HEADER IMMUNE SYSTEM/VIRAL PROTEIN 23-DEC-21 7WEF TITLE SARS-COV-2 OMICRON VARIANT SPIKE RBD IN COMPLEX WITH FAB XGV289 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THE HEAVY CHAIN OF FAB XGV289; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SPIKE PROTEIN S1; COMPND 7 CHAIN: E; COMPND 8 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: THE LIGHT CHAIN OF FAB XGV289; COMPND 12 CHAIN: L; 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 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 SARS-COV-2, OMICRON, SPIKE-FAB COMPLEX, VIRAL PROTEIN, IMMUNE SYSTEM- KEYWDS 2 VIRAL PROTEIN COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR X.WANG,L.WANG REVDAT 1 04-MAY-22 7WEF 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. 3.80 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 401170 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 7WEF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300026539. 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; FAB 289; SARS-COV-2 REMARK 245 OMICRON MUTATION SPIKE PROTEIN 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: C, E, 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 C 38 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 97 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 99 CG CD OE1 OE2 REMARK 470 ASP C 108 CG OD1 OD2 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 THR C 30 49.25 -84.53 REMARK 500 ASP C 65 -6.68 69.74 REMARK 500 ARG C 66 19.47 -140.25 REMARK 500 ASP C 72 85.19 -156.10 REMARK 500 PRO C 73 47.18 -77.79 REMARK 500 ALA C 91 -168.58 -165.81 REMARK 500 SER C 102 -164.61 62.85 REMARK 500 TRP C 103 -12.27 71.56 REMARK 500 THR E 333 -138.70 39.00 REMARK 500 ASN E 334 -163.64 64.39 REMARK 500 TYR E 423 116.00 -161.93 REMARK 500 ASP E 427 45.70 -89.61 REMARK 500 ASP E 428 20.87 -142.38 REMARK 500 ASN L 52 -6.52 68.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32449 RELATED DB: EMDB REMARK 900 SARS-COV-2 OMICRON VARIANT SPIKE RBD IN COMPLEX WITH FAB XGV289 DBREF 7WEF C 1 120 PDB 7WEF 7WEF 1 120 DBREF 7WEF E 330 530 UNP P0DTC2 SPIKE_SARS2 330 530 DBREF 7WEF L 2 112 PDB 7WEF 7WEF 2 112 SEQADV 7WEF ASP E 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 7WEF LEU E 371 UNP P0DTC2 SER 371 VARIANT SEQADV 7WEF PRO E 373 UNP P0DTC2 SER 373 VARIANT SEQADV 7WEF PHE E 375 UNP P0DTC2 SER 375 VARIANT SEQADV 7WEF ASN E 477 UNP P0DTC2 SER 477 VARIANT SEQADV 7WEF LYS E 478 UNP P0DTC2 THR 478 VARIANT SEQADV 7WEF ALA E 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7WEF ARG E 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 7WEF SER E 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 7WEF ARG E 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 7WEF TYR E 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 7WEF HIS E 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 C 120 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 C 120 PRO GLY ALA SER LEU LYS VAL SER CYS ARG ALA SER GLY SEQRES 3 C 120 TYR THR PHE THR SER HIS PHE ILE HIS TRP VAL ARG GLN SEQRES 4 C 120 ALA PRO GLY GLN GLY LEU GLU TRP MET GLY ILE ILE ASN SEQRES 5 C 120 PRO SER GLY GLY ALA SER