HEADER PROTEIN BINDING 25-JUL-21 7FG3 TITLE MAJOR CRYO-EM STRUCTURE OF S PROTEIN TRIMER OF SARS-COV2 WITH K-874, TITLE 2 COMPOSITE MAP COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: K-874A VHH; COMPND 8 CHAIN: D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS ANTIBODY, PROTEIN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR C.SONG,K.KATAYAMA,K.MURATA REVDAT 2 23-MAR-22 7FG3 1 JRNL REVDAT 1 29-SEP-21 7FG3 0 JRNL AUTH K.HAGA,R.TAKAI-TODAKA,Y.MATSUMURA,C.SONG,T.TAKANO,T.TOJO, JRNL AUTH 2 A.NAGAMI,Y.ISHIDA,H.MASAKI,M.TSUCHIYA,T.EBISUDANI, JRNL AUTH 3 S.SUGIMOTO,T.SATO,H.YASUDA,K.FUKUNAGA,A.SAWADA,N.NEMOTO, JRNL AUTH 4 K.MURATA,T.MORIMOTO,K.KATAYAMA JRNL TITL NASAL DELIVERY OF SINGLE-DOMAIN ANTIBODY IMPROVES SYMPTOMS JRNL TITL 2 OF SARS-COV-2 INFECTION IN AN ANIMAL MODEL. JRNL REF PLOS PATHOG. V. 17 09542 2021 JRNL REFN ESSN 1553-7374 JRNL PMID 34648602 JRNL DOI 10.1371/JOURNAL.PPAT.1009542 REMARK 2 REMARK 2 RESOLUTION. 3.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, CTFFIND, COOT, PHENIX, RELION, REMARK 3 RELION, RELION, RELION REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 146.000 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) : 3.900 REMARK 3 NUMBER OF PARTICLES : 115297 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 7FG3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1300023467. 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 : SEVERE ACUTE RESPIRATORY REMARK 245 SYNDROME-RELATED CORONAVIRUS 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 : 6552 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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 : 0.10 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 : 75000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 PHE A 2 REMARK 465 VAL A 3 REMARK 465 PHE A 4 REMARK 465 LEU A 5 REMARK 465 VAL A 6 REMARK 465 LEU A 7 REMARK 465 LEU A 8 REMARK 465 PRO A 9 REMARK 465 LEU A 10 REMARK 465 VAL A 11 REMARK 465 SER A 12 REMARK 465 SER A 13 REMARK 465 GLN A 14 REMARK 465 CYS A 15 REMARK 465 VAL A 16 REMARK 465 ASN A 17 REMARK 465 LEU A 18 REMARK 465 THR A 19 REMARK 465 THR A 20 REMARK 465 ARG A 21 REMARK 465 THR A 22 REMARK 465 GLN A 23 REMARK 465 LEU A 24 REMARK 465 PRO A 25 REMARK 465 PRO A 26 REMARK 465 VAL A 70 REMARK 465 SER A 71 REMARK 465 GLY A 72 REMARK 465 THR A 73 REMARK 465 ASN A 74 REMARK 465 GLY A 75 REMARK 465 THR A 76 REMARK 465 LYS A 77 REMARK 465 ARG A 78 REMARK 465 PHE A 79 REMARK 465 PHE A 140 REMARK 465 LEU A 141 REMARK 465 GLY A 142 REMARK 465 VAL A 143 REMARK 465 TYR A 144 REMARK 465 TYR A 145 REMARK 465 HIS A 146 REMARK 465 LYS A 147 REMARK 465 ASN A 148 REMARK 465 ASN A 149 REMARK 465 LYS A 150 REMARK 465 SER A 151 REMARK 465 TRP A 152 REMARK 465 MET A 153 REMARK 465 GLU A 154 REMARK 465 SER A 155 REMARK 