HEADER VIRAL PROTEIN 15-AUG-24 9J66 TITLE CRYO-EM STRUCTURE OF THE SARS-COV-2 S 6P TRIMER IN COMPLEX WITH THE TITLE 2 HUMAN NEUTRALIZING ANTIBODY FAB FRAGMENT CAV-C65 (LOCAL REFINEMENT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAV-C65 HEAVY CHAIN; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CAV-C65 LIGHT CHAIN; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SPIKE PROTEIN S1; COMPND 11 CHAIN: A, D; 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 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 13 2; SOURCE 14 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 15 ORGANISM_TAXID: 2697049; SOURCE 16 STRAIN: 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 SARS-COV-2, SPIKE GLYCOPROTEIN, NEUTRALIZING ANTIBODY, VIRAL PROTEIN- KEYWDS 2 IMMUNE SYSTEM COMPLEX (LOCAL REFINEMENT), VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR X.JING,Y.CHEN,P.GONG REVDAT 1 12-MAR-25 9J66 0 JRNL AUTH M.XU,Z.ZHANG,Y.SUN,H.MAI,S.LIU,S.LIU,K.LV,F.YU,Y.WANG,X.YUE, JRNL AUTH 2 J.ZHANG,X.CAI,R.ZHAO,H.LU,L.LIU,H.LUO,H.ZHAO,Y.WANG,P.GONG, JRNL AUTH 3 S.CHEN,X.JING,J.ZHAO,Y.Q.CHEN JRNL TITL IGA CLASS SWITCHING ENHANCES NEUTRALIZING POTENCY AGAINST JRNL TITL 2 SARS-COV-2 BY INCREASED ANTIBODY HINGE FLEXIBILITY. JRNL REF ANTIVIRAL RES. V. 235 06082 2025 JRNL REFN ISSN 0166-3542 JRNL PMID 39828085 JRNL DOI 10.1016/J.ANTIVIRAL.2025.106082 REMARK 2 REMARK 2 RESOLUTION. 3.55 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) : 3.550 REMARK 3 NUMBER OF PARTICLES : 579375 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 9J66 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 20-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1300047054. 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 THE SARS-COV-2 S 6P REMARK 245 TRIMER WITH THE HUMAN REMARK 245 NEUTRALIZING ANTIBODY FAB REMARK 245 FRAGMENT CAV-C65 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 : 8.00 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 : JEOL CRYO ARM 300 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 4000.00 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: B, C, A, D 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 SER B 125 REMARK 465 VAL B 126 REMARK 465 ARG B 127 REMARK 465 SER B 128 REMARK 465 THR B 129 REMARK 465 LYS B 130 REMARK 465 GLY B 131 REMARK 465 PRO B 132 REMARK 465 SER B 133 REMARK 465 VAL B 134 REMARK 465 PHE B 135 REMARK 465 PRO B 136 REMARK 465 LEU B 137 REMARK 465 ALA B 138 REMARK 465 PRO B 139 REMARK 465 SER B 140 REMARK 465 SER B 141 REMARK 465 LYS B 142 REMARK 465 SER B 143 REMARK 465 THR B 144 REMARK 465 SER B 145 REMARK 465 GLY B 146 REMARK 465 GLY B 147 REMARK 465 THR B 148 REMARK 465 ALA B 149 REMARK 465 ALA B 150 REMARK 465 LEU B 151 REMARK 465 GLY B 152 REMARK 465 CYS B 153 REMARK 465 LEU B 154 REMARK 465 VAL B 155 REMARK 465 LYS B 156 REMARK 465 ASP B 157 REMARK 465 TYR B 158 REMARK 465 PHE B 159 REMARK 465 PRO B 160 REMARK 465 GLU B 161 REMARK 465 PRO B 162 REMARK 465 VAL B 163 REMARK 465 THR B 164 REMARK 465 VAL B 165 REMARK 465 SER B 166 REMARK 465 TRP B 167 REMARK 465 ASN B 168 REMARK 465 SER B 169 REMARK 465 GLY B 170 REMARK 465 ALA B 171 REMARK 465 LEU B 172 REMARK 