HEADER VIRAL PROTEIN/IMMUNE SYSTEM 04-FEB-22 7WTG TITLE SARS-COV-2 OMICRON VARIANT SPIKE RBD IN COMPLEX WITH FAB XGV051 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: HEAVY CHAIN OF XGV051; COMPND 9 CHAIN: H; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: LIGHT CHAIN OF XGV051; 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, RBD-FAB COMPLEX, VIRAL PROTEIN, VIRAL PROTEIN- KEYWDS 2 IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR X.WANG,W.FU REVDAT 1 14-DEC-22 7WTG 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. 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 : 380727 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 7WTG 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_1300027483. 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 XGV051; SARS-COV-2 OMICRON REMARK 245 VARIANT SPIKE RBD; FAB XGV051 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, 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 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. = 8.1 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 ASN E 343 34.27 -97.60 REMARK 500 PHE E 464 65.45 62.27 REMARK 500 ASN E 481 -179.80 62.87 REMARK 500 LYS E 529 -138.44 57.29 REMARK 500 GLU H 10 -167.89 -117.75 REMARK 500 LYS H 63 -8.53 72.78 REMARK 500 MET H 114 -11.68 67.11 REMARK 500 CYS L 23 116.35 -161.31 REMARK 500 ASN L 31 14.39 -157.12 REMARK 500 ALA L 51 -115.29 57.05 REMARK 500 GLU L 81 32.93 -97.27 REMARK 500 GLN L 91 -151.76 55.18 REMARK 500 ASN L 92 -100.88 60.07 REMARK 500 ARG L 96 -179.33 60.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO E 337 PHE E 338 149.52 REMARK 500 CYS E 361 VAL E 362 141.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-32785 RELATED DB: EMDB REMARK 900 SARS-COV-2 OMICRON VARIANT SPIKE RBD IN COMPLEX WITH FAB XGV051 DBREF 7WTG E 330 530 UNP P0DTC2 SPIKE_SARS2 330 530 DBREF 7WTG H 2 121 PDB 7WTG 7WTG 2 121 DBREF 7WTG L 1 104 PDB 7WTG 7WTG 1 104 SEQADV 7WTG ASP E 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 7WTG LEU E 371 UNP P0DTC2 SER 371 VARIANT SEQADV 7WTG PRO E 373 UNP P0DTC2 SER 373 VARIANT SEQADV 7WTG PHE E 375 UNP P0DTC2 SER 375 VARIANT SEQADV 7WTG ASN E 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 7WTG LYS E 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 7WTG SER E 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 7WTG ASN E 477 UNP P0DTC2 SER 477 VARIANT SEQADV 7WTG LYS E 478 UNP P0DTC2 THR 478 VARIANT SEQADV 7WTG ALA E 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 7WTG ARG E 493 UNP P0DTC2 GLN 493 VARIANT SEQADV 7WTG SER E 496 UNP P0DTC2 GLY 496 VARIANT SEQADV 7WTG ARG E 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 7WTG TYR E 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 7WTG 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 120 VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS PRO SEQRES 2 H 120 GLY SER SER VAL LYS VAL SER CYS LYS ALA SER GLY GLY SEQRES 3 H 120 THR PHE SER ASN TYR ALA LEU SER TRP VAL ARG GLN ALA SEQRES 4 H 120 PRO GLY GLN GLY LEU GLU TRP MET GLY GLY ILE ILE PRO SEQRES 5 H 120 ILE PHE GLY THR THR ASN TYR ALA GLN LYS PHE GLN GLY SEQRES 6 H 120 ARG VAL THR ILE THR ALA ASP GLU SER THR SER THR ALA SEQRES 7 H 120 TYR MET GLU LEU SER SER LEU ARG SER GLU ASP THR ALA SEQRES 8 H 120 VAL TYR TYR CYS ALA ARG LEU ASP GLY TYR SER PHE GLY SEQRES 9 H 120 HIS ASP ARG TYR TYR GLN ASP GLY MET ASP ASP TRP GLY SEQRES 10 H 120 PRO GLY THR SEQRES 1 L 104 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 104 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 104 GLN ALA ILE ARG ASN ASP LEU GLY TRP TYR GLN GLN LYS SEQRES 4 L 104 PRO GLY LYS ALA PRO LYS CYS LEU ILE TYR ALA ALA SER SEQRES 5 L 104 SER LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 104 GLY SER GLY THR GLU PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 104 GLN PRO GLU ASP PHE ALA THR TYR PHE CYS LEU GLN GLN SEQRES 8 L 104 ASN ILE TYR PRO ARG THR PHE GLY GLN GLY THR LYS 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 ARG E 403 ASP E 405 5 3 HELIX 4 AA4 GLU E 406 ALA E 411 1 6 SHEET 1 AA1 4 LYS E 356 ILE E 358 0 SHEET 2 AA1 4 ASN E 394 ALA E 397 -1 O ALA E 397 N LYS E 356 SHEET 3 AA1 4 VAL E 511 GLU E 516 -1 O SER E 514 N TYR E 396 SHEET 4 AA1 4 VAL E 433 ILE E 434 -1 N ILE E 434 O VAL E 511 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 78 LEU H 83 -1 O LEU H 83 N VAL H 18 SHEET 4 AA4 4 VAL H 68 ASP H 73 -1 N THR H 69 O GLU H 82 SHEET 1 AA5 4 THR H 58 TYR H 60 0 SHEET 2 AA5 4 LEU H 45 ILE H 51 -1 N GLY H 50 O ASN H 59 SHEET 3 AA5 4 ALA H 33 GLN H 39 -1 N LEU H 34 O ILE H 51 SHEET 4 AA5 4 VAL H 93 ASP H 100 -1 O VAL H 93 N GLN H 39 SHEET 1 AA6 4 THR L 5 GLN L 6 0 SHEET 2 AA6 4 ILE L 21 ARG L 24 -1 O ARG L 24 N THR L 5 SHEET 3 AA6 4 GLU L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 AA6 4 PHE L 62 SER L 65 -1 N SER L 65 O THR L 72 SHEET 1 AA7 4 LYS L 45 ILE L 48 0 SHEET 2 AA7 4 GLY L 34 GLN L 38 -1 N GLN L 37 O LYS L 45 SHEET 3 AA7 4 ALA L 84 LEU L 89 -1 O THR L 85 N GLN L 38 SHEET 4 AA7 4 PHE L 98 GLY L 99 -1 O GLY L 99 N CYS L 88 SHEET 1 AA8 4 LYS L 45 ILE L 48 0 SHEET 2 AA8 4 GLY L 34 GLN L 38 -1 N GLN L 37 O LYS L 45 SHEET 3 AA8 4 ALA L 84 LEU L 89 -1 O THR L 85 N GLN L 38 SHEET 4 AA8 4 THR L 102 LYS L 103 -1 O LYS L 103 N ALA L 84 SSBOND 1 CYS E 336 CYS E 361 1555 1555 2.02 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 2.02 SSBOND 5 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 6 CYS L 23 CYS L 88 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