HEADER VIRAL PROTEIN/IMMUNE SYSTEM 23-DEC-21 7WED TITLE SARS-COV-2 OMICRON VARIANT SPIKE RBD IN COMPLEX WITH FAB XGV347 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: E; COMPND 4 SYNONYM: OMICRON VARIANT SPIKE PROTEIN, S GLYCOPROTEIN,E2,PEPLOMER COMPND 5 PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: THE HEAVY CHAIN OF FAB XGV347; COMPND 9 CHAIN: H; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: THE LIGHT CHAIN OF FAB XGV347; COMPND 13 CHAIN: L; COMPND 14 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 1 13-APR-22 7WED 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. 3.50 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 527413 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 7WED 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_1300026542. 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 45 CG CD NE CZ NH1 NH2 REMARK 470 GLU L 1 CG CD OE1 OE2 REMARK 470 ILE L 2 CG1 CG2 CD1 REMARK 470 GLU L 106 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS E 432 CA - CB - SG ANGL. DEV. = 8.4 DEGREES 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 PRO E 337 46.06 -86.46 REMARK 500 SER E 438 34.40 -140.02 REMARK 500 ALA E 484 -179.21 -68.12 REMARK 500 SER H 7 -168.21 -80.00 REMARK 500 THR H 16 -167.84 -75.94 REMARK 500 THR H 30 -131.04 41.92 REMARK 500 ILE H 49 -63.18 -103.16 REMARK 500 ALA H 93 -165.75 -162.62 REMARK 500 GLU H 104 -14.63 71.63 REMARK 500 THR H 105 -54.85 -122.96 REMARK 500 ILE L 31 -60.57 -98.47 REMARK 500 SER L 52 -3.45 68.42 REMARK 500 PRO L 96 122.13 -36.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32447 RELATED DB: EMDB REMARK 900 SARS-COV-2 OMICRON VARIANT SPIKE RBD IN COMPLEX WITH FAB XGV347 DBREF 7WED E 330 530 UNP P0DTC2 SPIKE_SARS2 330 530 DBREF 7WED H 1 123 PDB 7WED 7WED 1 123 DBREF 7WED L 1 107 PDB 7WED 7WED 1 107 SEQADV 7WED ASP E 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 7WED LEU E 371 UNP P0DTC2 SER 371 VARIANT SEQADV 7WED PRO E 373 UNP P0DTC2 SER 373 VARIANT SEQADV 7WED PHE E 375 UNP P0DTC2 SER 375 VARIANT SEQADV 7WED ASN E 477 UNP P0DTC2 SER 477 VARIANT SEQADV 7WED LYS E 478 UNP P0DTC2 THR 478 VARIANT SEQADV 7WED ALA E 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7WED ARG E 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 7WED SER E 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 7WED ARG E 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 7WED TYR E 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 7WED 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 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 H 123 GLN MET GLN LEU VAL GLN SER GLY PRO GLU VAL LYS LYS SEQRES 2 H 123 PRO GLY THR SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 H 123 PHE THR PHE THR ASP VAL SER SER LEU GLN TRP VAL ARG SEQRES 4 H 123 GLN ALA ARG GLY GLN ARG LEU GLU TRP ILE GLY TRP THR SEQRES 5 H 123 VAL VAL GLY THR GLY ASN THR ASN TYR ALA PRO ARG PHE SEQRES 6 H 123 GLN GLU ARG VAL THR ILE THR THR ASP LYS SER THR SER SEQRES 7 H 123 THR ALA TYR MET GLU LEU SER SER LEU ARG SER GLU ASP SEQRES 8 H 123 THR ALA VAL TYR TYR CYS ALA ALA