HEADER IMMUNE SYSTEM 21-OCT-24 9E21 TITLE CRYOEM STRUCTURE OF A BROADLY NEUTRALIZING ANTI-SARS-COV-2 ANTIBODY 52 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 52 FAB HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 52 FAB LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SARS XBB.1.5 SPIKE; COMPND 11 CHAIN: S; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 17 2; SOURCE 18 ORGANISM_TAXID: 2697049; SOURCE 19 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 20 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, ANTIBODY, RBD, IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM KEYWDS 2 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR D.JAISWAL,G.BAJIC REVDAT 1 30-JUL-25 9E21 0 JRNL AUTH D.JAISWAL,G.BAJIC JRNL TITL CRYOEM STRUCTURE OF A BROADLY NEUTRALIZING ANTI-SARS-COV-2 JRNL TITL 2 ANTIBODY 52 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 252670 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9E21 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1000288901. 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 : 52 FAB COMPLEX WITH RBD ON REMARK 245 XBB.1.5 SPIKE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 900.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2300.00 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) : 4895.00 REMARK 245 ILLUMINATION MODE : OTHER 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, S 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: 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 H 14 1.77 -64.71 REMARK 500 GLU H 101 -6.32 69.47 REMARK 500 ALA L 51 -7.06 72.20 REMARK 500 ALA S 352 74.33 -102.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-47426 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF A BROADLY NEUTRALIZING ANTI-SARS-COV-2 ANTIBODY REMARK 900 52 DBREF 9E21 H 2 118 PDB 9E21 9E21 2 118 DBREF 9E21 L 2 107 PDB 9E21 9E21 2 107 DBREF 9E21 S 327 527 PDB 9E21 9E21 327 527 SEQRES 1 H 117 VAL GLN LEU VAL GLN SER GLY GLY ASP LEU ALA PRO PRO SEQRES 2 H 117 GLY GLY SER LEU ARG LEU SER CYS GLU ALA SER GLY ILE SEQRES 3 H 117 ILE VAL SER SER ASN TYR MET THR TRP VAL ARG GLN ALA SEQRES 4 H 117 PRO GLY LYS GLY LEU GLU TRP VAL SER LEU ILE PHE ALA SEQRES 5 H 117 GLY GLY SER THR PHE TYR ALA ASP SER VAL LYS GLY ARG SEQRES 6 H 117 PHE THR VAL SER ARG ASP ASN SER LYS ASN THR LEU TYR SEQRES 7 H 117 LEU GLN MET SER SER LEU LYS PRO GLU ASP THR ALA VAL SEQRES 8 H 117 TYR PHE CYS ALA ARG ASP LEU ARG GLU MET GLY GLY LEU SEQRES 9 H 117 ASP PHE TRP GLY GLN GLY ALA LEU VAL THR VAL SER SER SEQRES 1 L 106 ILE GLN MET THR GLN SER PRO SER SER VAL SER ALA SER SEQRES 2 L 106 ILE GLY ASP THR VAL THR ILE THR CYS ARG ALA SER GLN SEQRES 3 L 106 GLY ILE PRO SER TRP VAL ALA TRP TYR GLN GLN LYS PRO SEQRES 4 L 106 GLY LYS ALA PRO LYS LEU LEU ILE TYR GLY ALA SER ASN SEQRES 5 L 106 LEU GLN ARG GLY VAL PRO SER ARG PHE SER GLY SER GLY SEQRES 6 L 106 SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU GLN SEQRES 7 L 106 PRO GLU ASP LEU ALA VAL TYR TYR CYS HIS GLN SER ASP SEQRES 8 L 106 SER LEU PRO GLY ILE PHE GLY GLY GLY THR LYS VAL GLU SEQRES 9 L 106 ILE LYS SEQRES 1 S 201 VAL ARG PHE PRO ASN ILE THR ASN LEU CYS PRO PHE HIS SEQRES 2 S 201 GLU VAL PHE ASN ALA THR THR PHE ALA SER VAL TYR ALA SEQRES 3 S 201 TRP ASN ARG LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SEQRES 4 S 201 SER VAL ILE TYR ASN PHE ALA PRO PHE PHE ALA PHE LYS SEQRES 5 S 201 CYS TYR GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS SEQRES 6 S 201 PHE THR ASN VAL TYR ALA ASP SER PHE VAL ILE ARG GLY SEQRES 7 S 201 ASN GLU VAL SER GLN ILE ALA PRO GLY GLN THR GLY ASN SEQRES 8 S 201 ILE ALA ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR SEQRES 9 S 201 GLY CYS VAL ILE ALA TRP ASN SER ASN LYS LEU ASP SER SEQRES 10 S 201 LYS PRO SER GLY ASN TYR ASN TYR LEU TYR ARG PHE LEU SEQRES 11 S 201 ARG LYS SER LYS LEU LYS PRO PHE GLU ARG ASP ILE SER SEQRES 12 S 201 THR GLU ILE TYR GLN VAL GLY ASN LYS PRO CYS ASN GLY SEQRES 13 S 201 VAL ALA GLY PRO ASN CYS TYR