465 GLU A 156 REMARK 465 PHE A 157 REMARK 465 ARG A 158 REMARK 465 LEU A 244 REMARK 465 HIS A 245 REMARK 465 ARG A 246 REMARK 465 SER A 247 REMARK 465 TYR A 248 REMARK 465 LEU A 249 REMARK 465 THR A 250 REMARK 465 PRO A 251 REMARK 465 GLY A 252 REMARK 465 ASP A 253 REMARK 465 SER A 254 REMARK 465 SER A 255 REMARK 465 SER A 256 REMARK 465 GLY A 257 REMARK 465 TRP A 258 REMARK 465 LYS A 835 REMARK 465 GLN A 836 REMARK 465 TYR A 837 REMARK 465 GLY A 838 REMARK 465 ASP A 839 REMARK 465 CYS A 840 REMARK 465 LEU A 841 REMARK 465 GLY A 842 REMARK 465 ASP A 843 REMARK 465 ILE A 844 REMARK 465 ALA A 845 REMARK 465 ALA A 846 REMARK 465 ARG A 847 REMARK 465 ASP A 848 REMARK 465 LEU A 849 REMARK 465 ILE A 850 REMARK 465 CYS A 851 REMARK 465 ALA A 852 REMARK 465 ASP A 1139 REMARK 465 PRO A 1140 REMARK 465 LEU A 1141 REMARK 465 GLN A 1142 REMARK 465 PRO A 1143 REMARK 465 GLU A 1144 REMARK 465 LEU A 1145 REMARK 465 ASP A 1146 REMARK 465 SER A 1147 REMARK 465 PHE A 1148 REMARK 465 LYS A 1149 REMARK 465 GLU A 1150 REMARK 465 GLU A 1151 REMARK 465 LEU A 1152 REMARK 465 ASP A 1153 REMARK 465 LYS A 1154 REMARK 465 TYR A 1155 REMARK 465 PHE A 1156 REMARK 465 LYS A 1157 REMARK 465 ASN A 1158 REMARK 465 HIS A 1159 REMARK 465 THR A 1160 REMARK 465 SER A 1161 REMARK 465 PRO A 1162 REMARK 465 ASP A 1163 REMARK 465 VAL A 1164 REMARK 465 ASP A 1165 REMARK 465 LEU A 1166 REMARK 465 GLY A 1167 REMARK 465 ASP A 1168 REMARK 465 ILE A 1169 REMARK 465 SER A 1170 REMARK 465 GLY A 1171 REMARK 465 ILE A 1172 REMARK 465 ASN A 1173 REMARK 465 ALA A 1174 REMARK 465 SER A 1175 REMARK 465 VAL A 1176 REMARK 465 VAL A 1177 REMARK 465 ASN A 1178 REMARK 465 ILE A 1179 REMARK 465 GLN A 1180 REMARK 465 LYS A 1181 REMARK 465 GLU A 1182 REMARK 465 ILE A 1183 REMARK 465 ASP A 1184 REMARK 465 ARG A 1185 REMARK 465 LEU A 1186 REMARK 465 ASN A 1187 REMARK 465 GLU A 1188 REMARK 465 VAL A 1189 REMARK 465 ALA A 1190 REMARK 465 LYS A 1191 REMARK 465 ASN A 1192 REMARK 465 LEU A 1193 REMARK 465 ASN A 1194 REMARK 465 GLU A 1195 REMARK 465 SER A 1196 REMARK 465 LEU A 1197 REMARK 465 ILE A 1198 REMARK 465 ASP A 1199 REMARK 465 LEU A 1200 REMARK 465 GLN A 1201 REMARK 465 GLU A 1202 REMARK 465 LEU A 1203 REMARK 465 GLY A 1204 REMARK 465 LYS A 1205 REMARK 465 TYR A 1206 REMARK 465 GLU A 1207 REMARK 465 GLN A 1208 REMARK 465 TYR A 1209 REMARK 465 ILE A 1210 REMARK 465 LYS A 1211 REMARK 465 TRP A 1212 REMARK 465 PRO A 1213 REMARK 465 TRP A 1214 REMARK 465 TYR A 1215 REMARK 465 ILE A 1216 REMARK 465 TRP A 1217 REMARK 465 LEU A 1218 REMARK 465 GLY A 1219 REMARK 465 PHE A 1220 REMARK 465 ILE A 1221 REMARK 465 ALA A 1222 REMARK 465 GLY A 1223 REMARK 465 LEU A 1224 REMARK 465 ILE A 1225 REMARK 465 ALA A 1226 REMARK 465 ILE A 1227 REMARK 465 VAL A 1228 REMARK 465 MET A 1229 REMARK 465 VAL A 1230 REMARK 465 THR A 1231 