HEADER VIRAL PROTEIN/IMMUNE SYSTEM 28-JAN-22 7WS2 TITLE STRUCTURES OF OMICRON SPIKE COMPLEXES ILLUMINATE BROAD-SPECTRUM TITLE 2 NEUTRALIZING ANTIBODY DEVELOPMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 510A5 LIGHT CHAIN; COMPND 3 CHAIN: D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SPIKE PROTEIN S1; COMPND 7 CHAIN: A; COMPND 8 FRAGMENT: RBD; COMPND 9 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 510A5 HEAVY CHAIN; COMPND 13 CHAIN: E; COMPND 14 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: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 8 2; SOURCE 9 ORGANISM_TAXID: 2697049; SOURCE 10 GENE: S, 2; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS COVID-19, SPIKE GLYCOPROTEIN, VIRUS, VIRAL PROTEIN, ANTIBODY, VIRAL KEYWDS 2 PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR H.GUO,Y.GAO,X.JI,H.YANG REVDAT 1 01-JUN-22 7WS2 0 JRNL AUTH H.GUO,Y.GAO,T.LI,T.LI,Y.LU,L.ZHENG,Y.LIU,T.YANG,F.LUO, JRNL AUTH 2 S.SONG,W.WANG,X.YANG,H.C.NGUYEN,H.ZHANG,A.HUANG,A.JIN, JRNL AUTH 3 H.YANG,Z.RAO,X.JI JRNL TITL STRUCTURES OF OMICRON SPIKE COMPLEXES AND IMPLICATIONS FOR JRNL TITL 2 NEUTRALIZING ANTIBODY DEVELOPMENT. JRNL REF CELL REP V. 39 10770 2022 JRNL REFN ESSN 2211-1247 JRNL PMID 35477022 JRNL DOI 10.1016/J.CELREP.2022.110770 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 : 230655 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 7WS2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1300027333. 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 SPIKE GLYCOPROTEIN REMARK 245 COMPLEX WITH 510A5 FAB; SPIKE REMARK 245 GLYCOPROTEIN; FAB 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 : SARS-COV-2 SPIKE PROTEIN REMARK 245 ECTODOMAIN; FAB FRAGMENT GENERATED BY PROTEOLYTIC CLEAVAGE OF REMARK 245 IGG ANTIBODY 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 : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2800.00 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 : SPOT SCAN 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: D, A, 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS D 108 CG CD CE NZ REMARK 470 HIS A 519 CG ND1 CD2 CE1 NE2 REMARK 470 LYS E 43 CG CD CE NZ REMARK 470 LYS E 76 CG CD CE NZ 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 D 52 40.10 -140.77 REMARK 500 PRO D 80 5.09 -64.48 REMARK 500 ASN A 487 -4.13 69.76 REMARK 500 ASP E 90 31.91 -96.08 REMARK 500 THR E 91 33.22 -96.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32741 RELATED DB: EMDB REMARK 900 STRUCTURES OF OMICRON SPIKE COMPLEXES ILLUMINATE BROAD-SPECTRUM REMARK 900 NEUTRALIZING ANTIBODY DEVELOPMENT DBREF 7WS2 D 1 108 PDB 7WS2 7WS2 1 108 DBREF 7WS2 A 331 530 UNP P0DTC2 SPIKE_SARS2 331 530 DBREF 7WS2 E 1 123 PDB 7WS2 7WS2 1 123 SEQRES 1 D 108 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 D 108 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 D 108 GLN SER ILE SER SER TYR LEU ASN TRP PHE GLN HIS LYS SEQRES 4 D 108 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR GLY ALA SER SEQRES 5 D 108 SER LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 D 108 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 D 108 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SER SEQRES 8 D 108 TYR SER THR PRO PRO TYR THR PHE GLY GLN GLY THR LYS SEQRES 9 D 108 LEU GLU ILE LYS SEQRES 1 A 200 ASN ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN SEQRES 2 A 200 ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS SEQRES 3 A 200 ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR SEQRES 4 A 200 ASN SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SEQRES 5 A 200 SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL SEQRES 6 A 200 TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG SEQRES 7 A 200 GLN ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR SEQRES 8 A 200 ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE SEQRES 9 A 200 ALA TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY SEQRES 10 A 200 ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN SEQRES 11 A 200 LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR SEQRES 12 A 200 GLN ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE SEQRES 13 A 200 ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO SEQRES 14 A 200 THR ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL SEQRES 15 A 200 LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS SEQRES 16 A 200 GLY PRO LYS LYS SER SEQRES 1 E 123 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 E 123 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 E 123 PHE THR PHE ASP ASP TYR ALA MET HIS TRP VAL ARG GLN SEQRES 4 E 123 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER GLY ILE SER SEQRES 5 E 123 TRP ASN SER ASP SER ILE ASP TYR ALA ASP SER VAL LYS SEQRES 6 E 123 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 E 123 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 E 123 ALA LEU TYR TYR CYS ALA LYS ASP ARG GLY TYR GLU ILE SEQRES 9 E 123 LEU THR PRO ALA SER PHE ASP TYR TRP GLY GLN GLY THR SEQRES 10 E 123 LEU VAL THR VAL SER SER HELIX 1 AA1 PHE A 338 ASN A 343 1 6 HELIX 2 AA2 TYR A 365 SER A 371 1 7 HELIX 3 AA3 SER A 383 ASP A 389 5 7 HELIX 4 AA4 GLY A 404 ILE A 410 5 7 HELIX 5 AA5 GLY A 416 ASN A 422 1 7 HELIX 6 AA6 GLY A 502 GLN A 506 5 5 HELIX 7 AA7 THR E 28 TYR E 32 5 5 HELIX 8 AA8 ASP E 62 LYS E 65 5 4 HELIX 9 AA9 ARG E 87 THR E 91 5 5 SHEET 1 AA1 4 MET D 4 GLN D 6 0 SHEET 2 AA1 4 VAL D 19 ALA D 25 -1 O ARG D 24 N THR D 5 SHEET 3 AA1 4 ASP D 70 ILE D 75 -1 O LEU D 73 N ILE D 21 SHEET 4 AA1 4 SER D 63 SER D 67 -1 N SER D 65 O THR D 72 SHEET 1 AA2 2 SER D 10 LEU D 11 0 SHEET 2 AA2 2 LYS D 104 LEU D 105 1 O LYS D 104 N LEU D 11 SHEET 1 AA3 5 SER D 53 LEU D 54 0 SHEET 2 AA3 5 LYS D 45 TYR D 49 -1 N TYR D 49 O SER D 53 SHEET 3 AA3 5 LEU D 33 HIS D 38 -1 N GLN D 37 O LYS D 45 SHEET 4 AA3 5 THR D 85 GLN D 90 -1 O THR D 85 N HIS D 38 SHEET 5 AA3 5 THR D 98 PHE D 99 -1 O THR D 98 N GLN D 90 SHEET 1 AA4 5 LYS A 356 ILE A 358 0 SHEET 2 AA4 5 ASN A 394 ILE A 402 -1 O VAL A 395 N ILE A 358 SHEET 3 AA4 5 TYR A 508 GLU A 516 -1 O VAL A 510 N PHE A 400 SHEET 4 AA4 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA4 5 THR A 376 TYR A 380 -1 N LYS A 378 O VAL A 433 SHEET 1 AA5 2 CYS A 361 VAL A 362 0 SHEET 2 AA5 2 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 1 AA6 2 LEU A 452 ARG A 454 0 SHEET 2 AA6 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA7 4 LEU E 4 SER E 7 0 SHEET 2 AA7 4 LEU E 18 ALA E 24 -1 O ALA E 23 N VAL E 5 SHEET 3 AA7 4 SER E 78 MET E 83 -1 O LEU E 81 N LEU E 20 SHEET 4 AA7 4 PHE E 68 ASP E 73 -1 N ASP E 73 O SER E 78 SHEET 1 AA8 2 LEU E 11 VAL E 12 0 SHEET 2 AA8 2 THR E 120 VAL E 121 1 O THR E 120 N VAL E 12 SHEET 1 AA9 5 ILE E 58 TYR E 60 0 SHEET 2 AA9 5 LEU E 45 ILE E 51 -1 N GLY E 50 O ASP E 59 SHEET 3 AA9 5 MET E 34 GLN E 39 -1 N ARG E 38 O GLU E 46 SHEET 4 AA9 5 LEU E 93 ASP E 99 -1 O LEU E 93 N GLN E 39 SHEET 5 AA9 5 PHE E 110 TYR E 112 -1 O TYR E 112 N LYS E 98 SHEET 1 AB1 5 ILE E 58 TYR E 60 0 SHEET 2 AB1 5 LEU E 45 ILE E 51 -1 N GLY E 50 O ASP E 59 SHEET 3 AB1 5 MET E 34 GLN E 39 -1 N ARG E 38 O GLU E 46 SHEET 4 AB1 5 LEU E 93 ASP E 99 -1 O LEU E 93 N GLN E 39 SHEET 5 AB1 5 THR E 117 LEU E 118 -1 O THR E 117 N TYR E 94 SSBOND 1 CYS D 23 CYS D 88 1555 1555 2.04 SSBOND 2 CYS A 336 CYS A 361 1555 1555 2.02 SSBOND 3 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 4 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 5 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 6 CYS E 22 CYS E 96 1555 1555 2.04 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