465 THR B 173 REMARK 465 SER B 174 REMARK 465 GLY B 175 REMARK 465 VAL B 176 REMARK 465 HIS B 177 REMARK 465 THR B 178 REMARK 465 PHE B 179 REMARK 465 PRO B 180 REMARK 465 ALA B 181 REMARK 465 VAL B 182 REMARK 465 LEU B 183 REMARK 465 GLN B 184 REMARK 465 SER B 185 REMARK 465 SER B 186 REMARK 465 GLY B 187 REMARK 465 LEU B 188 REMARK 465 TYR B 189 REMARK 465 SER B 190 REMARK 465 LEU B 191 REMARK 465 SER B 192 REMARK 465 SER B 193 REMARK 465 VAL B 194 REMARK 465 VAL B 195 REMARK 465 THR B 196 REMARK 465 VAL B 197 REMARK 465 PRO B 198 REMARK 465 SER B 199 REMARK 465 SER B 200 REMARK 465 SER B 201 REMARK 465 LEU B 202 REMARK 465 GLY B 203 REMARK 465 THR B 204 REMARK 465 GLN B 205 REMARK 465 THR B 206 REMARK 465 TYR B 207 REMARK 465 ILE B 208 REMARK 465 CYS B 209 REMARK 465 ASN B 210 REMARK 465 VAL B 211 REMARK 465 ASN B 212 REMARK 465 HIS B 213 REMARK 465 LYS B 214 REMARK 465 PRO B 215 REMARK 465 SER B 216 REMARK 465 ASN B 217 REMARK 465 THR B 218 REMARK 465 LYS B 219 REMARK 465 VAL B 220 REMARK 465 ASP B 221 REMARK 465 LYS B 222 REMARK 465 LYS B 223 REMARK 465 VAL B 224 REMARK 465 GLU B 225 REMARK 465 PRO B 226 REMARK 465 LYS B 227 REMARK 465 SER B 228 REMARK 465 CYS B 229 REMARK 465 SER B 230 REMARK 465 GLY B 231 REMARK 465 ARG C 108 REMARK 465 THR C 109 REMARK 465 VAL C 110 REMARK 465 ALA C 111 REMARK 465 ALA C 112 REMARK 465 PRO C 113 REMARK 465 SER C 114 REMARK 465 VAL C 115 REMARK 465 PHE C 116 REMARK 465 ILE C 117 REMARK 465 PHE C 118 REMARK 465 PRO C 119 REMARK 465 PRO C 120 REMARK 465 SER C 121 REMARK 465 ASP C 122 REMARK 465 GLU C 123 REMARK 465 GLN C 124 REMARK 465 LEU C 125 REMARK 465 LYS C 126 REMARK 465 SER C 127 REMARK 465 GLY C 128 REMARK 465 THR C 129 REMARK 465 ALA C 130 REMARK 465 SER C 131 REMARK 465 VAL C 132 REMARK 465 VAL C 133 REMARK 465 CYS C 134 REMARK 465 LEU C 135 REMARK 465 LEU C 136 REMARK 465 ASN C 137 REMARK 465 ASN C 138 REMARK 465 PHE C 139 REMARK 465 TYR C 140 REMARK 465 PRO C 141 REMARK 465 ARG C 142 REMARK 465 GLU C 143 REMARK 465 ALA C 144 REMARK 465 LYS C 145 REMARK 465 VAL C 146 REMARK 465 GLN C 147 REMARK 465 TRP C 148 REMARK 465 LYS C 149 REMARK 465 VAL C 150 REMARK 465 ASP C 151 REMARK 465 ASN C 152 REMARK 465 ALA C 153 REMARK 465 LEU C 154 REMARK 465 GLN C 155 REMARK 465 SER C 156 REMARK 465 GLY C 157 REMARK 465 ASN C 158 REMARK 465 SER C 159 REMARK 465 GLN C 160 REMARK 465 GLU C 161 REMARK 465 SER C 162 REMARK 465 VAL C 163 REMARK 465 THR C 164 REMARK 465 GLU C 165 REMARK 465 GLN C 166 REMARK 465 ASP C 167 REMARK 465 SER C 168 REMARK 465 LYS C 169 REMARK 465 ASP C 170 REMARK 465 SER C 171 REMARK 465 THR C 172 REMARK 465 TYR C 173 REMARK 465 SER C 174 REMARK 465 LEU C 175 REMARK 465 SER C 176 REMARK 465 SER C 177 REMARK 465 THR C 178 REMARK 465 LEU C 179 REMARK 465 THR C 180 REMARK 465 LEU C 181 REMARK 465 SER C 182 REMARK 465 LYS C 183 REMARK 465 ALA C 184 REMARK 465 ASP C 185 REMARK 465 TYR C 186 REMARK 465 GLU C 187 REMARK 465 LYS C 188 REMARK 465 HIS C 189 REMARK 465 LYS C 190 REMARK 465 VAL C 191 REMARK 465 TYR C 192 REMARK 465 ALA C 193 REMARK 465 CYS C 194 REMARK 465 GLU C 195 REMARK 465 VAL C 196 REMARK 465 THR C 197 REMARK 465 HIS C 198 REMARK 465 GLN C 199 REMARK 465 