REMARK 465 ILE A 1232 REMARK 465 MET A 1233 REMARK 465 LEU A 1234 REMARK 465 CYS A 1235 REMARK 465 CYS A 1236 REMARK 465 MET A 1237 REMARK 465 THR A 1238 REMARK 465 SER A 1239 REMARK 465 CYS A 1240 REMARK 465 CYS A 1241 REMARK 465 SER A 1242 REMARK 465 CYS A 1243 REMARK 465 LEU A 1244 REMARK 465 LYS A 1245 REMARK 465 GLY A 1246 REMARK 465 CYS A 1247 REMARK 465 CYS A 1248 REMARK 465 SER A 1249 REMARK 465 CYS A 1250 REMARK 465 GLY A 1251 REMARK 465 SER A 1252 REMARK 465 CYS A 1253 REMARK 465 CYS A 1254 REMARK 465 LYS A 1255 REMARK 465 PHE A 1256 REMARK 465 ASP A 1257 REMARK 465 GLU A 1258 REMARK 465 ASP A 1259 REMARK 465 ASP A 1260 REMARK 465 SER A 1261 REMARK 465 GLU A 1262 REMARK 465 PRO A 1263 REMARK 465 VAL A 1264 REMARK 465 LEU A 1265 REMARK 465 LYS A 1266 REMARK 465 GLY A 1267 REMARK 465 VAL A 1268 REMARK 465 LYS A 1269 REMARK 465 LEU A 1270 REMARK 465 HIS A 1271 REMARK 465 TYR A 1272 REMARK 465 THR A 1273 REMARK 465 ALA D 1 REMARK 465 GLU D 118 REMARK 465 PRO D 119 REMARK 465 LYS D 120 REMARK 465 THR D 121 REMARK 465 PRO D 122 REMARK 465 LYS D 123 REMARK 465 PRO D 124 REMARK 465 GLN D 125 REMARK 465 SER D 126 REMARK 465 HIS D 127 REMARK 465 HIS D 128 REMARK 465 HIS D 129 REMARK 465 HIS D 130 REMARK 465 HIS D 131 REMARK 465 HIS D 132 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O TYR A 38 OH TYR A 204 1.93 REMARK 500 O ASN A 710 OG1 THR A 1077 2.04 REMARK 500 OE2 GLU A 298 OG1 THR A 315 2.05 REMARK 500 NE2 GLN A 321 O PRO A 621 2.07 REMARK 500 O GLU A 661 OH TYR A 695 2.08 REMARK 500 OH TYR A 37 O LEU A 54 2.10 REMARK 500 O ILE A 934 OG SER A 937 2.13 REMARK 500 O ASN A 925 OG SER A 929 2.13 REMARK 500 OG1 THR A 95 O ALA A 264 2.14 REMARK 500 NH1 ARG A 273 OD1 ASP A 290 2.14 REMARK 500 OD2 ASP A 398 OH TYR A 423 2.15 REMARK 500 O GLN A 872 OG SER A 875 2.15 REMARK 500 O THR A 827 N ASP A 830 2.16 REMARK 500 OG SER A 708 O SER A 711 2.16 REMARK 500 O PRO A 322 N ASN A 616 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 291 CA - CB - SG ANGL. DEV. = 8.8 DEGREES REMARK 500 CYS A 590 CA - C - N ANGL. DEV. = -19.4 DEGREES REMARK 500 CYS A 590 O - C - N ANGL. DEV. = 10.6 DEGREES REMARK 500 PRO A1069 CA - N - CD ANGL. DEV. = -9.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 40 -165.46 -161.96 REMARK 500 PHE A 43 59.02 -94.71 REMARK 500 PHE A 59 25.38 48.19 REMARK 500 ASP A 88 19.90 55.60 REMARK 500 SER A 116 -168.34 -125.56 REMARK 500 SER A 162 109.99 -162.68 REMARK 500 MET A 177 -137.70 -154.14 REMARK 500 ASP A 178 -137.90 -59.12 REMARK 500 LEU A 179 -26.01 -9.10 REMARK 500 GLU A 180 -18.16 -48.57 REMARK 500 ASN A 185 -0.22 65.13 REMARK 500 THR A 236 -31.69 -132.78 REMARK 500 ARG A 273 -169.51 -118.74 REMARK 500 CYS A 291 87.85 63.80 REMARK 500 ALA A 292 22.26 86.70 REMARK 500 LEU A 293 -138.48 -144.23 REMARK 500 ASP A 294 -5.87 -6.85 REMARK 500 PRO A 295 -23.61 -20.52 REMARK 500 LYS A 300 -162.63 -169.50 REMARK 500 LYS A 304 -2.88 64.15 REMARK 500 ASN A 317 51.98 -94.42 REMARK 500 ARG A 319 -72.84 -62.41 REMARK 500 VAL A 327 32.27 -99.53 REMARK 500 ASN A 331 55.15 32.45 REMARK 500 THR A 345 -6.85 -56.31 REMARK 500 TRP A 353 109.98 -60.00 REMARK 500 SER A 359 -166.03 -78.77 REMARK 500 ASN A 360 90.35 -68.64 REMARK 500 ASP A 364 76.76 -69.86 REMARK 500 TYR A 365 -9.11 -53.69 REMARK 500 PRO A 384 2.69 -64.64 REMARK 500 PHE A 400 147.82 -172.98 REMARK 500 ASN A 422 -33.00 -131.08 REMARK 500 TYR A 423 113.75 -163.82 REMARK 500 PRO A 426 -175.87 -68.47 REMARK 500 TYR A 449 15.96 -140.35 REMARK 500 LEU A 455 -71.74 -83.30 REMARK 500 PHE A 456 30.83 -149.52 REMARK 500 ASN A 460 -5.76 72.08 REMARK 500 LEU A 461 70.64 55.85 REMARK 500 ARG A 466 78.70 -103.92 REMARK 500 TYR A 505 23.63 -141.62 REMARK 500 ALA A 520 55.89 -155.49 REMARK 500 ALA A 522 -168.92 -162.21 REMARK 500 CYS A 525 40.64 -93.93 REMARK 500 PRO A 527 54.14 -100.54 REMARK 500 LYS A 529 -159.51 -164.00 REMARK 500 SER A 530 66.14 65.98 REMARK 500 LEU A 533 -62.81 -92.87 REMARK 500 VAL A 534 145.40 -170.73 REMARK 500 REMARK 500 THIS ENTRY HAS 96 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 176 MET A 177 -143.54 REMARK 500 ASP A 178 LEU A 179 -130.97 REMARK 500 VAL A 289 ASP A 290 -139.38 REMARK 500 ASP A 294 PRO A 295 -118.78 REMARK 500 LYS A 300 CYS A 301 145.72 REMARK 500 LEU A 303 LYS A 304 148.56 REMARK 500 PHE A 318 ARG A 319 -140.12 REMARK 500 ASN A 448 TYR A 449 -142.06 REMARK 500 VAL A 524 CYS A 525 135.53 REMARK 500 CYS A 525 GLY A 526 142.21 REMARK 500 LYS A 535 ASN A 536 147.81 REMARK 500 ASN A 544 GLY A 545 -139.54 REMARK 500 GLY A 545 LEU A 546 -141.52 REMARK 500 GLN A 563 GLN A 564 149.02 REMARK 500 ASP A 578 PRO A 579 142.39 REMARK 500 ASP A 586 ILE A 587 -117.60 REMARK 500 THR A 588 PRO A 589 -147.10 REMARK 500 SER A 591 PHE A 592 145.86 REMARK 500 ALA A 623 ILE A 624 -142.32 REMARK 500 PHE A 833 ILE A 834 149.22 REMARK 500 TRP A 886 THR A 887 -148.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-31576 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-31575 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-31574 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-31573 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-31572 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-31578 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-31577 RELATED DB: EMDB REMARK 900 MAJOR CRYO-EM STRUCTURE OF S PROTEIN TRIMER OF SARS-COV2 WITH K-874, REMARK 900 COMPOSITE MAP DBREF 7FG3 A 1 1273 UNP P0DTC2 SPIKE_SARS2 1 1273 DBREF 7FG3 D 1 132 PDB 7FG3 7FG3 1 132 SEQRES 1 A 1273 MET PHE VAL PHE LEU VAL LEU LEU PRO LEU VAL SER SER SEQRES 2 A 1273 GLN CYS VAL ASN LEU THR THR ARG THR