HEADER VIRAL PROTEIN 27-JUN-22 8A96 TITLE SARS COV2 SPIKE RBD IN COMPLEX WITH FAB47 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB47 HEAVY CHAIN (VARIABLE DOMAIN); COMPND 7 CHAIN: K; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: FAB47 LIGHT CHAIN (VARIABLE DOMAIN); COMPND 11 CHAIN: J; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS; SOURCE 3 ORGANISM_TAXID: 2901879; SOURCE 4 GENE: S, 2; 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: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 20 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SPIKE, ANTIBODY, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR B.M.HALLBERG,H.DAS REVDAT 1 03-MAY-23 8A96 0 JRNL AUTH P.PUSHPARAJ,A.NICOLETTO,D.J.SHEWARD,H.DAS,X.CASTRO DOPICO, JRNL AUTH 2 L.PEREZ VIDAKOVICS,L.HANKE,M.CHERNYSHEV,S.NARANG,S.KIM, JRNL AUTH 3 J.FISCHBACH,S.EKSTROM,G.MCINERNEY,B.M.HALLBERG,B.MURRELL, JRNL AUTH 4 M.CORCORAN,G.B.KARLSSON HEDESTAM JRNL TITL IMMUNOGLOBULIN GERMLINE GENE POLYMORPHISMS INFLUENCE THE JRNL TITL 2 FUNCTION OF SARS-COV-2 NEUTRALIZING ANTIBODIES. JRNL REF IMMUNITY V. 56 193 2023 JRNL REFN ISSN 1074-7613 JRNL PMID 36574772 JRNL DOI 10.1016/J.IMMUNI.2022.12.005 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CRYOSPARC, UCSF CHIMERA, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, COOT, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7A29 REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY 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) : 2.700 REMARK 3 NUMBER OF PARTICLES : 139021 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 8A96 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1292123966. 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 SPIKE IN COMPLEX REMARK 245 WITH FAB47 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.90 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 : LOCALIZED RECONSTRUCTION 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 5600.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 163000 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: C, K, J 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 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 ILE C 332 CG1 CG2 CD1 REMARK 470 LYS C 528 CG CD CE NZ REMARK 470 LYS C 529 CG CD CE NZ 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 C 430 71.16 -109.56 REMARK 500 ASN C 481 13.13 57.61 REMARK 500 GLN K 6 -166.43 -117.93 REMARK 500 THR K 76 -6.96 80.69 REMARK 500 SER K 122 -161.80 -124.93 REMARK 500 SER J 12 32.52 -91.74 REMARK 500 LEU J 13 30.50 -96.28 REMARK 500 GLU J 17 -126.98 59.81 REMARK 500 THR J 20 59.81 -102.43 REMARK 500 PRO J 96 46.68 -77.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-15271 RELATED DB: EMDB REMARK 900 SARS COV2 SPIKE RBD IN COMPLEX WITH FAB47 DBREF 8A96 C 327 531 UNP P0DTC2 SPIKE_SARS2 327 531 DBREF 8A96 K 2 123 PDB 8A96 8A96 2 123 DBREF 8A96 J 1 106 PDB 8A96 8A96 1 106 SEQADV 8A96 ALA C 333 UNP P0DTC2 THR 333 CONFLICT SEQRES 1 C 205 VAL ARG PHE PRO ASN ILE ALA ASN LEU CYS PRO PHE GLY SEQRES 2 C 205 GLU VAL PHE ASN ALA THR ARG PHE ALA SER VAL TYR ALA SEQRES 3 C 205 TRP ASN ARG LYS ARG ILE SER ASN CYS VAL ALA ASP TYR SEQRES 4 C 205 SER VAL LEU TYR ASN SER ALA SER PHE SER THR PHE LYS SEQRES 5 C 205 CYS TYR GLY VAL SER PRO THR LYS LEU ASN ASP LEU CYS SEQRES 6 C 205 PHE THR ASN VAL TYR ALA ASP SER PHE VAL ILE ARG GLY SEQRES 7 C 205 ASP GLU VAL ARG GLN ILE ALA PRO GLY GLN THR GLY LYS SEQRES 8 C 205 ILE ALA ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE THR SEQRES 9 C 205 GLY CYS VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SER SEQRES 10 C 205 LYS VAL GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU PHE SEQRES 11 C 205 