HEADER VIRAL PROTEIN/IMMUNE SYSTEM 05-JUN-22 7Y0O TITLE INTERFACE OF SARS-COV-2 WT SPIKE IN COMPLEX WITH R15 FAB AND P14 TITLE 2 NANOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RBD; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HEAVY CHAIN OF R15; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: LIGHT CHAIN OF R15; COMPND 12 CHAIN: L; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: P14 NANOBODY; COMPND 16 CHAIN: B; COMPND 17 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; SOURCE 18 MOL_ID: 4; SOURCE 19 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 20 ORGANISM_TAXID: 30538; SOURCE 21 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 22 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, SPIKE, BISPECIFIC ANTIBODY, SYZJ001, R15-F7, P14-F8-35, KEYWDS 2 STRUCTURAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR L.WANG REVDAT 1 06-SEP-23 7Y0O 0 JRNL AUTH L.WANG JRNL TITL SARS-COV-2 WT SPIKE IN COMPLEX WITH R15 FAB AND P14 NANOBODY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.40 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) : 4.400 REMARK 3 NUMBER OF PARTICLES : 372940 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 7Y0O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030038. 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 : COMPLEX OF SARS-COV-2 SPIKE IN REMARK 245 COMPLEX WITH R15-F7 AND P14-F18- REMARK 245 35; SARS-COV-2 SPIKE; R15; P14 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 TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2700.00 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L, B 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 ARG A 357 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 405 CG OD1 OD2 REMARK 470 GLU A 406 CG CD OE1 OE2 REMARK 470 ASP A 427 CG OD1 OD2 REMARK 470 ASP A 428 CG OD1 OD2 REMARK 470 GLU A 516 CG CD OE1 OE2 REMARK 470 ASP L 70 CG OD1 OD2 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 A 364 47.30 -140.19 REMARK 500 CYS A 379 175.42 179.88 REMARK 500 SER A 443 40.14 -97.16 REMARK 500 LYS A 444 -177.78 -67.92 REMARK 500 SER A 459 -113.69 60.22 REMARK 500 CYS A 480 -70.38 -64.76 REMARK 500 ASN A 481 -32.89 -136.00 REMARK 500 CYS A 488 145.83 -171.76 REMARK 500 VAL A 503 -21.16 -144.88 REMARK 500 TYR H 27 -153.85 53.47 REMARK 500 ALA H 91 -167.13 -168.12 REMARK 500 TYR H 111 60.48 61.59 REMARK 500 SER L 14 -168.37 -125.02 REMARK 500 ALA L 51 -2.21 64.34 REMARK 500 SER L 52 15.03 -143.04 REMARK 500 LYS B 43 -138.55 59.68 REMARK 500 ALA B 44 73.57 56.60 REMARK 500 SER B 101 -89.09 56.80 REMARK 500 THR B 104 -169.35 -104.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 217 DISTANCE = 6.97 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33551 RELATED DB: EMDB REMARK 900 INTERFACE OF SARS-COV-2 WT SPIKE IN COMPLEX WITH R15 FAB AND P14 REMARK 900 NANOBODY DBREF 7Y0O A 334 527 UNP P0DTC2 SPIKE_SARS2 334 527 DBREF 7Y0O H 1 116 PDB 7Y0O 7Y0O 1 116 DBREF 7Y0O L 0 107 PDB 7Y0O 7Y0O 0 107 DBREF 7Y0O B 1 123 PDB 7Y0O 7Y0O 1 123 SEQRES 1 A 194 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 2 A 194 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 A 194 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 A 194 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 A 194 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 A 194 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 A 194 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 8 A 194 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 A 194 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 A 194 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 A 194 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 A 194 SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 A 194 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 A 194 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 A 194 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 1 H 116 GLN MET GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 H 116 PRO GLY ALA SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 H 116 TYR THR PHE THR SER TYR ALA ILE SER TRP VAL ARG GLN SEQRES 4 H 116 ALA PRO GLY GLN GLY LEU GLU TRP MET GLY ARG ILE ILE SEQRES 5 H 116 PRO ILE LEU GLY ILE ALA ASN TYR ALA GLN LYS PHE GLN SEQRES 6 H 116 GLY ARG VAL THR ILE THR ALA ASP GLU SER THR SER THR SEQRES 7 H 116 ALA TYR MET GLU LEU SER SER ARG SER GLU ASP THR ALA SEQRES 8 H 116 VAL TYR TYR CYS ALA SER GLY ALA PHE TYR TYR GLY SER SEQRES 9 H 116 GLY SER TYR PRO PHE ASP TYR TRP GLY GLN GLY THR SEQRES 1 L 108 GLY ASP ILE GLN LEU THR GLN SER PRO SER SER LEU SER SEQRES 2 L 108 ALA SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SEQRES 3 L 108 SER GLN ASP ILE SER ASP TYR LEU ASN TRP TYR GLN GLN SEQRES 4 L 108 LYS PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SEQRES 5 L 108 SER SER LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SEQRES 6 L 108 SER GLY SER GLY THR ASP PHE THR LEU THR ILE SER ASN SEQRES 7 L 108 LEU GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SEQRES 8 L 108 SER TYR SER ALA PRO ARG THR PHE GLY GLN GLY THR LYS SEQRES 9 L 108 VAL GLU ILE LYS SEQRES 1 B 123 GLU GLU GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 123 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 123 PHE ARG PHE GLY SER TYR TYR MET SER TRP VAL ARG GLN SEQRES 4 B 123 ALA PRO GLY LYS ALA PRO GLU TRP VAL SER ASP ILE ASN SEQRES 5 B 123 THR ARG GLY GLU THR THR ARG TYR SER ASP SER VAL LYS SEQRES 6 B 123 GLY ARG PHE THR ILE ALA ARG ASP ASN ALA ASN ASN THR SEQRES 7 B 123 VAL PHE LEU PHE MET ASN ARG LEU LYS PRO GLU ASP THR SEQRES 8 B 123 ALA VAL TYR TYR CYS ALA VAL ALA ALA SER GLY ASP THR SEQRES 9 B 123 PHE GLU GLY ARG SER ASP PRO ASP TYR TRP GLY GLN GLY SEQRES 10 B 123 THR LEU VAL THR VAL SER FORMUL 5 HOH *18(H2 O) HELIX 1 AA1 PHE A 338 ASN A 343 1 6 HELIX 2 AA2 TYR A 365 SER A 371 1 7 HELIX 3 AA3 SER A 383 LEU A 387 5 5 HELIX 4 AA4 ASP A 405 ILE A 410 5 6 HELIX 5 AA5 LYS A 417 ASN A 422 1 6 HELIX 6 AA6 ALA H 61 GLN H 65 5 5 HELIX 7 AA7 GLN L 79 PHE L 83 5 5 SHEET 1 AA1 5 LYS A 356 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O TYR A 508 N ILE A 402 SHEET 4 AA1 5 CYS A 432 ASN A 437 -1 N CYS A 432 O LEU A 513 SHEET 5 AA1 5 THR A 376 CYS A 379 -1 N THR A 376 O ALA A 435 SHEET 1 AA2 2 LEU A 452 ARG A 454 0 SHEET 2 AA2 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA3 2 ALA H 16 SER H 17 0 SHEET 2 AA3 2 SER H 84 SER H 85 -1 O SER H 85 N ALA H 16 SHEET 1 AA4 3 CYS H 22 LYS H 23 0 SHEET 2 AA4 3 THR H 78 GLU H 82 -1 O ALA H 79 N CYS H 22 SHEET 3 AA4 3 THR H 69 ASP H 73 -1 N THR H 71 O TYR H 80 SHEET 1 AA5 3 LEU H 45 ILE H 51 0 SHEET 2 AA5 3 ILE H 34 GLN H 39 -1 N ILE H 34 O ILE H 51 SHEET 3 AA5 3 CYS H 95 ALA H 96 -1 O ALA H 96 N SER H 35 SHEET 1 AA6 2 THR L 5 SER L 7 0 SHEET 2 AA6 2 THR L 22 ARG L 24 -1 O THR L 22 N SER L 7 SHEET 1 AA7 6 SER L 10 ALA L 13 0 SHEET 2 AA7 6 THR L 102 ILE L 106 1 O LYS L 103 N LEU L 11 SHEET 3 AA7 6 THR L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 AA7 6 LEU L 33 GLN L 38 -1 N ASN L 34 O GLN L 89 SHEET 5 AA7 6 LYS L 45 TYR L 49 -1 O LYS L 45 N GLN L 37 SHEET 6 AA7 6 SER L 53 LEU L 54 -1 O SER L 53 N TYR L 49 SHEET 1 AA8 2 PHE L 62 SER L 67 0 SHEET 2 AA8 2 ASP L 70 ILE L 75 -1 O THR L 74 N SER L 63 SHEET 1 AA9 4 GLU B 6 SER B 7 0 SHEET 2 AA9 4 SER B 21 ALA B 23 -1 O SER B 21 N SER B 7 SHEET 3 AA9 4 THR B 78 PHE B 82 -1 N VAL B 79 O CYS B 22 SHEET 4 AA9 4 THR B 69 ALA B 71 -1 N THR B 69 O PHE B 82 SHEET 1 AB1 2 LEU B 11 VAL B 12 0 SHEET 2 AB1 2 THR B 121 VAL B 122 1 O THR B 121 N VAL B 12 SHEET 1 AB2 4 THR B 58 TYR B 60 0 SHEET 2 AB2 4 LYS B 43 ILE B 51 -1 N ASP B 50 O ARG B 59 SHEET 3 AB2 4 SER B 35 ALA B 40 -1 N ARG B 38 O GLU B 46 SHEET 4 AB2 4 VAL B 93 CYS B 96 -1 O TYR B 95 N VAL B 37 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.05 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.04 SSBOND 5 CYS H 22 CYS H 95 1555 1555 2.03 SSBOND 6 CYS L 23 CYS L 88 1555 1555 2.04 SSBOND 7 CYS B 22 CYS B 96 1555 1555 2.04 CISPEP 1 SER L 7 PRO L 8 0 -9.57 CISPEP 2 ALA L 94 PRO L 95 0 2.71 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