GLN LEU PRO PRO SEQRES 3 A 1273 ALA TYR THR ASN SER PHE THR ARG GLY VAL TYR TYR PRO SEQRES 4 A 1273 ASP LYS VAL PHE ARG SER SER VAL LEU HIS SER THR GLN SEQRES 5 A 1273 ASP LEU PHE LEU PRO PHE PHE SER ASN VAL THR TRP PHE SEQRES 6 A 1273 HIS ALA ILE HIS VAL SER GLY THR ASN GLY THR LYS ARG SEQRES 7 A 1273 PHE ASP ASN PRO VAL LEU PRO PHE ASN ASP GLY VAL TYR SEQRES 8 A 1273 PHE ALA SER THR GLU LYS SER ASN ILE ILE ARG GLY TRP SEQRES 9 A 1273 ILE PHE GLY THR THR LEU ASP SER LYS THR GLN SER LEU SEQRES 10 A 1273 LEU ILE VAL ASN ASN ALA THR ASN VAL VAL ILE LYS VAL SEQRES 11 A 1273 CYS GLU PHE GLN PHE CYS ASN ASP PRO PHE LEU GLY VAL SEQRES 12 A 1273 TYR TYR HIS LYS ASN ASN LYS SER TRP MET GLU SER GLU SEQRES 13 A 1273 PHE ARG VAL TYR SER SER ALA ASN ASN CYS THR PHE GLU SEQRES 14 A 1273 TYR VAL SER GLN PRO PHE LEU MET ASP LEU GLU GLY LYS SEQRES 15 A 1273 GLN GLY ASN PHE LYS ASN LEU ARG GLU PHE VAL PHE LYS SEQRES 16 A 1273 ASN ILE ASP GLY TYR PHE LYS ILE TYR SER LYS HIS THR SEQRES 17 A 1273 PRO ILE ASN LEU VAL ARG ASP LEU PRO GLN GLY PHE SER SEQRES 18 A 1273 ALA LEU GLU PRO LEU VAL ASP LEU PRO ILE GLY ILE ASN SEQRES 19 A 1273 ILE THR ARG PHE GLN THR LEU LEU ALA LEU HIS ARG SER SEQRES 20 A 1273 TYR LEU THR PRO GLY ASP SER SER SER GLY TRP THR ALA SEQRES 21 A 1273 GLY ALA ALA ALA TYR TYR VAL GLY TYR LEU GLN PRO ARG SEQRES 22 A 1273 THR PHE LEU LEU LYS TYR ASN GLU ASN GLY THR ILE THR SEQRES 23 A 1273 ASP ALA VAL ASP CYS ALA LEU ASP PRO LEU SER GLU THR SEQRES 24 A 1273 LYS CYS THR LEU LYS SER PHE THR VAL GLU LYS GLY ILE SEQRES 25 A 1273 TYR GLN THR SER ASN PHE ARG VAL GLN PRO THR GLU SER SEQRES 26 A 1273 ILE VAL ARG PHE PRO ASN ILE THR ASN LEU CYS PRO PHE SEQRES 27 A 1273 GLY GLU VAL PHE ASN ALA THR ARG PHE ALA SER VAL TYR SEQRES 28 A 1273 ALA TRP ASN ARG LYS ARG ILE SER ASN CYS VAL ALA ASP SEQRES 29 A 1273 TYR SER VAL LEU TYR ASN SER ALA SER PHE SER THR PHE SEQRES 30 A 1273 LYS CYS TYR GLY VAL SER PRO THR LYS LEU ASN ASP LEU SEQRES 31 A 1273 CYS PHE THR ASN VAL TYR ALA ASP SER PHE VAL ILE ARG SEQRES 32 A 1273 GLY ASP GLU VAL ARG GLN ILE ALA PRO GLY GLN THR GLY SEQRES 33 A 1273 LYS ILE ALA ASP TYR ASN TYR LYS LEU PRO ASP ASP PHE SEQRES 34 A 1273 THR GLY CYS VAL ILE ALA TRP ASN SER ASN ASN LEU ASP SEQRES 35 A 1273 SER LYS VAL GLY GLY ASN TYR ASN TYR LEU TYR ARG LEU SEQRES 36 A 1273 PHE ARG LYS SER ASN LEU LYS PRO PHE GLU ARG ASP ILE SEQRES 37 A 1273 SER THR GLU ILE TYR GLN ALA GLY SER THR PRO CYS ASN SEQRES 38 A 1273 GLY VAL GLU GLY PHE ASN CYS TYR PHE PRO LEU GLN SER SEQRES 39 A 1273 TYR GLY PHE GLN PRO THR ASN GLY VAL GLY TYR GLN PRO SEQRES 40 A 1273 TYR ARG VAL VAL VAL LEU SER PHE GLU LEU LEU HIS ALA SEQRES 41 A 1273 PRO ALA THR VAL CYS GLY PRO LYS LYS SER THR ASN LEU SEQRES 42 A 1273 VAL LYS ASN LYS CYS VAL ASN PHE ASN PHE ASN GLY LEU SEQRES 43 A 1273 THR GLY