ARG LYS SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SER SEQRES 12 C 205 THR GLU ILE TYR GLN ALA GLY SER THR PRO CYS ASN GLY SEQRES 13 C 205 VAL GLU GLY PHE ASN CYS TYR PHE PRO LEU GLN SER TYR SEQRES 14 C 205 GLY PHE GLN PRO THR ASN GLY VAL GLY TYR GLN PRO TYR SEQRES 15 C 205 ARG VAL VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO SEQRES 16 C 205 ALA THR VAL CYS GLY PRO LYS LYS SER THR SEQRES 1 K 122 VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS PRO SEQRES 2 K 122 GLY SER SER VAL LYS VAL SER CYS LYS ALA SER GLY GLY SEQRES 3 K 122 THR PHE ASN THR TYR ALA ILE ASN TRP VAL ARG GLN ALA SEQRES 4 K 122 PRO GLY GLN GLY LEU GLU TRP MET GLY ARG ILE ILE PRO SEQRES 5 K 122 MET PHE GLY ILE ALA ASN TYR ALA GLN LYS PHE GLN GLY SEQRES 6 K 122 THR VAL THR PHE THR ALA ASP LYS SER THR SER THR ALA SEQRES 7 K 122 TYR MET GLU LEU SER SER LEU ARG TYR GLU ASP THR ALA SEQRES 8 K 122 VAL TYR TYR CYS ALA ARG SER ALA TYR TYR SER GLU SER SEQRES 9 K 122 SER GLY TYR TYR LEU ASP TYR TRP GLY GLN GLY THR LEU SEQRES 10 K 122 VAL THR VAL SER SER SEQRES 1 J 106 GLU ILE VAL LEU THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 J 106 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 J 106 GLN SER VAL SER GLY SER TYR LEU ALA TRP TYR GLN GLN SEQRES 4 J 106 LYS PRO GLY GLN ALA PRO SER LEU LEU ILE TYR GLY ALA SEQRES 5 J 106 SER SER ARG ALA THR GLY ILE PRO ASP ARG PHE SER GLY SEQRES 6 J 106 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER ARG SEQRES 7 J 106 LEU GLU PRO GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN SEQRES 8 J 106 TYR VAL ASN SER PRO ARG THR PHE GLY GLN GLY THR LYS SEQRES 9 J 106 LEU GLU HELIX 1 AA1 PRO C 337 ASN C 343 1 7 HELIX 2 AA2 TYR C 365 ALA C 372 1 8 HELIX 3 AA3 ASP C 405 VAL C 407 5 3 HELIX 4 AA4 GLY C 416 ASN C 422 1 7 HELIX 5 AA5 SER C 438 SER C 443 1 6 HELIX 6 AA6 GLY C 502 TYR C 505 5 4 HELIX 7 AA7 GLY K 27 THR K 31 1 5 HELIX 8 AA8 ARG K 87 THR K 91 5 5 HELIX 9 AA9 VAL J 29 SER J 32 5 4 SHEET 1 AA1 5 ASN C 354 ILE C 358 0 SHEET 2 AA1 5 VAL C 395 ARG C 403 -1 O VAL C 395 N ILE C 358 SHEET 3 AA1 5 PRO C 507 PHE C 515 -1 O SER C 514 N TYR C 396 SHEET 4 AA1 5 GLY C 431 ASN C 437 -1 N CYS C 432 O LEU C 513 SHEET 5 AA1 5 THR C 376 CYS C 379 -1 N LYS C 378 O VAL C 433 SHEET 1 AA2 2 LEU C 452 ARG C 454 0 SHEET 2 AA2 2 LEU C 492 SER C 494 -1 O GLN C 493 N TYR C 453 SHEET 1 AA3 2 TYR C 473 GLN C 474 0 SHEET 2 AA3 2 CYS C 488 TYR C 489 -1 O TYR C 489 N TYR C 473 SHEET 1 AA4 6 ALA K 9 VAL K 11 0 SHEET 2 AA4 6 THR K 117 THR K 120 1 O LEU K 118 N GLU K 10 SHEET 3 AA4 6 VAL K 93 ALA K 100 -1 N TYR K 94 O THR K 117 SHEET 4 AA4 6 TYR K 32 GLN K 39 -1 N ASN K 35 O ALA K 97 SHEET 5 AA4 6 LEU K 45 ILE K 52 -1 O ILE K 51 N ILE K 34 SHEET 6 AA4 6 ILE K 57 TYR K 60 -1 O ILE K 57 N ILE K 52 SHEET 1 AA5 3 VAL K 18 LYS K 19 0 SHEET 2 AA5 3 THR K 78 LEU K 83 -1 O LEU K 83 N VAL K 18 SHEET 3 AA5 3 CYS K 22 LYS K 23 -1 N CYS K 22 O ALA K 79 SHEET 1 AA6 3 VAL K 18 LYS K 19 0 SHEET 2 AA6 3 THR K 78 LEU K 83 -1 O LEU K 83 N VAL K 18 SHEET 3 AA6 3 VAL K 68 ASP K 73 -1 N THR K 71 O TYR K 80 SHEET 1 AA7 2 LEU J 4 GLN J 6 0 SHEET 2 AA7 2 CYS J 23 ALA J 25 -1 O ARG J 24 N THR J 5 SHEET 1 AA8 2 ALA J 19 THR J 20 0 SHEET 2 AA8 2 THR J 75 ILE J 76 -1 N ILE J 76 O ALA J 19 SHEET 1 AA9 4 SER J 54 ARG J 55 0 SHEET 2 AA9 4 SER J 46 TYR J 50 -1 N TYR J 50 O SER J 54 SHEET 3 AA9 4 LEU J 34 GLN J 39 -1 N TRP J 36 O LEU J 48 SHEET 4 AA9 4 VAL J 86 GLN J 91 -1 O VAL J 86 N GLN J 39 SSBOND 1 CYS C 336 CYS C 361 1555 1555 2.03 SSBOND 2 CYS C 379 CYS C 432 1555 1555 2.03 SSBOND 3 CYS C 480 CYS C 488 1555 1555 2.03 SSBOND 4 CYS K 22 CYS K 96 1555 1555 2.04 SSBOND 5 CYS J 23 CYS J 89 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