HEADER VIRAL PROTEIN/IMMUNE SYSTEM 13-JAN-22 7WLC TITLE SARS-COV-2 OMICRON VARIANT SPIKE RBD IN COMPLEX WITH FAB XGV282 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: E; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HEAVY CHAIN OF XGV282; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: LIGHT CHAIN OF XGV282; COMPND 12 CHAIN: L; COMPND 13 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_TAXID: 9606; 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 SARS-COV-2, OMICRON, SPIKE-FAB COMPLEX, VIRAL PROTEIN, VIRAL PROTEIN- KEYWDS 2 IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR X.WANG,L.WANG REVDAT 2 04-MAY-22 7WLC 1 TITLE REVDAT 1 13-APR-22 7WLC 0 JRNL AUTH K.WANG,Z.JIA,L.BAO,L.WANG,L.CAO,H.CHI,Y.HU,Q.LI,Y.ZHOU, JRNL AUTH 2 Y.JIANG,Q.ZHU,Y.DENG,P.LIU,N.WANG,L.WANG,M.LIU,Y.LI,B.ZHU, JRNL AUTH 3 K.FAN,W.FU,P.YANG,X.PEI,Z.CUI,L.QIN,P.GE,J.WU,S.LIU,Y.CHEN, JRNL AUTH 4 W.HUANG,Q.WANG,C.F.QIN,Y.WANG,C.QIN,X.WANG JRNL TITL MEMORY B CELL REPERTOIRE FROM TRIPLE VACCINEES AGAINST JRNL TITL 2 DIVERSE SARS-COV-2 VARIANTS. JRNL REF NATURE V. 603 919 2022 JRNL REFN ESSN 1476-4687 JRNL PMID 35090164 JRNL DOI 10.1038/S41586-022-04466-X REMARK 2 REMARK 2 RESOLUTION. 4.00 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) : 4.000 REMARK 3 NUMBER OF PARTICLES : 119800 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7WLC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300026954. 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 OMICRON MUTATION REMARK 245 SPIKE PROTEIN IN COMPLEX WITH REMARK 245 FAB 265; SARS-COV-2 OMICRON REMARK 245 MUTATION SPIKE PROTEIN; FAB 265 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 : 8.50 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 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 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 : 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: E, H, L 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 ARG H 98 CG CD NE CZ NH1 NH2 REMARK 470 PHE H 105 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PHE H 106 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR H 107 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG L 51 CG CD NE CZ NH1 NH2 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 LYS E 386 30.58 -96.07 REMARK 500 TYR E 423 118.49 -162.69 REMARK 500 ASN E 487 -4.11 74.13 REMARK 500 LYS H 12 -169.14 -126.01 REMARK 500 ASP H 109 -62.13 -93.97 REMARK 500 ASN L 52 -2.77 68.