HEADER VIRAL PROTEIN/IMMUNE SYSTEM 04-FEB-22 7WTH TITLE SARS-COV-2 OMICRON VARIANT SPIKE RBD IN COMPLEX WITH FAB XGV264 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: E; COMPND 4 FRAGMENT: RBD; COMPND 5 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: LIGHT CHAIN OF XGV264; COMPND 9 CHAIN: L; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HEAVY CHAIN OF XGV264; COMPND 13 CHAIN: H; 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,W.FU REVDAT 1 14-DEC-22 7WTH 0 JRNL AUTH L.WANG,W.FU,L.BAO,Z.JIA,Y.ZHANG,Y.ZHOU,W.WU,J.WU,Q.ZHANG, JRNL AUTH 2 Y.GAO,K.WANG,Q.WANG,C.QIN,X.WANG JRNL TITL SELECTION AND STRUCTURAL BASES OF POTENT BROADLY JRNL TITL 2 NEUTRALIZING ANTIBODIES FROM 3-DOSE VACCINEES THAT ARE JRNL TITL 3 HIGHLY EFFECTIVE AGAINST DIVERSE SARS-COV-2 VARIANTS, JRNL TITL 4 INCLUDING OMICRON SUBLINEAGES. JRNL REF CELL RES. V. 32 691 2022 JRNL REFN ISSN 1001-0602 JRNL PMID 35672388 JRNL DOI 10.1038/S41422-022-00677-Z REMARK 2 REMARK 2 RESOLUTION. 4.30 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) : 4.300 REMARK 3 NUMBER OF PARTICLES : 494849 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 7WTH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1300027487. 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 VARIANT REMARK 245 SPIKE RBD IN COMPLEX WITH FAB REMARK 245 XGV264; SARS-COV-2 OMICRON REMARK 245 VARIANT SPIKE RBD; FAB XGV264 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 : 8.00 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 K2 BASE (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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, L, H 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 PRO E 330 REMARK 465 ASN E 331 REMARK 465 LYS E 529 REMARK 465 SER E 530 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 E 378 CG CD CE NZ REMARK 470 HIS E 519 CG ND1 CD2 CE1 NE2 REMARK 470 GLN L 6 CG CD OE1 NE2 REMARK 470 LYS L 68 CG CD CE NZ REMARK 470 THR H 75 OG1 CG2 REMARK 470 ARG H 79 CG CD NE CZ NH1 NH2 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 OD2 ASP H 74 OG SER H 76 2.17 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 PHE E 377 24.63 -140.31 REMARK 500 SER E 399 115.10 -160.10 REMARK 500 CYS E 432 -167.19 -161.87 REMARK 500 PHE E 464 60.23 62.73 REMARK 500 ARG E 498 159.19 64.69 REMARK 500 SER L 17 63.54 60.30 REMARK 500 ASN L 31 -127.12 60.14 REMARK 500 PHE L 32 -11.15 72.64 REMARK 500 VAL L 53 -69.79 65.15 REMARK 500 THR L 97 -111.99 52.29 REMARK 500 ARG L 107 119.00 -160.60 REMARK 500 LYS H 45 -132.94 52.73 REMARK 500 SER H 64 -6.17 72.27 REMARK 500 THR H 75 -1.78 68.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32786 RELATED DB: EMDB REMARK 900 SARS-COV-2 OMICRON VARIANT SPIKE RBD IN COMPLEX WITH FAB XGV264 DBREF 7WTH E 330 530 UNP P0DTC2 SPIKE_SARS2 330 530 DBREF 7WTH L 3 108 PDB 7WTH 7WTH 3 108 DBREF 7WTH H 2 119 PDB 7WTH 7WTH 2 119 SEQADV 7WTH ASP E 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 7WTH LEU E 371 UNP P0DTC2 SER 371 VARIANT SEQADV 7WTH PRO E 373 UNP P0DTC2 SER 373 VARIANT SEQADV 7WTH PHE E 375 UNP P0DTC2 SER 375 VARIANT SEQADV 7WTH ASN E 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 7WTH LYS E 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 7WTH SER E 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 