GLY C 200 REMARK 465 LEU C 201 REMARK 465 SER C 202 REMARK 465 SER C 203 REMARK 465 PRO C 204 REMARK 465 VAL C 205 REMARK 465 THR C 206 REMARK 465 LYS C 207 REMARK 465 SER C 208 REMARK 465 PHE C 209 REMARK 465 ASN C 210 REMARK 465 ARG C 211 REMARK 465 GLY C 212 REMARK 465 GLU C 213 REMARK 465 CYS C 214 REMARK 465 LEU A 518 REMARK 465 HIS A 519 REMARK 465 LYS D 356 REMARK 465 ARG D 357 REMARK 465 ILE D 358 REMARK 465 LEU D 368 REMARK 465 TYR D 369 REMARK 465 ASN D 370 REMARK 465 SER D 371 REMARK 465 ALA D 372 REMARK 465 SER D 373 REMARK 465 PHE D 374 REMARK 465 LYS D 386 REMARK 465 LEU D 387 REMARK 465 ASN D 388 REMARK 465 ASP D 389 REMARK 465 VAL D 445 REMARK 465 GLY D 446 REMARK 465 PHE D 464 REMARK 465 GLU D 465 REMARK 465 ARG D 466 REMARK 465 ASP D 467 REMARK 465 ILE D 468 REMARK 465 SER D 469 REMARK 465 THR D 470 REMARK 465 GLU D 471 REMARK 465 ILE D 472 REMARK 465 TYR D 473 REMARK 465 GLN D 474 REMARK 465 ALA D 475 REMARK 465 GLY D 476 REMARK 465 SER D 477 REMARK 465 THR D 478 REMARK 465 PRO D 479 REMARK 465 CYS D 480 REMARK 465 ASN D 481 REMARK 465 GLY D 482 REMARK 465 VAL D 483 REMARK 465 GLU D 484 REMARK 465 GLY D 485 REMARK 465 PHE D 486 REMARK 465 ASN D 487 REMARK 465 CYS D 488 REMARK 465 TYR D 489 REMARK 465 PHE D 490 REMARK 465 PRO D 491 REMARK 465 LEU D 492 REMARK 465 GLN D 493 REMARK 465 SER D 494 REMARK 465 TYR D 495 REMARK 465 GLY D 496 REMARK 465 PHE D 497 REMARK 465 LEU D 518 REMARK 465 HIS D 519 REMARK 465 ALA D 520 REMARK 465 PRO D 521 REMARK 465 ALA D 522 REMARK 465 THR D 523 REMARK 465 VAL D 524 REMARK 465 CYS D 525 REMARK 465 GLY D 526 REMARK 465 PRO D 527 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 GLN B 1 CG CD OE1 NE2 REMARK 470 LYS B 13 CG CD CE NZ REMARK 470 LYS B 19 CG CD CE NZ REMARK 470 LYS B 23 CG CD CE NZ REMARK 470 PHE B 29 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 74 CG CD CE NZ REMARK 470 LEU B 86 CG CD1 CD2 REMARK 470 ARG B 87 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 89 CG CD OE1 OE2 REMARK 470 ASP B 90 CG OD1 OD2 REMARK 470 THR B 91 OG1 CG2 REMARK 470 THR B 99 OG1 CG2 REMARK 470 GLU B 102 CG CD OE1 OE2 REMARK 470 MET B 103 CG SD CE REMARK 470 GLU B 107 CG CD OE1 OE2 REMARK 470 LEU B 118 CG CD1 CD2 REMARK 470 ASP C 1 CG OD1 OD2 REMARK 470 VAL C 19 CG1 CG2 REMARK 470 ARG C 24 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 27 CG CD OE1 NE2 REMARK 470 SER C 30 OG REMARK 470 LYS C 42 CG CD CE NZ REMARK 470 SER C 53 OG REMARK 470 SER C 67 OG REMARK 470 THR C 69 OG1 CG2 REMARK 470 ASP C 70 CG OD1 OD2 REMARK 470 GLN C 79 CG CD OE1 NE2 REMARK 470 ASP C 82 CG OD1 OD2 REMARK 470 SER C 93 OG REMARK 470 LYS C 103 CG CD CE NZ REMARK 470 LYS C 107 CG CD CE NZ REMARK 470 ASP A 389 CG OD1 OD2 REMARK 470 GLU A 406 CG CD OE1 OE2 REMARK 470 THR A 415 OG1 CG2 REMARK 470 LYS A 417 CG CD CE NZ REMARK 470 LEU A 441 CG CD1 CD2 REMARK 470 LYS A 444 CG CD CE NZ REMARK 470 LYS A 462 CG CD CE NZ REMARK 470 GLU A 465 CG CD OE1 OE2 REMARK 470 GLN A 474 CG CD OE1 NE2 REMARK 470 ASN A 481 CG OD1 ND2 REMARK 470 TYR A 505 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG D 346 CG CD NE CZ NH1 NH2 REMARK 470 TYR D 351 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN D 354 CG OD1 ND2 REMARK 470 ASP D 364 CG OD1 OD2 REMARK 470 TYR D 365 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL D 367 CG1 CG2 REMARK 470 LEU D 390 CG CD1 CD2 REMARK 470 CYS D 391 SG REMARK 470 PHE D 392 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN D 394 CG OD1 ND2 REMARK 470 ASP D 398 CG OD1 OD2 REMARK 470 ARG D 403 CG CD NE CZ NH1 NH2 REMARK 470 ASP D 405 CG OD1 OD2 REMARK 470 GLU D 406 CG CD OE1 OE2 REMARK 470 ARG D 408 CG CD NE CZ NH1 NH2 REMARK 470 GLN D 409 CG CD OE1 NE2 REMARK 470 GLN D 414 CG CD OE1 NE2 REMARK 470 LYS D 417 CG CD CE NZ REMARK 470 ILE D 418 CG1 CG2 CD1 REMARK 470 ASP D 420 CG OD1 OD2 REMARK 470 LYS D 424 CG CD CE NZ REMARK 470 ASP D 427 CG OD1 OD2 REMARK 470 ASP D 428 CG OD1 OD2 REMARK 470 LYS D 444 CG CD CE NZ REMARK 470 ASN D 448 CG OD1 ND2 REMARK 470 TYR D 449 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN D 450 CG OD1 ND2 REMARK 470 TYR D 451 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG D 454 CG CD NE CZ NH1 NH2 REMARK 470 PHE D 456 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG D 457 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 458 CG CD CE NZ REMARK 470 SER D 459 OG REMARK 470 ASN D 460 CG OD1 ND2 REMARK 470 LYS D 462 CG CD CE NZ REMARK 470 GLN D 498 CG CD OE1 NE2 REMARK 470 THR D 500 OG1 CG2 REMARK 470 TYR D 505 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU D 516 CG CD OE1 OE2 REMARK 470 LEU D 517 CG CD1 CD2 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 SER B 88 -126.86 60.24 REMARK 500 MET B 103 -95.41 57.13 REMARK 500 SER C 30 -126.34 56.29 REMARK 500 ALA C 51 -4.08 67.83 REMARK 500 PHE C 83 64.25 -101.77 REMARK 500 PRO C 95 79.15 -67.48 REMARK 500 VAL A 341 -61.78 -108.62 REMARK 500 ASN A 388 47.54 -85.68 REMARK 500 THR A 523 18.12 -140.42 REMARK 500 ASN D 360 54.39 38.29 REMARK 500 CYS D 361 -169.39 -126.29 REMARK 500 SER D 366 53.54 -91.75 REMARK 500 TYR D 449 -169.01 -163.00 REMARK 500 PHE D 456 14.85 -140.18 REMARK 500 LYS D 458 -110.57 50.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61167 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE SARS-COV-2 S 6P TRIMER IN COMPLEX WITH THE REMARK 900 HUMAN NEUTRALIZING ANTIBODY FAB FRAGMENT CAV-C65 (LOCAL REFINEMENT) DBREF 9J66 B 1 231 PDB 9J66 9J66 1 231 DBREF 9J66 C 1 214 PDB 9J66 9J66 1 214 DBREF 9J66 A 333 527 UNP P0DTC2 SPIKE_SARS2 333 527 DBREF 9J66 D 333 527 UNP P0DTC2 SPIKE_SARS2 333 527 SEQRES 1 B 231 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 B 231 PRO GLY SER SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 B 231 GLY THR PHE SER SER TYR THR ILE SER TRP VAL ARG GLN SEQRES 4 B 231 ALA PRO GLY GLN GLY LEU GLU TRP MET GLY ARG ILE ILE SEQRES 5 B 231 PRO ILE PHE GLY ILE ALA ASN TYR ALA GLN LYS PHE GLN SEQRES 6 B 231 GLY ARG VAL THR ILE THR ALA ASP LYS SER THR SER THR SEQRES 7 B 231 ALA TYR MET GLU LEU SER SER LEU ARG SER GLU ASP THR SEQRES 8 B 231 ALA VAL TYR TYR CYS ALA ARG THR PRO LEU GLU MET ALA SEQRES 9 B 231 THR GLU GLU GLY TYR PHE ASP TYR TRP GLY GLN GLY THR SEQRES 10 B 231 LEU VAL THR VAL SER SER ALA SER VAL ARG SER THR LYS SEQRES 11 B 231 GLY PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SER SEQRES 12 B 231 THR SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS SEQRES 13 B 231 ASP TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER SEQRES 14 B 231 GLY ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL SEQRES 15 B 231 LEU GLN SER SER GLY LEU TYR SER LEU SER SER VAL VAL SEQRES 16 B 231 THR VAL PRO SER SER SER LEU GLY THR GLN THR TYR ILE SEQRES 17 B 231 CYS ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP SEQRES 18 B 231 LYS LYS VAL GLU PRO LYS SER CYS SER GLY SEQRES 1 C 214 ASP ILE GLN MET THR GLN SER PRO SER SER VAL SER ALA SEQRES 2 C 214 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 C 214 GLN GLY ILE SER SER TRP LEU ALA TRP TYR GLN GLN THR SEQRES 4 C 214 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SER SEQRES 5 C 214 SER LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 C 214 GLY SER GLY THR ASP PHE THR LEU THR ILE SER SER LEU SEQRES 7 C 214 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN ALA SEQRES 8 C 214 ASN SER PHE PRO PHE THR PHE GLY PRO GLY THR LYS VAL SEQRES 9 C 214 ASP ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 C 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 C 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 C 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 C 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 C 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 C 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 C 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 C 214 PHE ASN ARG GLY GLU CYS SEQRES 1 A 195 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 A 195 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 A 195 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 A 195 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 A 195 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 A 195 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 A 195 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 A 195 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 A 195 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 A 195 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 A 195 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 A 195 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 A 195 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 A 195 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 A 195 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 1 D 195 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 D 195 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 D 195 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 D 195 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 D 195 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 D 195 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 D 195 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 D 195 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 D 195 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 D 195 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 D 195 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 D 195 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 D 195 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 