THR GLY VAL LEU THR GLU SER ASN LYS LYS PHE SEQRES 44 A 1273 LEU PRO PHE GLN GLN PHE GLY ARG ASP ILE ALA ASP THR SEQRES 45 A 1273 THR ASP ALA VAL ARG ASP PRO GLN THR LEU GLU ILE LEU SEQRES 46 A 1273 ASP ILE THR PRO CYS SER PHE GLY GLY VAL SER VAL ILE SEQRES 47 A 1273 THR PRO GLY THR ASN THR SER ASN GLN VAL ALA VAL LEU SEQRES 48 A 1273 TYR GLN ASP VAL ASN CYS THR GLU VAL PRO VAL ALA ILE SEQRES 49 A 1273 HIS ALA ASP GLN LEU THR PRO THR TRP ARG VAL TYR SER SEQRES 50 A 1273 THR GLY SER ASN VAL PHE GLN THR ARG ALA GLY CYS LEU SEQRES 51 A 1273 ILE GLY ALA GLU HIS VAL ASN ASN SER TYR GLU CYS ASP SEQRES 52 A 1273 ILE PRO ILE GLY ALA GLY ILE CYS ALA SER TYR GLN THR SEQRES 53 A 1273 GLN THR ASN SER PRO ARG ARG ALA ARG SER VAL ALA SER SEQRES 54 A 1273 GLN SER ILE ILE ALA TYR THR MET SER LEU GLY ALA GLU SEQRES 55 A 1273 ASN SER VAL ALA TYR SER ASN ASN SER ILE ALA ILE PRO SEQRES 56 A 1273 THR ASN PHE THR ILE SER VAL THR THR GLU ILE LEU PRO SEQRES 57 A 1273 VAL SER MET THR LYS THR SER VAL ASP CYS THR MET TYR SEQRES 58 A 1273 ILE CYS GLY ASP SER THR GLU CYS SER ASN LEU LEU LEU SEQRES 59 A 1273 GLN TYR GLY SER PHE CYS THR GLN LEU ASN ARG ALA LEU SEQRES 60 A 1273 THR GLY ILE ALA VAL GLU GLN ASP LYS ASN THR GLN GLU SEQRES 61 A 1273 VAL PHE ALA GLN VAL LYS GLN ILE TYR LYS THR PRO PRO SEQRES 62 A 1273 ILE LYS ASP PHE GLY GLY PHE ASN PHE SER GLN ILE LEU SEQRES 63 A 1273 PRO ASP PRO SER LYS PRO SER LYS ARG SER PHE ILE GLU SEQRES 64 A 1273 ASP LEU LEU PHE ASN LYS VAL THR LEU ALA ASP ALA GLY SEQRES 65 A 1273 PHE ILE LYS GLN TYR GLY ASP CYS LEU GLY ASP ILE ALA SEQRES 66 A 1273 ALA ARG ASP LEU ILE CYS ALA GLN LYS PHE ASN GLY LEU SEQRES 67 A 1273 THR VAL LEU PRO PRO LEU LEU THR ASP GLU MET ILE ALA SEQRES 68 A 1273 GLN TYR THR SER ALA LEU LEU ALA GLY THR ILE THR SER SEQRES 69 A 1273 GLY TRP THR PHE GLY ALA GLY ALA ALA LEU GLN ILE PRO SEQRES 70 A 1273 PHE ALA MET GLN MET ALA TYR ARG PHE ASN GLY ILE GLY SEQRES 71 A 1273 VAL THR GLN ASN VAL LEU TYR GLU ASN GLN LYS LEU ILE SEQRES 72 A 1273 ALA ASN GLN PHE ASN SER ALA ILE GLY LYS ILE GLN ASP SEQRES 73 A 1273 SER LEU SER SER THR ALA SER ALA LEU GLY LYS LEU GLN SEQRES 74 A 1273 ASP VAL VAL ASN GLN ASN ALA GLN ALA LEU ASN THR LEU SEQRES 75 A 1273 VAL LYS GLN LEU SER SER ASN PHE GLY ALA ILE SER SER SEQRES 76 A 1273 VAL LEU ASN ASP ILE LEU SER ARG LEU ASP LYS VAL GLU SEQRES 77 A 1273 ALA GLU VAL GLN ILE ASP ARG LEU ILE THR GLY ARG LEU SEQRES 78 A 1273 GLN SER LEU GLN THR TYR VAL THR GLN GLN LEU ILE ARG SEQRES 79 A 1273 ALA ALA GLU ILE ARG ALA SER ALA ASN LEU ALA ALA THR SEQRES 80 A 1273 LYS MET SER GLU CYS VAL LEU GLY GLN SER LYS ARG VAL SEQRES 81 A 1273 ASP PHE CYS GLY LYS GLY TYR HIS LEU MET SER PHE PRO SEQRES 82 A 1273 GLN SER ALA PRO HIS GLY VAL VAL PHE LEU HIS VAL THR SEQRES 83 A 1273 TYR VAL PRO ALA GLN GLU LYS ASN PHE THR