7WTH ASN E 477 UNP P0DTC2 SER 477 VARIANT SEQADV 7WTH LYS E 478 UNP P0DTC2 THR 478 VARIANT SEQADV 7WTH ALA E 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7WTH ARG E 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 7WTH SER E 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 7WTH ARG E 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 7WTH TYR E 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 7WTH 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 L 106 ALA LEU THR GLN PRO ALA SER VAL SER GLY SER PRO GLY SEQRES 2 L 106 GLN SER ILE THR VAL SER CYS THR GLY THR SER SER ASP SEQRES 3 L 106 LEU GLY ASN PHE GLN TYR VAL SER TRP TYR GLN HIS HIS SEQRES 4 L 106 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR GLU VAL SER SEQRES 5 L 106 LYS ARG PRO SER GLY VAL SER ASN ARG PHE SER GLY SER SEQRES 6 L 106 LYS SER GLY ASN THR ALA SER LEU THR ILE SER GLY LEU SEQRES 7 L 106 GLN ALA GLU ASP GLU ALA ASP TYR TYR CYS CYS SER TYR SEQRES 8 L 106 THR THR THR THR ILE PRO VAL ALA PHE GLY GLY GLY THR SEQRES 9 L 106 ARG LEU SEQRES 1 H 118 ILE THR LEU LYS GLU SER GLY PRO THR LEU VAL LYS PRO SEQRES 2 H 118 THR GLN THR LEU THR LEU THR CYS ALA PHE SER GLY PHE SEQRES 3 H 118 SER LEU ASN THR GLY GLY ALA GLY VAL GLY TRP ILE ARG SEQRES 4 H 118 GLN PRO PRO GLY LYS ALA LEU GLU TRP LEU ALA LEU ILE SEQRES 5 H 118 TYR TRP ASP GLY ASP LYS ARG TYR ASN PRO SER LEU LYS SEQRES 6 H 118 SER ARG LEU ALA ILE ILE MET ASP THR SER LYS ASN ARG SEQRES 7 H 118 VAL VAL LEU THR MET THR ASN MET ASP PRO VAL ASP THR SEQRES 8 H 118 ALA THR TYR TYR CYS ALA HIS HIS LYS ILE GLU TYR ILE SEQRES 9 H 118 PHE ASP TYR TRP GLY GLN GLY THR LEU VAL ALA VAL SER SEQRES 10 H 118 SER HELIX 1 AA1 PRO E 337 PHE E 342 1 6 HELIX 2 AA2 SER E 366 LEU E 371 5 6 HELIX 3 AA3 LYS E 386 LEU E 390 5 5 HELIX 4 AA4 ARG E 403 ILE E 410 5 8 HELIX 5 AA5 LEU H 65 SER H 67 5 3 HELIX 6 AA6 ASP H 88 THR H 92 5 5 SHEET 1 AA1 2 LYS E 356 ILE E 358 0 SHEET 2 AA1 2 VAL E 395 ALA E 397 -1 O VAL E 395 N ILE E 358 SHEET 1 AA2 2 CYS E 361 VAL E 362 0 SHEET 2 AA2 2 VAL E 524 CYS E 525 1 O CYS E 525 N CYS E 361 SHEET 1 AA3 3 PHE E 374 THR E 376 0 SHEET 2 AA3 3 VAL E 433 TRP E 436 -1 O ALA E 435 N THR E 376 SHEET 3 AA3 3 VAL E 510 VAL E 512 -1 O VAL E 511 N ILE E 434 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 3 THR L 19 THR L 23 0 SHEET 2 AA5 3 THR L 72 ILE L 77 -1 O ALA L 73 N CYS L 22 SHEET 3 AA5 3 PHE L 64 SER L 69 -1 N SER L 69 O THR L 72 SHEET 1 AA6 4 LYS L 44 ILE L 50 0 SHEET 2 AA6 4 SER L 36 HIS L 41 -1 N TRP L 37 O LEU L 49 SHEET 3 AA6 4 ASP L 87 TYR L 93 -1 O TYR L 89 N TYR L 38 SHEET 4 AA6 4 VAL L 100 ALA L 101 -1 O ALA L 101 N SER L 92 SHEET 1 AA7 4 THR H 3 SER H 7 0 SHEET 2 AA7 4 LEU H 18 SER H 25 -1 O ALA H 23 N LYS H 5 SHEET 3 AA7 4 VAL H 80 MET H 84 -1 O LEU H 82 N LEU H 20 SHEET 4 AA7 4 LEU H 69 MET H 73 -1 N ALA H 70 O THR H 83 SHEET 1 AA8 5 LEU H 11 VAL H 12 0 SHEET 2 AA8 5 THR H 113 VAL H 117 1 O ALA H 116 N VAL H 12 SHEET 3 AA8 5 ALA H 93 HIS H 100 -1 N TYR H 95 O THR H 113 SHEET 4 AA8 5 GLY H 35 GLN H 41 -1 N ILE H 39 O TYR H 96 SHEET 5 AA8 5 GLU H 48 TYR H 54 -1 O ILE H 53 N VAL H 36 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 L 22 CYS L 90 1555 1555 2.04 SSBOND 6 CYS H 22 CYS H 97 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