HEADER VIRAL PROTEIN/IMMUNE SYSTEM 13-APR-23 8J1T TITLE LOCAL REFINED CRYO-EM STRUCTURE OF OMICRON BA.5 RBD IN COMPLEX WITH 8- TITLE 2 9D FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: 8-9D HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 8-9D LIGHT CHAIN; COMPND 7 CHAIN: K; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN; COMPND 11 CHAIN: F; COMPND 12 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 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 15 2; SOURCE 16 ORGANISM_TAXID: 2697049; SOURCE 17 GENE: S, 2; SOURCE 18 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 20 EXPRESSION_SYSTEM_CELL_LINE: HEK293 KEYWDS VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Y.XIANG,R.LI REVDAT 2 20-DEC-23 8J1T 1 JRNL REVDAT 1 29-NOV-23 8J1T 0 JRNL AUTH W.TAI,K.YANG,Y.LIU,R.LI,S.FENG,B.CHAI,X.ZHUANG,S.QI,H.SHI, JRNL AUTH 2 Z.LIU,J.LEI,E.MA,W.WANG,C.TIAN,T.LE,J.WANG,Y.CHEN,M.TIAN, JRNL AUTH 3 Y.XIANG,G.YU,G.CHENG JRNL TITL A LUNG-SELECTIVE DELIVERY OF MRNA ENCODING BROADLY JRNL TITL 2 NEUTRALIZING ANTIBODY AGAINST SARS-COV-2 INFECTION. JRNL REF NAT COMMUN V. 14 8042 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 38052844 JRNL DOI 10.1038/S41467-023-43798-8 REMARK 2 REMARK 2 RESOLUTION. 3.30 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 : FLEXIBLE FIT 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 161014 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 8J1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300036652. 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 : SEVERE ACUTE RESPIRATORY REMARK 245 SYNDROME CORONAVIRUS 2 OMICRON REMARK 245 BA.5 RBD BOUND 8-9D FAB; 8-9D REMARK 245 FAB; SARS-COV2 OMICRON BA.5 RBD 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 : 7.70 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 KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 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) : 5000.00 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: H, K, F 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 LEU F 517 REMARK 465 LEU F 518 REMARK 465 HIS F 519 REMARK 465 ALA F 520 REMARK 465 PRO F 521 REMARK 465 ALA F 522 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 H 91 46.35 -140.86 REMARK 500 SER K 9 -128.18 53.23 REMARK 500 ALA K 50 -142.43 59.74 REMARK 500 LEU K 54 153.25 65.67 REMARK 500 GLN K 79 71.26 59.15 REMARK 500 ASN K 92 -162.82 -124.87 REMARK 500 MET K 97 -117.84 60.32 REMARK 500 PRO F 337 45.03 -81.32 REMARK 500 ASN F 343 46.82 -102.47 REMARK 500 GLN F 414 153.60 67.65 REMARK 500 TYR F 449 0.79 -65.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-35932 RELATED DB: EMDB REMARK 900 LOCAL REFINED CRYO-EM STRUCTURE OF OMICRON BA.5 RBD IN COMPLEX WITH REMARK 900 8-9D FAB DBREF 8J1T H 3 117 PDB 8J1T 8J1T 3 117 DBREF 8J1T K 1 108 PDB 8J1T 8J1T 1 108 DBREF 8J1T F 334 527 UNP P0DTC2 SPIKE_SARS2 334 527 SEQADV 8J1T ASP F 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 8J1T PHE F 371 UNP P0DTC2 SER 371 VARIANT SEQADV 8J1T PRO F 373 UNP P0DTC2 SER 373 VARIANT SEQADV 8J1T PHE F 375 UNP P0DTC2 SER 375 VARIANT SEQADV 8J1T ALA F 376 UNP P0DTC2 THR 376 CONFLICT SEQADV 8J1T ASN F 405 UNP P0DTC2 ASP 405 CONFLICT SEQADV 8J1T SER F 408 UNP P0DTC2 ARG 408 CONFLICT SEQADV 8J1T ASN F 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 8J1T LYS F 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 8J1T ARG F 452 UNP P0DTC2 LEU 452 CONFLICT SEQADV 8J1T ASN F 477 UNP P0DTC2 SER 477 VARIANT SEQADV 8J1T LYS F 478 UNP P0DTC2 THR 478 VARIANT SEQADV 8J1T ALA F 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 8J1T VAL F 486 UNP P0DTC2 PHE 486 CONFLICT SEQADV 8J1T ARG F 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 8J1T TYR F 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 8J1T HIS F 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 H 115 VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN PRO SEQRES 2 H 115 GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY