HEADER ANTIVIRAL PROTEIN 27-JUN-26 43DZ TITLE THE COMPLEX STRUCTURE OF RBD AND KXD-I42 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: THE HEAVY CHAIN OF KXD-I42 FAB; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: THE LIGHT CHAIN OF KXD-I42 FAB; COMPND 11 CHAIN: C; COMPND 12 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 KEYWDS COMPLEX, SPIKE, NEUTRALIZING ANTIBODY, ANTIVIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.GE,C.NIE REVDAT 1 11-NOV-26 43DZ 0 JRNL AUTH J.GE,C.NIE JRNL TITL THE COMPLEX STRUCTURE OF RBD AND KXD-I42 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC 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) : 3.560 REMARK 3 NUMBER OF PARTICLES : 88662 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 43DZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 30-JUN-26. REMARK 100 THE DEPOSITION ID IS D_1300076320. 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 RBD AND KXD-I42 FAB 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 : 7.20 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 : TFS FALCON 4I (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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: A, B, C 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 ARG A 457 REMARK 465 GLN A 474 REMARK 465 ALA A 475 REMARK 465 SER A 477 REMARK 465 THR A 478 REMARK 465 PRO A 479 REMARK 465 CYS A 480 REMARK 465 ASN A 481 REMARK 465 GLY A 482 REMARK 465 VAL A 483 REMARK 465 GLU A 484 REMARK 465 GLY A 485 REMARK 465 PHE A 486 REMARK 465 ASN A 487 REMARK 465 LYS A 528 REMARK 465 LYS A 529 REMARK 465 GLU B 1 REMARK 465 SER B 121 REMARK 465 GLN C 1 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 LYS A 386 CG CD CE NZ REMARK 470 TYR A 495 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 16 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 87 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 17 CG CD NE CZ NH1 NH2 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 A 337 48.75 -79.63 REMARK 500 GLN A 409 44.32 -91.64 REMARK 500 ASP A 428 35.33 -98.98 REMARK 500 SER B 55 11.79 59.99 REMARK 500 LEU B 101 -134.83 58.68 REMARK 500 PRO B 107 -175.18 -69.93 REMARK 500 ASN C 52 -13.27 71.88 REMARK 500 ASN C 53 -23.10 -140.99 REMARK 500 ASN C 97 76.46 58.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 403 0.29 SIDE CHAIN REMARK 500 ARG A 466 0.26 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-81809 RELATED DB: EMDB REMARK 900 THE COMPLEX STRUCTURE OF RBD AND KXD-I42 DBREF 43DZ A 334 529 UNP P0DTC2 SPIKE_SARS2 334 529 DBREF 43DZ B 1 121 PDB 43DZ 43DZ 1 121 DBREF 43DZ C 1 109 PDB 43DZ 43DZ 1 109 SEQRES 1 A 196 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 2 A 196 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 A 196 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 A 196 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 A 196 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 A 196 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 A 196 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 8 A 196 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 A 196 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 A 196 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 A 196 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 A 196 SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 A 196 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 A 196 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 