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32581 RELATED DB: EMDB REMARK 900 SARS-COV-2 OMICRON VARIANT SPIKE PROTEIN IN COMPLEX WITH FAB XGV265 DBREF 7WLC E 330 530 UNP P0DTC2 SPIKE_SARS2 330 530 DBREF 7WLC H 2 119 PDB 7WLC 7WLC 2 119 DBREF 7WLC L 1 111 PDB 7WLC 7WLC 1 111 SEQADV 7WLC ASP E 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 7WLC LEU E 371 UNP P0DTC2 SER 371 VARIANT SEQADV 7WLC PRO E 373 UNP P0DTC2 SER 373 VARIANT SEQADV 7WLC PHE E 375 UNP P0DTC2 SER 375 VARIANT SEQADV 7WLC ASN E 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 7WLC LYS E 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 7WLC SER E 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 7WLC ASN E 477 UNP P0DTC2 SER 477 VARIANT SEQADV 7WLC LYS E 478 UNP P0DTC2 THR 478 VARIANT SEQADV 7WLC ALA E 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7WLC ARG E 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 7WLC SER E 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 7WLC ARG E 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 7WLC TYR E 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 7WLC HIS E 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 E 201 PRO ASN ILE THR ASN LEU CYS PRO PHE ASP GLU VAL PHE SEQRES 2 E 201 ASN ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG SEQRES 3 E 201 LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU SEQRES 4 E 201 TYR ASN LEU ALA PRO PHE PHE THR PHE LYS CYS TYR GLY SEQRES 5 E 201 VAL SER PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN SEQRES 6 E 201 VAL TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL SEQRES 7 E 201 ARG GLN ILE ALA PRO GLY GLN THR GLY ASN ILE ALA ASP SEQRES 8 E 201 TYR ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL SEQRES 9 E 201 ILE ALA TRP ASN SER ASN LYS LEU ASP SER LYS VAL SER SEQRES 10 E 201 GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER SEQRES 11 E 201 ASN LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE SEQRES 12 E 201 TYR GLN ALA GLY ASN LYS PRO CYS ASN GLY VAL ALA GLY SEQRES 13 E 201 PHE ASN CYS TYR PHE PRO LEU ARG SER TYR SER PHE ARG SEQRES 14 E 201 PRO THR TYR GLY VAL GLY HIS GLN PRO TYR ARG VAL VAL SEQRES 15 E 201 VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL SEQRES 16 E 201 CYS GLY PRO LYS LYS SER SEQRES 1 H 118 VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS PRO SEQRES 2 H 118 GLY SER SER VAL LYS VAL SER CYS LYS ALA SER GLY ASP SEQRES 3 H 118 THR PHE SER SER TYR THR PHE SER TRP VAL ARG GLN ALA SEQRES 4 H 118 PRO GLY GLN GLY LEU GLU TRP MET GLY ARG SER ILE PRO SEQRES 5 H 118 ILE VAL GLY LYS ALA ILE TYR ALA GLN GLU PHE GLN GLY SEQRES 6 H 118 ARG VAL THR ILE SER ALA ASP ARG SER THR THR THR VAL SEQRES 7 H 118 TYR MET GLU LEU SER SER LEU ARG SER ASP ASP THR ALA SEQRES 8 H 118 VAL TYR TYR CYS ALA ARG ASP GLN SER GLY PHE ASP PHE SEQRES 9 H 118 PHE TYR TYR ASP HIS TRP GLY GLN GLY THR LEU VAL ALA SEQRES 10 H 118 VAL SEQRES 1 L 111 GLN SER VAL LEU THR GLN PRO PRO SER ALA SER GLY THR SEQRES 2 L 111 PRO GLY GLN ARG VAL THR