THR ALA PRO SEQRES 84 A 1273 ALA ILE CYS HIS ASP GLY LYS ALA HIS PHE PRO ARG GLU SEQRES 85 A 1273 GLY VAL PHE VAL SER ASN GLY THR HIS TRP PHE VAL THR SEQRES 86 A 1273 GLN ARG ASN PHE TYR GLU PRO GLN ILE ILE THR THR ASP SEQRES 87 A 1273 ASN THR PHE VAL SER GLY ASN CYS ASP VAL VAL ILE GLY SEQRES 88 A 1273 ILE VAL ASN ASN THR VAL TYR ASP PRO LEU GLN PRO GLU SEQRES 89 A 1273 LEU ASP SER PHE LYS GLU GLU LEU ASP LYS TYR PHE LYS SEQRES 90 A 1273 ASN HIS THR SER PRO ASP VAL ASP LEU GLY ASP ILE SER SEQRES 91 A 1273 GLY ILE ASN ALA SER VAL VAL ASN ILE GLN LYS GLU ILE SEQRES 92 A 1273 ASP ARG LEU ASN GLU VAL ALA LYS ASN LEU ASN GLU SER SEQRES 93 A 1273 LEU ILE ASP LEU GLN GLU LEU GLY LYS TYR GLU GLN TYR SEQRES 94 A 1273 ILE LYS TRP PRO TRP TYR ILE TRP LEU GLY PHE ILE ALA SEQRES 95 A 1273 GLY LEU ILE ALA ILE VAL MET VAL THR ILE MET LEU CYS SEQRES 96 A 1273 CYS MET THR SER CYS CYS SER CYS LEU LYS GLY CYS CYS SEQRES 97 A 1273 SER CYS GLY SER CYS CYS LYS PHE ASP GLU ASP ASP SER SEQRES 98 A 1273 GLU PRO VAL LEU LYS GLY VAL LYS LEU HIS TYR THR SEQRES 1 D 132 ALA GLU VAL GLN LEU VAL GLU SER GLY GLY GLY GLN VAL SEQRES 2 D 132 GLU THR GLY GLY SER LEU ARG LEU SER CYS GLN ALA SER SEQRES 3 D 132 GLY SER THR PHE SER ASP TYR VAL MET ALA TRP PHE ARG SEQRES 4 D 132 GLN ARG PRO GLY LYS GLU ARG GLU PHE VAL ALA THR ILE SEQRES 5 D 132 SER ARG ASN GLY GLY THR THR THR TYR GLY SER SER VAL SEQRES 6 D 132 LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS SER SEQRES 7 D 132 THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP SEQRES 8 D 132 THR ALA VAL TYR TYR CYS TYR ALA VAL GLY GLY ASP GLY SEQRES 9 D 132 ASP SER TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 10 D 132 GLU PRO LYS THR PRO LYS PRO GLN SER HIS HIS HIS HIS SEQRES 11 D 132 HIS HIS HELIX 1 AA1 PHE A 338 ALA A 344 1 7 HELIX 2 AA2 ASP A 364 ASN A 370 1 7 HELIX 3 AA3 GLY A 416 ASN A 422 1 7 HELIX 4 AA4 ASN A 616 VAL A 620 5 5 HELIX 5 AA5 ASP A 737 CYS A 743 1 7 HELIX 6 AA6 SER A 746 TYR A 756 1 11 HELIX 7 AA7 SER A 758 PHE A 782 1 25 HELIX 8 AA8 SER A 816 VAL A 826 1 11 HELIX 9 AA9 THR A 866 SER A 884 1 19 HELIX 10 AB1 PHE A 898 GLY A 908 1 11 HELIX 11 AB2 GLN A 913 THR A 941 1 29 HELIX 12 AB3 LEU A 945 SER A 967 1 23 HELIX 13 AB4 LEU A 977 LEU A 984 1 8 HELIX 14 AB5 ASP A 985 VAL A 1033 1 49 HELIX 15 AB6 LYS D 88 THR D 92 5 5 SHEET 1 AA1 2 TYR A 28 THR A 29 0 SHEET 2 AA1 2 VAL A 62 THR A 63 -1 O VAL A 62 N THR A 29 SHEET 1 AA2 3 HIS A 49 PHE A 55 0 SHEET 2 AA2 3 GLN A 271 TYR A 279 -1 O LEU A 277 N HIS A 49 SHEET 3 AA2 3 ILE A 285 ASP A 287 -1 O THR A 286 N LYS A 278 SHEET 1 AA3 5 LEU A 84 PRO A 85 0 SHEET 2 AA3 5 ARG A 237 THR A 240 -1 O PHE A 238 N LEU A 84 SHEET 3 AA3 5 TRP A 104 GLY A 107 -1 N ILE A 105 O GLN A 239 SHEET 4 AA3 5 SER A 116 ASN A 121 -1 O LEU A 117 N PHE A 106 SHEET 5 AA3 5 VAL A 126 