PRO PHE CYS SER GLU SEQRES 9 H 123 THR SER CYS SER ASP GLY PHE ASP LEU TRP GLY GLN GLY SEQRES 10 H 123 THR LYS VAL THR VAL SER SEQRES 1 L 107 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 L 107 SER PRO GLY ASP ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 107 GLN SER VAL ARG ILE SER TYR LEU ALA TRP TYR GLN GLN SEQRES 4 L 107 LYS PRO GLY GLN ALA PRO ARG LEU LEU ILE SER GLY SER SEQRES 5 L 107 SER SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER ALA SEQRES 6 L 107 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG SEQRES 7 L 107 LEU GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN SEQRES 8 L 107 TYR ALA ASN SER PRO TRP THR PHE GLY GLN GLY THR LYS SEQRES 9 L 107 VAL GLU VAL HELIX 1 AA1 PRO E 337 ASN E 343 1 7 HELIX 2 AA2 TYR E 365 ASN E 370 1 6 HELIX 3 AA3 THR E 385 LEU E 390 5 6 HELIX 4 AA4 ASP E 405 ALA E 411 5 7 HELIX 5 AA5 GLY E 416 TYR E 421 1 6 HELIX 6 AA6 PRO H 63 GLN H 66 5 4 SHEET 1 AA1 5 ASN E 354 ILE E 358 0 SHEET 2 AA1 5 PHE E 392 ARG E 403 -1 O ALA E 397 N LYS E 356 SHEET 3 AA1 5 PRO E 507 LEU E 517 -1 O VAL E 510 N PHE E 400 SHEET 4 AA1 5 GLY E 431 ASN E 437 -1 N ILE E 434 O VAL E 511 SHEET 5 AA1 5 THR E 376 CYS E 379 -1 N THR E 376 O ALA E 435 SHEET 1 AA2 2 LEU E 452 ARG E 454 0 SHEET 2 AA2 2 LEU E 492 SER E 494 -1 O ARG E 493 N TYR E 453 SHEET 1 AA3 2 TYR E 473 GLN E 474 0 SHEET 2 AA3 2 CYS E 488 TYR E 489 -1 O TYR E 489 N TYR E 473 SHEET 1 AA4 4 GLN H 3 GLN H 6 0 SHEET 2 AA4 4 VAL H 18 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 AA4 4 THR H 79 LEU H 84 -1 O MET H 82 N VAL H 20 SHEET 4 AA4 4 VAL H 69 ASP H 74 -1 N THR H 72 O TYR H 81 SHEET 1 AA5 6 GLU H 10 LYS H 12 0 SHEET 2 AA5 6 THR H 118 VAL H 122 1 O LYS H 119 N GLU H 10 SHEET 3 AA5 6 ALA H 93 ALA H 99 -1 N ALA H 93 O VAL H 120 SHEET 4 AA5 6 SER H 34 GLN H 40 -1 N VAL H 38 O TYR H 96 SHEET 5 AA5 6 LEU H 46 VAL H 53 -1 O GLU H 47 N ARG H 39 SHEET 6 AA5 6 THR H 59 TYR H 61 -1 O ASN H 60 N TRP H 51 SHEET 1 AA6 4 GLU H 10 LYS H 12 0 SHEET 2 AA6 4 THR H 118 VAL H 122 1 O LYS H 119 N GLU H 10 SHEET 3 AA6 4 ALA H 93 ALA H 99 -1 N ALA H 93 O VAL H 120 SHEET 4 AA6 4 LEU H 113 TRP H 114 -1 O LEU H 113 N ALA H 99 SHEET 1 AA7 4 THR L 5 SER L 7 0 SHEET 2 AA7 4 ALA L 19 ARG L 24 -1 O SER L 22 N SER L 7 SHEET 3 AA7 4 ASP L 71 ILE L 76 -1 O ILE L 76 N ALA L 19 SHEET 4 AA7 4 PHE L 63 SER L 66 -1 N SER L 64 O THR L 75 SHEET 1 AA8 6 THR L 10 SER L 12 0 SHEET 2 AA8 6 THR L 103 GLU L 106 1 O GLU L 106 N LEU L 11 SHEET 3 AA8 6 VAL L 86 GLN L 91 -1 N TYR L 87 O THR L 103 SHEET 4 AA8 6 LEU L 34 GLN L 39 -1 N TYR L 37 O TYR L 88 SHEET 5 AA8 6 ARG L 46 SER L 50 -1 O ILE L 49 N TRP L 36 SHEET 6 AA8 6 SER L 54 ARG L 55 -1 O SER L 54 N SER L 50 SSBOND 1 CYS E 336 CYS E 361 1555 1555 2.03 SSBOND 2 CYS E 379 CYS E 432 1555 1555 2.05 SSBOND 3 CYS E 391 CYS E 525 1555 1555 2.04 SSBOND 4 CYS E 480 CYS E 488 1555 1555 2.03 SSBOND 5 CYS H 22 CYS H 97 1555 1555 2.04 SSBOND 6 CYS H 102 CYS H 107 1555 1555 2.04 SSBOND 7 CYS L 23 CYS L 89 1555 1555 2.04 CISPEP 1 ASN E 331 ILE E 332 0 -10.60 CISPEP 2 SER L 7 PRO L 8 0 -11.01 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