SER PRO LEU GLN SER TYR SEQRES 14 S 201 GLY PHE ARG PRO THR TYR GLY VAL GLY HIS GLN PRO TYR SEQRES 15 S 201 ARG VAL VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO SEQRES 16 S 201 ALA THR VAL CYS GLY PRO HET NAG S 601 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 NAG C8 H15 N O6 HELIX 1 AA1 ILE H 28 ASN H 32 5 5 HELIX 2 AA2 LYS H 86 THR H 90 5 5 HELIX 3 AA3 PRO S 337 ASN S 343 1 7 HELIX 4 AA4 SER S 383 LEU S 390 5 8 HELIX 5 AA5 GLU S 406 ILE S 410 5 5 HELIX 6 AA6 GLY S 416 ASN S 422 1 7 HELIX 7 AA7 GLY S 502 GLN S 506 5 5 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 LEU H 18 SER H 25 -1 O SER H 25 N GLN H 3 SHEET 3 AA1 4 THR H 77 MET H 82 -1 O MET H 82 N LEU H 18 SHEET 4 AA1 4 PHE H 67 ASP H 72 -1 N THR H 68 O GLN H 81 SHEET 1 AA2 6 LEU H 11 ALA H 12 0 SHEET 2 AA2 6 ALA H 112 VAL H 116 1 O THR H 115 N ALA H 12 SHEET 3 AA2 6 ALA H 91 LEU H 99 -1 N TYR H 93 O ALA H 112 SHEET 4 AA2 6 TYR H 33 GLN H 39 -1 N TYR H 33 O ASP H 98 SHEET 5 AA2 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA2 6 THR H 57 TYR H 59 -1 O PHE H 58 N LEU H 50 SHEET 1 AA3 4 LEU H 11 ALA H 12 0 SHEET 2 AA3 4 ALA H 112 VAL H 116 1 O THR H 115 N ALA H 12 SHEET 3 AA3 4 ALA H 91 LEU H 99 -1 N TYR H 93 O ALA H 112 SHEET 4 AA3 4 GLY H 104 TRP H 108 -1 O PHE H 107 N ARG H 97 SHEET 1 AA4 4 MET L 4 GLN L 6 0 SHEET 2 AA4 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AA4 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 AA4 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 AA5 6 VAL L 11 ALA L 13 0 SHEET 2 AA5 6 THR L 102 ILE L 106 1 O GLU L 105 N ALA L 13 SHEET 3 AA5 6 VAL L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AA5 6 VAL L 33 GLN L 38 -1 N ALA L 34 O HIS L 89 SHEET 5 AA5 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AA5 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 AA6 5 ASN S 354 ILE S 358 0 SHEET 2 AA6 5 ASN S 394 ILE S 402 -1 O SER S 399 N ASN S 354 SHEET 3 AA6 5 TYR S 508 GLU S 516 -1 O VAL S 510 N PHE S 400 SHEET 4 AA6 5 GLY S 431 ASN S 437 -1 N CYS S 432 O LEU S 513 SHEET 5 AA6 5 ALA S 376 TYR S 380 -1 N LYS S 378 O VAL S 433 SHEET 1 AA7 2 LEU S 452 ARG S 454 0 SHEET 2 AA7 2 LEU S 492 SER S 494 -1 O GLN S 493 N TYR S 453 SHEET 1 AA8 2 TYR S 473 GLN S 474 0 SHEET 2 AA8 2 CYS S 488 TYR S 489 -1 O TYR S 489 N TYR S 473 SSBOND 1 CYS H 22 CYS H 95 1555 1555 2.03 SSBOND 2 CYS S 336 CYS S 361 1555 1555 2.03 SSBOND 3 CYS S 379 CYS S 432 1555 1555 2.03 SSBOND 4 CYS S 480 CYS S 488 1555 1555 2.03 LINK ND2 ASN S 331 C1 NAG S 601 1555 1555 1.44 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 TER 883 SER H 118 TER 1672 LYS L 107 TER 3274 PRO S 527 HETATM 3275 C1 NAG S 601 195.588 174.121 239.186 1.00 38.30 C HETATM 3276 C2 NAG S 601 196.038 172.880 238.409 1.00 35.96 C HETATM 3277 C3 NAG S 601 194.830 172.259 237.715 1.00 34.67 C HETATM 3278 C4 NAG S 601 193.726 171.983 238.729 1.00 37.56 C HETATM 3279 C5 NAG S 601 193.418 173.264 239.512 1.00 45.38 C HETATM 3280 C6 NAG S 601 192.361 173.092 240.581 1.00 47.31 C HETATM 3281 C7 NAG S 601 198.349 172.802 237.562 1.00 44.06 C HETATM 3282 C8 NAG S 601 199.257 173.263 236.449 1.00 38.89 C HETATM 3283 N2 NAG S 601 197.070 173.205 237.460 1.00 41.05 N HETATM 3284 O3 NAG S 601 195.258 171.090 237.070 1.00 40.53 O HETATM 3285 O4 NAG S 601 192.601 171.528 238.014 1.00 35.11 O HETATM 3286 O5 NAG S 601 194.604 173.737 240.116 1.00 45.80 O HETATM 3287 O6 NAG S 601 192.740 172.068 241.470 1.00 47.08 O HETATM 3288 O7 NAG S 601 198.768 172.114 238.480 1.00 47.23 O CONECT 142 710 CONECT 710 142 CONECT 1716 3275 CONECT 1753 1962 CONECT 1962 1753 CONECT 2111 2518 CONECT 2518 2111 CONECT 2919 2968 CONECT 2968 2919 CONECT 3275 1716 3276 3286 CONECT 3276 3275 3277 3283 CONECT 3277 3276 3278 3284 CONECT 3278 3277 3279 3285 CONECT 3279 3278 3280 3286 CONECT 3280 3279 3287 CONECT 3281 3282 3283 3288 CONECT 3282 3281 CONECT 3283 3276 3281 CONECT 3284 3277 CONECT 3285 3278 CONECT 3286 3275 3279 CONECT 3287 3280 CONECT 3288 3281 MASTER 121 0 1 7 33 0 0 6 3285 3 23 34 END