LYS A 129 -1 O LYS A 129 N LEU A 118 SHEET 1 AA4 4 THR A 208 ILE A 210 0 SHEET 2 AA4 4 LYS A 187 PHE A 194 -1 N LYS A 187 O ILE A 210 SHEET 3 AA4 4 TYR A 204 SER A 205 -1 O TYR A 204 N VAL A 193 SHEET 4 AA4 4 GLU A 224 PRO A 225 -1 O GLU A 224 N SER A 205 SHEET 1 AA5 4 THR A 208 ILE A 210 0 SHEET 2 AA5 4 LYS A 187 PHE A 194 -1 N LYS A 187 O ILE A 210 SHEET 3 AA5 4 VAL A 90 GLU A 96 -1 N PHE A 92 O PHE A 192 SHEET 4 AA5 4 ALA A 264 TYR A 265 -1 O ALA A 264 N THR A 95 SHEET 1 AA6 2 ASN A 196 ILE A 197 0 SHEET 2 AA6 2 TYR A 200 PHE A 201 -1 O TYR A 200 N ILE A 197 SHEET 1 AA7 2 GLY A 311 TYR A 313 0 SHEET 2 AA7 2 VAL A 597 THR A 599 -1 O VAL A 597 N TYR A 313 SHEET 1 AA8 3 ASN A 354 LYS A 356 0 SHEET 2 AA8 3 VAL A 395 SER A 399 -1 O ALA A 397 N LYS A 356 SHEET 3 AA8 3 LEU A 513 PHE A 515 -1 O SER A 514 N TYR A 396 SHEET 1 AA9 3 THR A 376 TYR A 380 0 SHEET 2 AA9 3 THR A 430 ASN A 437 -1 O VAL A 433 N LYS A 378 SHEET 3 AA9 3 TYR A 508 VAL A 510 -1 O ARG A 509 N TRP A 436 SHEET 1 AB1 2 TYR A 451 TYR A 453 0 SHEET 2 AB1 2 GLN A 493 TYR A 495 -1 O TYR A 495 N TYR A 451 SHEET 1 AB2 2 GLN A 644 THR A 645 0 SHEET 2 AB2 2 GLY A 648 CYS A 649 -1 O GLY A 648 N THR A 645 SHEET 1 AB3 2 ILE A 670 CYS A 671 0 SHEET 2 AB3 2 TYR A 695 THR A 696 -1 O TYR A 695 N CYS A 671 SHEET 1 AB4 3 ASN A 717 SER A 721 0 SHEET 2 AB4 3 GLY A1059 ALA A1070 -1 O VAL A1068 N THR A 719 SHEET 3 AB4 3 GLU A 725 PRO A 728 -1 N GLU A 725 O PHE A1062 SHEET 1 AB5 3 ASN A 717 SER A 721 0 SHEET 2 AB5 3 GLY A1059 ALA A1070 -1 O VAL A1068 N THR A 719 SHEET 3 AB5 3 TYR A1047 PRO A1053 -1 N PHE A1052 O LEU A1063 SHEET 1 AB6 3 ILE A1081 HIS A1083 0 SHEET 2 AB6 3 LYS A1086 PRO A1090 -1 O LYS A1086 N HIS A1083 SHEET 3 AB6 3 THR A1120 SER A1123 -1 O SER A1123 N ALA A1087 SHEET 1 AB7 2 VAL A1094 SER A1097 0 SHEET 2 AB7 2 TRP A1102 THR A1105 -1 O PHE A1103 N VAL A1096 SHEET 1 AB8 3 LEU D 5 SER D 8 0 SHEET 2 AB8 3 LEU D 19 ALA D 25 -1 O GLN D 24 N VAL D 6 SHEET 3 AB8 3 LEU D 82 MET D 84 -1 O MET D 84 N LEU D 19 SHEET 1 AB9 3 GLN D 12 VAL D 13 0 SHEET 2 AB9 3 THR D 111 VAL D 115 1 O THR D 114 N VAL D 13 SHEET 3 AB9 3 ALA D 93 TYR D 95 -1 N TYR D 95 O THR D 111 SHEET 1 AC1 2 PHE D 38 ARG D 39 0 SHEET 2 AC1 2 GLU D 47 PHE D 48 -1 O GLU D 47 N ARG D 39 SHEET 1 AC2 2 ARG D 73 ASP D 74 0 SHEET 2 AC2 2 THR D 79 VAL D 80 -1 O THR D 79 N ASP D 74 SSBOND 1 CYS A 131 CYS A 166 1555 1555 2.02 SSBOND 2 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 3 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 4 CYS A 391 CYS A 525 1555 1555 2.21 SSBOND 5 CYS A 617 CYS A 649 1555 1555 2.04 SSBOND 6 CYS A 662 CYS A 671 1555 1555 2.04 SSBOND 7 CYS A 743 CYS A 749 1555 1555 2.03 SSBOND 8 CYS A 1032 CYS A 1043 1555 1555 2.03 SSBOND 9 CYS D 23 CYS D 97 1555 1555 2.04 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