ILE SER CYS SER GLY SER GLY SEQRES 3 L 111 SER ASN ILE GLY SER ASN THR ILE ASN TRP TYR GLN GLN SEQRES 4 L 111 LEU PRO GLY THR ALA PRO LYS VAL LEU ILE TYR ARG ASN SEQRES 5 L 111 ASN GLU ARG PRO SER GLY VAL PRO ASP ARG PHE SER GLY SEQRES 6 L 111 SER LYS SER GLY THR SER ALA SER LEU THR ILE SER GLY SEQRES 7 L 111 LEU GLN SER GLU ASP GLU ALA TYR TYR HIS CYS ALA ALA SEQRES 8 L 111 TRP ASP ASP SER LEU ASN GLY PRO VAL PHE GLY GLY GLY SEQRES 9 L 111 THR LYS LEU THR VAL LEU GLY HELIX 1 AA1 PRO E 337 PHE E 342 1 6 HELIX 2 AA2 TYR E 365 ASN E 370 1 6 HELIX 3 AA3 LYS E 386 ASP E 389 5 4 HELIX 4 AA4 ASP E 405 ALA E 411 5 7 HELIX 5 AA5 ASN E 417 ASN E 422 1 6 HELIX 6 AA6 GLN H 62 GLN H 65 5 4 HELIX 7 AA7 ARG H 87 THR H 91 5 5 SHEET 1 AA1 4 LYS E 356 ILE E 358 0 SHEET 2 AA1 4 VAL E 395 ARG E 403 -1 O ALA E 397 N LYS E 356 SHEET 3 AA1 4 PRO E 507 PHE E 515 -1 O VAL E 510 N PHE E 400 SHEET 4 AA1 4 CYS E 432 ASN E 437 -1 N CYS E 432 O LEU E 513 SHEET 1 AA2 2 CYS E 391 PHE E 392 0 SHEET 2 AA2 2 VAL E 524 CYS E 525 -1 O VAL E 524 N PHE E 392 SHEET 1 AA3 2 TYR E 453 ARG E 454 0 SHEET 2 AA3 2 LEU E 492 ARG E 493 -1 O ARG E 493 N TYR E 453 SHEET 1 AA4 2 TYR E 473 GLN E 474 0 SHEET 2 AA4 2 CYS E 488 TYR E 489 -1 O TYR E 489 N TYR E 473 SHEET 1 AA5 4 GLN H 3 GLN H 6 0 SHEET 2 AA5 4 SER H 17 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 AA5 4 THR H 78 SER H 84 -1 O VAL H 79 N CYS H 22 SHEET 4 AA5 4 VAL H 68 ASP H 73 -1 N SER H 71 O TYR H 80 SHEET 1 AA6 6 GLU H 10 VAL H 11 0 SHEET 2 AA6 6 THR H 115 ALA H 118 1 O LEU H 116 N GLU H 10 SHEET 3 AA6 6 ALA H 92 ARG H 98 -1 N TYR H 94 O THR H 115 SHEET 4 AA6 6 PHE H 34 GLN H 39 -1 N GLN H 39 O VAL H 93 SHEET 5 AA6 6 LEU H 45 SER H 51 -1 O GLY H 49 N TRP H 36 SHEET 6 AA6 6 ALA H 58 TYR H 60 -1 O ILE H 59 N ARG H 50 SHEET 1 AA7 5 SER L 9 GLY L 12 0 SHEET 2 AA7 5 THR L 105 VAL L 109 1 O LYS L 106 N ALA L 10 SHEET 3 AA7 5 ALA L 85 ASP L 93 -1 N ALA L 85 O LEU L 107 SHEET 4 AA7 5 ASN L 35 GLN L 39 -1 N ASN L 35 O ALA L 90 SHEET 5 AA7 5 LYS L 46 ILE L 49 -1 O LYS L 46 N GLN L 38 SHEET 1 AA8 4 SER L 9 GLY L 12 0 SHEET 2 AA8 4 THR L 105 VAL L 109 1 O LYS L 106 N ALA L 10 SHEET 3 AA8 4 ALA L 85 ASP L 93 -1 N ALA L 85 O LEU L 107 SHEET 4 AA8 4 GLY L 98 PHE L 101 -1 O VAL L 100 N ALA L 91 SHEET 1 AA9 3 VAL L 18 SER L 23 0 SHEET 2 AA9 3 SER L 71 ILE L 76 -1 O ALA L 72 N CYS L 22 SHEET 3 AA9 3 PHE L 63 SER L 68 -1 N SER L 64 O THR L 75 SSBOND 1 CYS E 336 CYS E 361 1555 1555 2.03 SSBOND 2 CYS E 379 CYS E 432 1555 1555 2.04 SSBOND 3 CYS E 391 CYS E 525 1555 1555 2.03 SSBOND 4 CYS E 480 CYS E 488 1555 1555 2.03 SSBOND 5 CYS H 22 CYS H 96 1555 1555 2.04 SSBOND 6 CYS L 22 CYS L 89 1555 1555 2.03 CISPEP 1 ASN E 331 ILE E 332 0 -4.76 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