TYR ALA GLN ASN PHE ARG ASP SEQRES 6 C 120 ARG VAL THR MET THR THR ASP PRO SER THR SER THR VAL SEQRES 7 C 120 TYR MET GLU LEU GLY SER LEU ARG SER GLU ASP THR ALA SEQRES 8 C 120 VAL TYR TYR CYS ALA ARG ALA GLU GLY SER SER TRP LEU SEQRES 9 C 120 GLY TRP PHE ASP PRO TRP GLY GLN GLY THR LEU VAL THR SEQRES 10 C 120 VAL SER SER 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 LYS 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 ASN LEU ASP SER LYS VAL GLY 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 L 111 SER VAL LEU THR GLN PRO PRO SER ALA SER GLY THR PRO SEQRES 2 L 111 GLY GLN ARG VAL THR ILE PRO CYS SER GLY SER SER SER SEQRES 3 L 111 ASN ILE GLY ASN ASN TYR VAL TYR TRP TYR GLN GLN LEU SEQRES 4 L 111 PRO GLY THR ALA PRO LYS LEU LEU VAL TYR GLY ASN ASN SEQRES 5 L 111 GLN ARG PRO SER GLY VAL PRO ASP ARG PHE SER VAL SER SEQRES 6 L 111 LYS SER GLY THR SER ALA SER LEU ALA ILE SER GLY LEU SEQRES 7 L 111 ARG SER GLU ASP GLU ALA ASP TYR TYR CYS ALA ALA TRP SEQRES 8 L 111 ASP ASP GLY LEU SER GLY SER GLY TRP VAL PHE GLY GLY SEQRES 9 L 111 GLY THR LYS LEU THR VAL LEU HELIX 1 AA1 THR C 28 HIS C 32 5 5 HELIX 2 AA2 ARG C 86 THR C 90 5 5 HELIX 3 AA3 PRO E 337 ASN E 343 1 7 HELIX 4 AA4 SER E 366 LEU E 371 1 6 HELIX 5 AA5 GLY E 404 ALA E 411 5 8 SHEET 1 AA1 4 GLN C 3 VAL C 5 0 SHEET 2 AA1 4 LEU C 18 SER C 25 -1 O ARG C 23 N VAL C 5 SHEET 3 AA1 4 THR C 77 LEU C 82 -1 O LEU C 82 N LEU C 18 SHEET 4 AA1 4 VAL C 67 THR C 70 -1 N THR C 68 O GLU C 81 SHEET 1 AA2 5 ALA C 57 TYR C 59 0 SHEET 2 AA2 5 GLU C 46 ILE C 51 -1 N ILE C 50 O SER C 58 SHEET 3 AA2 5 ILE C 34 GLN C 39 -1 N TRP C 36 O MET C 48 SHEET 4 AA2 5 ALA C 91 ARG C 97 -1 O ALA C 96 N HIS C 35 SHEET 5 AA2 5 THR C 114 VAL C 116 -1 O VAL C 116 N ALA C 91 SHEET 1 AA3 5 ASN E 354 ILE E 358 0 SHEET 2 AA3 5 VAL E 395 ILE E 402 -1 O VAL E 395 N ILE E 358 SHEET 3 AA3 5 TYR E 508 SER E 514 -1 O TYR E 508 N ILE E 402 SHEET 4 AA3 5 GLY E 431 ASN E 437 -1 N CYS E 432 O LEU E 513 SHEET 5 AA3 5 LYS E 378 CYS E 379 -1 N LYS E 378 O VAL E 433 SHEET 1 AA4 2 LEU E 452 ARG E 454 0 SHEET 2 AA4 2 LEU E 492 SER E 494 -1 O ARG E 493 N TYR E 453 SHEET 1 AA5 2 TYR E 473 GLN E 474 0 SHEET 2 AA5 2 CYS E 488 TYR E 489 -1 O TYR E 489 N TYR E 473 SHEET 1 AA6 5 SER L 9 GLY L 12 0 SHEET 2 AA6 5 THR L 107 VAL L 111 1 O LYS L 108 N ALA L 10 SHEET 3 AA6 5 ASP L 86 ASP L 94 -1 N TYR L 87 O THR L 107 SHEET 4 AA6 5 TYR L 35 GLN L 39 -1 N GLN L 39 O ASP L 86 SHEET 5 AA6 5 LYS L 46 VAL L 49 -1 O VAL L 49 N TRP L 36 SHEET 1 AA7 4 SER L 9 GLY L 12 0 SHEET 2 AA7 4 THR L 107 VAL L 111 1 O LYS L 108 N ALA L 10 SHEET 3 AA7 4 ASP L 86 ASP L 94 -1 N TYR L 87 O THR L 107 SHEET 4 AA7 4 SER L 99 VAL L 102 -1 O GLY L 100 N ASP L 93 SHEET 1 AA8 3 VAL L 18 SER L 23 0 SHEET 2 AA8 3 SER L 71 ILE L 76 -1 O ALA L 72 N CYS L 22 SHEET 3 AA8 3 PHE L 63 SER L 68 -1 N SER L 66 O SER L 73 SSBOND 1 CYS C 22 CYS C 95 1555 1555 2.03 SSBOND 2 CYS E 336 CYS E 361 1555 1555 2.03 SSBOND 3 CYS E 379 CYS E 432 1555 1555 2.04 SSBOND 4 CYS E 391 CYS E 525 1555 1555 2.04 SSBOND 5 CYS E 480 CYS E 488 1555 1555 2.03 SSBOND 6 CYS L 22 CYS L 89 1555 1555 2.03 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