SHEET 2 AA8 6 THR B 111 VAL B 115 1 O THR B 114 N ILE B 12 SHEET 3 AA8 6 GLY B 91 ASP B 98 -1 N GLY B 91 O VAL B 113 SHEET 4 AA8 6 MET B 34 GLN B 39 -1 N VAL B 37 O TYR B 94 SHEET 5 AA8 6 LEU B 45 ILE B 51 -1 O VAL B 48 N TRP B 36 SHEET 6 AA8 6 THR B 57 TYR B 59 -1 O PHE B 58 N VAL B 50 SHEET 1 AA9 4 LEU B 11 ILE B 12 0 SHEET 2 AA9 4 THR B 111 VAL B 115 1 O THR B 114 N ILE B 12 SHEET 3 AA9 4 GLY B 91 ASP B 98 -1 N GLY B 91 O VAL B 113 SHEET 4 AA9 4 PHE B 104 TRP B 107 -1 O ASP B 105 N ARG B 97 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 5 CYS D 23 CYS D 88 1555 1555 2.04 SSBOND 6 CYS B 22 CYS B 95 1555 1555 2.03 CISPEP 1 SER D 94 PRO D 95 0 2.28 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