HEADER VIRAL PROTEIN/IMMUNE SYSTEM 31-MAR-23 8IX3 TITLE CRYO-EM STRUCTURE OF SARS-COV-2 BA.4/5 SPIKE PROTEIN IN COMPLEX WITH TITLE 2 1G11 (LOCAL REFINEMENT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGHT CHAIN OF 1G11; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN OF 1G11; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: BA.4/5 VARIANT SPIKE PROTEIN; COMPND 11 CHAIN: G; COMPND 12 SYNONYM: SPIKE PROTEIN S2'; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 13 2; SOURCE 14 ORGANISM_TAXID: 2697049; SOURCE 15 GENE: S, 2; SOURCE 16 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS SARS-COV-2, NEUTRALIZING ANTIBODY, CRYO-EM, VIRAL PROTEIN, VIRAL KEYWDS 2 PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR H.SUN,Y.JIANG,Z.ZHENG,Q.ZHENG,S.LI REVDAT 2 13-DEC-23 8IX3 1 JRNL REVDAT 1 15-NOV-23 8IX3 0 JRNL AUTH H.SUN,Y.WANG,X.CHEN,Y.JIANG,S.WANG,Y.HUANG,L.LIU,Y.LI,M.LAN, JRNL AUTH 2 H.GUO,Q.YUAN,Y.ZHANG,T.LI,H.YU,Y.GU,J.ZHANG,S.LI,Z.ZHENG, JRNL AUTH 3 Q.ZHENG,N.XIA JRNL TITL STRUCTURAL BASIS FOR BROAD NEUTRALIZATION OF HUMAN ANTIBODY JRNL TITL 2 AGAINST OMICRON SUBLINEAGES AND EVASION BY XBB VARIANT. JRNL REF J.VIROL. V. 97 13723 2023 JRNL REFN ESSN 1098-5514 JRNL PMID 37855619 JRNL DOI 10.1128/JVI.01137-23 REMARK 2 REMARK 2 RESOLUTION. 3.98 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) : 3.980 REMARK 3 NUMBER OF PARTICLES : 275583 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8IX3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300036561. 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 BA.4/5 SPIKE PROTEIN REMARK 245 IN COMPLEX WITH 1G11; SARS-COV- REMARK 245 2 BA.4/5 SPIKE PROTEIN; NAB 1G11 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 : 7.40 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 TECNAI F30 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT 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: L, H, G 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 LYS G 527 REMARK 465 LYS G 528 REMARK 465 PHE G 529 REMARK 465 ASN G 530 REMARK 465 PHE G 531 REMARK 465 ASN G 532 REMARK 465 GLY G 533 REMARK 465 LEU G 534 REMARK 465 THR G 535 REMARK 465 GLY G 536 REMARK 465 THR G 537 REMARK 465 GLY G 538 REMARK 465 VAL G 539 REMARK 465 LEU G 540 REMARK 465 THR G 541 REMARK 465 GLU G 542 REMARK 465 SER G 543 REMARK 465 ASN G 544 REMARK 465 LYS G 545 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 ASP L 30 61.97 60.35 REMARK 500 LYS L 31 -7.92 72.96 REMARK 500 ALA L 51 -3.82 66.91 REMARK 500 LEU L 91 34.62 -140.73 REMARK 500 VAL H 48 -61.48 -92.54 REMARK 500 SER H 104 -165.87 -163.33 REMARK 500 SER H 124 -39.00 -130.60 REMARK 500 TYR G 365 31.57 -94.99 REMARK 500 GLU G 516 76.88 -102.