A 196 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO LYS SEQRES 16 A 196 LYS SEQRES 1 B 121 GLU VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 121 PRO GLY ARG SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 121 PHE THR PHE ASP ASP TYR ALA MET TYR TRP ILE ARG GLN SEQRES 4 B 121 ALA PRO GLY ARG GLY LEU GLU TRP VAL SER GLY ILE SER SEQRES 5 B 121 TRP ASN SER GLY ASN ILE GLU TYR ALA ASP SER VAL LYS SEQRES 6 B 121 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 B 121 LEU TYR LEU GLN MET ASN ARG LEU ARG PRO GLU ASP THR SEQRES 8 B 121 ALA PHE TYR TYR CYS ALA LYS GLY GLN LEU GLY GLU PHE SEQRES 9 B 121 PRO PHE PRO VAL ASP PHE TRP GLY GLN GLY THR THR VAL SEQRES 10 B 121 THR VAL SER SER SEQRES 1 C 109 GLN ALA VAL VAL THR GLN PRO PRO SER ALA SER GLY THR SEQRES 2 C 109 PRO GLY GLN ARG VAL SER ILE SER CYS SER GLY SER SER SEQRES 3 C 109 SER ASN ILE GLY THR TYR PRO VAL SER TRP TYR GLN GLN SEQRES 4 C 109 LEU PRO GLY THR ALA PRO LYS LEU LEU ILE TYR SER ASN SEQRES 5 C 109 ASN GLN ARG PRO SER GLY VAL PRO ASP ARG PHE SER GLY SEQRES 6 C 109 SER LYS SER GLY THR SER ALA SER LEU ALA ILE THR GLY SEQRES 7 C 109 LEU GLN SER GLU ASP GLU THR ASP CYS TYR CYS ALA VAL SEQRES 8 C 109 TRP ASP ASP ARG VAL ASN GLY LEU VAL PHE GLY GLY GLY SEQRES 9 C 109 THR GLU LEU THR VAL HELIX 1 AA1 PRO A 337 ASN A 343 1 7 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 SER A 383 ASN A 388 5 6 HELIX 4 AA4 ARG A 403 ILE A 410 5 8 HELIX 5 AA5 LYS A 417 ASN A 422 1 6 HELIX 6 AA6 ASP B 62 LYS B 65 5 4 HELIX 7 AA7 ARG B 87 THR B 91 5 5 HELIX 8 AA8 GLN C 80 GLU C 84 5 5 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ILE A 402 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 TYR A 508 GLU A 516 -1 O VAL A 510 N PHE A 400 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 PHE A 374 TYR A 380 -1 N TYR A 380 O GLY A 431 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 4 GLN B 3 SER B 7 0 SHEET 2 AA3 4 LEU B 18 SER B 25 -1 O SER B 25 N GLN B 3 SHEET 3 AA3 4 SER B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA3 4 PHE B 68 ASP B 73 -1 N THR B 69 O GLN B 82 SHEET 1 AA4 6 GLY B 10 VAL B 12 0 SHEET 2 AA4 6 THR B 115 VAL B 119 1 O THR B 118 N GLY B 10 SHEET 3 AA4 6 ALA B 92 GLY B 99 -1 N TYR B 94 O THR B 115 SHEET 4 AA4 6 MET B 34 GLN B 39 -1 N ILE B 37 O TYR B 95 SHEET 5 AA4 6 LEU B 45 ILE B 51 -1 O SER B 49 N TRP B 36 SHEET 6 AA4 6 ILE B 58 TYR B 60 -1 O GLU B 59 N GLY B 50 SHEET 1 AA5 4 GLY B 10 VAL B 12 0 SHEET 2 AA5 4 THR B 115 VAL B 119 1 O THR B 118 N GLY B 10 SHEET 3 AA5 4 ALA B 92 GLY B 99 -1 N TYR B 94 O THR B 115 SHEET 4 AA5 4 VAL B 108 TRP B 111 -1 O ASP B 109 N LYS B 98 SHEET 1 AA6 3 VAL C 18 SER C 23 0 SHEET 2 AA6 3 SER C 71 ILE C 76 -1 O LEU C 74 N ILE C 20 SHEET 3 AA6 3 PHE C 63 SER C 68 -1 N SER C 64 O ALA C 75 SHEET 1 AA7 4 LYS C 46 ILE C 49 0 SHEET 2 AA7 4 VAL C 34 GLN C 39 -1 N GLN C 38 O LYS C 46 SHEET 3 AA7 4 THR C 85 ASP C 93 -1 O ALA C 90 N SER C 35 SHEET 4 AA7 4 GLY C 98 PHE C 101 -1 O VAL C 100 N VAL C 91 SHEET 1 AA8 4 LYS C 46 ILE C 49 0 SHEET 2 AA8 4 VAL C 34 GLN C 39 -1 N GLN C 38 O LYS C 46 SHEET 3 AA8 4 THR C 85 ASP C 93 -1 O ALA C 90 N SER C 35 SHEET 4 AA8 4 THR C 105 LEU C 107 -1 O THR C 105 N CYS C 87 SSBOND 1 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 2 CYS A 391 CYS A 525 1555 1555 2.87 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 CONECT 369 778 CONECT 455 1412 CONECT 778 369 CONECT 1412 455 MASTER 177 0 0 8 32 0 0 6 3126 3 4 35 END