D 195 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 D 195 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO HELIX 1 AA1 PRO A 337 VAL A 341 5 5 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 TYR A 365 ASN A 370 1 6 HELIX 4 AA4 SER A 383 LEU A 390 5 8 HELIX 5 AA5 GLY A 404 ARG A 408 1 5 HELIX 6 AA6 LYS A 417 ASN A 422 1 6 HELIX 7 AA7 GLY A 502 TYR A 505 5 4 HELIX 8 AA8 PRO D 337 PHE D 342 1 6 HELIX 9 AA9 ASP D 405 ILE D 410 5 6 HELIX 10 AB1 GLY D 416 TYR D 421 1 6 SHEET 1 AA1 4 GLN B 3 GLN B 6 0 SHEET 2 AA1 4 SER B 21 SER B 25 -1 O LYS B 23 N VAL B 5 SHEET 3 AA1 4 THR B 78 LEU B 86 -1 O ALA B 79 N CYS B 22 SHEET 4 AA1 4 SER B 16 VAL B 18 -1 N SER B 16 O LEU B 86 SHEET 1 AA2 4 GLN B 3 GLN B 6 0 SHEET 2 AA2 4 SER B 21 SER B 25 -1 O LYS B 23 N VAL B 5 SHEET 3 AA2 4 THR B 78 LEU B 86 -1 O ALA B 79 N CYS B 22 SHEET 4 AA2 4 VAL B 68 ASP B 73 -1 N THR B 71 O TYR B 80 SHEET 1 AA3 4 LEU B 45 ARG B 50 0 SHEET 2 AA3 4 TYR B 32 GLN B 39 -1 N ARG B 38 O GLU B 46 SHEET 3 AA3 4 ALA B 92 GLU B 102 -1 O TYR B 95 N VAL B 37 SHEET 4 AA3 4 TYR B 112 TRP B 113 -1 O TYR B 112 N ARG B 98 SHEET 1 AA4 3 THR B 105 GLU B 106 0 SHEET 2 AA4 3 ALA B 92 GLU B 102 -1 N GLU B 102 O THR B 105 SHEET 3 AA4 3 THR B 117 VAL B 119 -1 O THR B 117 N TYR B 94 SHEET 1 AA5 3 VAL C 19 ARG C 24 0 SHEET 2 AA5 3 ASP C 70 ILE C 75 -1 O LEU C 73 N ILE C 21 SHEET 3 AA5 3 PHE C 62 SER C 67 -1 N SER C 63 O THR C 74 SHEET 1 AA6 4 SER C 53 LEU C 54 0 SHEET 2 AA6 4 ILE C 48 TYR C 49 -1 N TYR C 49 O SER C 53 SHEET 3 AA6 4 ALA C 34 TRP C 35 -1 N TRP C 35 O ILE C 48 SHEET 4 AA6 4 CYS C 88 GLN C 89 -1 O GLN C 89 N ALA C 34 SHEET 1 AA7 2 THR C 85 TYR C 86 0 SHEET 2 AA7 2 THR C 102 LYS C 103 -1 O THR C 102 N TYR C 86 SHEET 1 AA8 5 ASN A 354 ILE A 358 0 SHEET 2 AA8 5 VAL A 395 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA8 5 PRO A 507 PHE A 515 -1 O VAL A 510 N PHE A 400 SHEET 4 AA8 5 GLY A 431 ASN A 437 -1 N CYS A 432 O LEU A 513 SHEET 5 AA8 5 THR A 376 CYS A 379 -1 N THR A 376 O ALA A 435 SHEET 1 AA9 2 LEU A 452 ARG A 454 0 SHEET 2 AA9 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AB1 2 TYR A 473 GLN A 474 0 SHEET 2 AB1 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AB2 3 VAL D 395 ARG D 403 0 SHEET 2 AB2 3 PRO D 507 PHE D 515 -1 O TYR D 508 N ILE D 402 SHEET 3 AB2 3 CYS D 432 ASN D 437 -1 N ILE D 434 O VAL D 511 SSBOND 1 CYS B 22 CYS B 96 1555 1555 2.03 SSBOND 2 CYS C 23 CYS C 88 1555 1555 2.04 SSBOND 3 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 4 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 5 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 6 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 7 CYS D 336 CYS D 361 1555 1555 2.03 SSBOND 8 CYS D 379 CYS D 432 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 TER 887 ALA B 124 TER 1648 LYS C 107 TER 3133 PRO A 527 TER 4048 LEU D 517 CONECT 144 686 CONECT 686 144 CONECT 1045 1509 CONECT 1509 1045 CONECT 1677 1884 CONECT 1884 1677 CONECT 2024 2424 CONECT 2111 3120 CONECT 2424 2024 CONECT 2796 2850 CONECT 2850 2796 CONECT 3120 2111 CONECT 3162 3325 CONECT 3325 3162 CONECT 3397 3714 CONECT 3714 3397 MASTER 503 0 0 10 36 0 0 6 4044 4 16 65 END