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-35788 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SARS-COV-2 BA.4/5 SPIKE PROTEIN IN COMPLEX REMARK 900 WITH 1G11 (LOCAL REFINEMENT) DBREF 8IX3 L 1 107 PDB 8IX3 8IX3 1 107 DBREF 8IX3 H 1 125 PDB 8IX3 8IX3 1 125 DBREF 8IX3 G 333 545 UNP P0DTC2 SPIKE_SARS2 333 557 SEQADV 8IX3 ASP G 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 8IX3 PHE G 371 UNP P0DTC2 SER 371 VARIANT SEQADV 8IX3 PRO G 373 UNP P0DTC2 SER 373 VARIANT SEQADV 8IX3 PHE G 375 UNP P0DTC2 SER 375 VARIANT SEQADV 8IX3 ALA G 376 UNP P0DTC2 THR 376 VARIANT SEQADV 8IX3 ASN G 405 UNP P0DTC2 ASP 405 VARIANT SEQADV 8IX3 SER G 408 UNP P0DTC2 ARG 408 VARIANT SEQADV 8IX3 ASN G 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 8IX3 LYS G 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 8IX3 ARG G 452 UNP P0DTC2 LEU 452 VARIANT SEQADV 8IX3 ASN G 477 UNP P0DTC2 SER 477 VARIANT SEQADV 8IX3 LYS G 478 UNP P0DTC2 THR 478 VARIANT SEQADV 8IX3 ALA G 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 8IX3 VAL G 486 UNP P0DTC2 PHE 486 VARIANT SEQADV 8IX3 ARG G 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 8IX3 TYR G 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 8IX3 HIS G 505 UNP P0DTC2 TYR 505 VARIANT SEQADV 8IX3 LYS G 527 UNP P0DTC2 PRO 527 VARIANT SEQADV 8IX3 G UNP P0DTC2 LYS 529 DELETION SEQADV 8IX3 G UNP P0DTC2 SER 530 DELETION SEQADV 8IX3 G UNP P0DTC2 THR 531 DELETION SEQADV 8IX3 G UNP P0DTC2 ASN 532 DELETION SEQADV 8IX3 G UNP P0DTC2 LEU 533 DELETION SEQADV 8IX3 G UNP P0DTC2 VAL 534 DELETION SEQADV 8IX3 G UNP P0DTC2 LYS 535 DELETION SEQADV 8IX3 G UNP P0DTC2 ASN 536 DELETION SEQADV 8IX3 G UNP P0DTC2 LYS 537 DELETION SEQADV 8IX3 G UNP P0DTC2 CYS 538 DELETION SEQADV 8IX3 G UNP P0DTC2 VAL 539 DELETION SEQADV 8IX3 G UNP P0DTC2 ASN 540 DELETION SEQRES 1 L 107 ASP ILE GLN LEU THR GLN SER PRO SER PHE LEU SER ALA SEQRES 2 L 107 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 107 GLN GLY ILE ASP LYS TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 107 PRO GLY GLN ALA PRO LYS VAL LEU ILE TYR ALA ALA SER SEQRES 5 L 107 THR LEU HIS SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 L 107 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 107 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN LEU SEQRES 8 L 107 TYR THR PHE PRO VAL THR PHE GLY PRO GLY THR LYS VAL SEQRES 9 L 107 ASP VAL ARG SEQRES 1 H 125 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 125 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 125 PHE LYS PHE ASP ASP TYR ALA MET HIS TRP VAL ARG GLN SEQRES 4 H 125 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER GLY THR SER SEQRES 5 H 125 TRP ASN SER GLY THR THR GLY TYR ALA ASP SER VAL ARG SEQRES 6 H 125 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS LYS SER SEQRES 7 H 125 LEU TYR LEU GLN MET ASN SER LEU GLY VAL GLU ASP THR SEQRES 8 H 125 ALA PHE TYR TYR CYS VAL LYS ASP SER ASN TYR ASP SER SEQRES 9 H 125 SER GLY TYR LEU ILE ASN ASN PHE ASP TYR TRP GLY GLN SEQRES 10 H 125 GLY ILE LEU VAL THR VAL SER SER SEQRES 1 G 213 THR ASN LEU CYS PRO PHE ASP GLU VAL PHE ASN ALA THR SEQRES 2 G 213 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 G 213 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN PHE SEQRES 4 G 213 ALA PRO PHE PHE ALA PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 G 213 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 G 213 ASP SER PHE VAL ILE ARG GLY ASN GLU VAL SER GLN ILE SEQRES 7 G 213 ALA PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN TYR SEQRES 8 G 213 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 G 213 ASN SER ASN LYS LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 G 213 ASN TYR ARG TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 G 213 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 G 213 GLY ASN LYS PRO CYS ASN GLY VAL ALA GLY VAL ASN CYS SEQRES 13 G 213 TYR PHE PRO LEU GLN SER TYR GLY PHE ARG PRO THR TYR SEQRES 14 G 213 GLY VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 G 213 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY LYS SEQRES 16 G 213 LYS PHE ASN PHE ASN GLY LEU THR GLY THR GLY VAL LEU SEQRES 17 G 213 THR GLU SER ASN LYS HELIX 1 AA1 GLY H 87 THR H 91 5 5 HELIX 2 AA2 SER G 366 ASN G 370 5 5 HELIX 3 AA3 GLU G 406 ILE G 410 5 5 SHEET 1 AA1 4 LEU L 4 SER L 7 0 SHEET 2 AA1 4 VAL L 19 ALA L 25 -1 O THR L 22 N SER L 7 SHEET 3 AA1 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 AA1 4 PHE L 62 SER L 65 -1 N SER L 63 O THR L 74 SHEET 1 AA2 6 PHE L 10 SER L 12 0 SHEET 2 AA2 6 THR L 102 ASP L 105 1 O ASP L 105 N LEU L 11 SHEET 3 AA2 6 THR L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AA2 6 LEU L 33 GLN L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 AA2 6 LYS L 45 TYR L 49 -1 O ILE L 48 N TRP L 35 SHEET 6 AA2 6 THR L 53 LEU L 54 -1 O THR L 53 N TYR L 49 SHEET 1 AA3 4 GLN H 3 SER H 7 0 SHEET 2 AA3 4 SER H 17 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 AA3 4 SER H 78 ASN H 84 -1 O LEU H 81 N LEU H 20 SHEET 4 AA3 4 PHE H 68 ASP H 73 -1 N THR H 69 O GLN H 82 SHEET 1 AA4 5 GLY H 59 TYR H 60 0 SHEET 2 AA4 5 LEU H 45 THR H 51 -1 N GLY H 50 O GLY H 59 SHEET 3 AA4 5 MET H 34 GLN H 39 -1 N MET H 34 O THR H 51 SHEET 4 AA4 5 ALA H 92 LYS H 98 -1 O TYR H 95 N VAL H 37 SHEET 5 AA4 5 TYR H 114 TRP H 115 -1 O TYR H 114 N LYS H 98 SHEET 1 AA5 5 GLY H 59 TYR H 60 0 SHEET 2 AA5 5 LEU H 45 THR H 51 -1 N GLY H 50 O GLY H 59 SHEET 3 AA5 5 MET H 34 GLN H 39 -1 N MET H 34 O THR H 51 SHEET 4 AA5 5 ALA H 92 LYS H 98 -1 O TYR H 95 N VAL H 37 SHEET 5 AA5 5 ILE H 119 VAL H 121 -1 O ILE H 119 N TYR H 94 SHEET 1 AA6 4 ALA G 376 CYS G 379 0 SHEET 2 AA6 4 CYS G 432 ASN G 437 -1 O VAL G 433 N LYS G 378 SHEET 3 AA6 4 TYR G 508 SER G 514 -1 O VAL G 511 N ILE G 434 SHEET 4 AA6 4 TYR G 396 ALA G 397 -1 N TYR G 396 O SER G 514 SHEET 1 AA7 4 ALA G 376 CYS G 379 0 SHEET 2 AA7 4 CYS G 432 ASN G 437 -1 O VAL G 433 N LYS G 378 SHEET 3 AA7 4 TYR G 508 SER G 514 -1 O VAL G 511 N ILE G 434 SHEET 4 AA7 4 PHE G 400 ILE G 402 -1 N ILE G 402 O TYR G 508 SHEET 1 AA8 2 ARG G 452 ARG G 454 0 SHEET 2 AA8 2 LEU G 492 SER G 494 -1 O GLN G 493 N TYR G 453 SHEET 1 AA9 2 TYR G 473 GLN G 474 0 SHEET 2 AA9 2 CYS G 488 TYR G 489 -1 O TYR G 489 N TYR G 473 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.03 SSBOND 2 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 3 CYS G 336 CYS G 361 1555 1555 2.02 SSBOND 4 CYS G 379 CYS G 432 1555 1555 2.03 SSBOND 5 CYS G 480 CYS G 488 1555 1555 2.03 CISPEP 1 SER L 7 PRO L 8 0 0.64 CISPEP 2 PHE L 94 PRO L 95 0 0.97 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