LEU SEQRES 3 H 115 THR VAL SER SER ASN TYR MET ASN TRP VAL ARG GLN ALA SEQRES 4 H 115 PRO GLY LYS GLY LEU GLU TRP VAL SER VAL PHE TYR PRO SEQRES 5 H 115 GLY GLY SER THR PHE TYR ALA ASP SER VAL ARG GLY ARG SEQRES 6 H 115 PHE THR ILE SER ARG ASP ASN SER LYS ASN THR LEU TYR SEQRES 7 H 115 LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR ALA VAL SEQRES 8 H 115 TYR TYR CYS ALA ARG ASP HIS SER GLY HIS ALA LEU ASP SEQRES 9 H 115 ILE TRP GLY GLN GLY THR MET VAL THR VAL SER SEQRES 1 K 108 ASP ILE GLN MET THR GLN SER PRO SER PHE LEU SER ALA SEQRES 2 K 108 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 K 108 GLN GLY ILE SER SER TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 K 108 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SER SEQRES 5 K 108 THR LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 K 108 GLY SER GLY THR GLU PHE THR LEU THR ILE SER SER LEU SEQRES 7 K 108 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN HIS LEU SEQRES 8 K 108 ASN SER TYR PRO SER MET TYR THR PHE GLY GLN GLY THR SEQRES 9 K 108 LYS VAL ASP ILE SEQRES 1 F 194 ASN LEU CYS PRO PHE ASP GLU VAL PHE ASN ALA THR ARG SEQRES 2 F 194 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 F 194 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN PHE ALA SEQRES 4 F 194 PRO PHE PHE ALA PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 F 194 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 F 194 SER PHE VAL ILE ARG GLY ASN GLU VAL SER GLN ILE ALA SEQRES 7 F 194 PRO GLY GLN THR GLY ASN ILE ALA ASP TYR ASN TYR LYS SEQRES 8 F 194 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 F 194 SER ASN LYS LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 F 194 TYR ARG TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 F 194 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 F 194 ASN LYS PRO CYS ASN GLY VAL ALA GLY VAL ASN CYS TYR SEQRES 13 F 194 PHE PRO LEU GLN SER TYR GLY PHE ARG PRO THR TYR GLY SEQRES 14 F 194 VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 F 194 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO HELIX 1 AA1 THR H 29 ASN H 33 5 5 HELIX 2 AA2 ALA H 61 ARG H 65 5 5 HELIX 3 AA3 PRO F 337 ASN F 343 1 7 HELIX 4 AA4 SER F 366 ALA F 372 1 7 HELIX 5 AA5 PRO F 384 ASN F 388 5 5 HELIX 6 AA6 ASN F 405 ILE F 410 5 6 HELIX 7 AA7 GLY F 416 ASN F 422 1 7 SHEET 1 AA1 4 GLN H 4 SER H 8 0 SHEET 2 AA1 4 LEU H 19 SER H 26 -1 O ALA H 24 N VAL H 6 SHEET 3 AA1 4 THR H 78 MET H 83 -1 O LEU H 79 N CYS H 23 SHEET 4 AA1 4 PHE H 68 ASP H 73 -1 N THR H 69 O GLN H 82 SHEET 1 AA2 5 GLY H 11 VAL H 13 0 SHEET 2 AA2 5 THR H 112 VAL H 116 1 O THR H 115 N GLY H 11 SHEET 3 AA2 5 ALA H 92 ASP H 99 -1 N TYR H 94 O THR H 112 SHEET 4 AA2 5 TYR H 34 GLN H 40 -1 N VAL H 38 O TYR H 95 SHEET 5 AA2 5 LEU H 46 PHE H 52 -1 O GLU H 47 N ARG H 39 SHEET 1 AA3 4 MET K 4 GLN K 6 0 SHEET 2 AA3 4 VAL K 19 ALA K 25 -1 O ARG K 24 N THR K 5 SHEET 3 AA3 4 GLU K 70 ILE K 75 -1 O LEU K 73 N ILE K 21 SHEET 4 AA3 4 PHE K 62 SER K 63 -1 N SER K 63 O THR K 74 SHEET 1 AA4 4 LYS K 45 ILE K 48 0 SHEET 2 AA4 4 TRP K 35 GLN K 37 -1 N TRP K 35 O ILE K 48 SHEET 3 AA4 4 THR K 85 TYR K 87 -1 O TYR K 87 N TYR K 36 SHEET 4 AA4 4 THR K 104 LYS K 105 -1 O THR K 104 N TYR K 86 SHEET 1 AA5 5 ASN F 354 ARG F 355 0 SHEET 2 AA5 5 ASP F 398 ARG F 403 -1 O SER F 399 N ASN F 354 SHEET 3 AA5 5 PRO F 507 SER F 514 -1 O VAL F 512 N ASP F 398 SHEET 4 AA5 5 GLY F 431 ASN F 437 -1 N ILE F 434 O VAL F 511 SHEET 5 AA5 5 ALA F 376 TYR F 380 -1 N LYS F 378 O VAL F 433 SHEET 1 AA6 2 CYS F 391 PHE F 392 0 SHEET 2 AA6 2 VAL F 524 CYS F 525 -1 O VAL F 524 N PHE F 392 SHEET 1 AA7 2 ARG F 452 ARG F 454 0 SHEET 2 AA7 2 LEU F 492 SER F 494 -1 O GLN F 493 N TYR F 453 SSBOND 1 CYS H 23 CYS H 96 1555 1555 2.04 SSBOND 2 CYS K 23 CYS K 88 1555 1555 2.04 SSBOND 3 CYS F 336 CYS F 361 1555 1555 2.03 SSBOND 4 CYS F 379 CYS F 432 1555 1555 2.03 SSBOND 5 CYS F 391 CYS F 525 1555 1555 2.03 SSBOND 6 CYS F 480 CYS F 488 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