HEADER VIRAL PROTEIN/IMMUNE SYSTEM 08-NOV-22 8HES TITLE CRYSTAL STRUCTURE OF SARS-COV-2 RBD AND NIV-10 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: NIV-10 FAB H-CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SPIKE PROTEIN S1; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: NIV-10 FAB L-CHAIN; COMPND 11 CHAIN: L; 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: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 8 2; SOURCE 9 ORGANISM_COMMON: 2019-NCOV,SARS-COV-2; SOURCE 10 ORGANISM_TAXID: 2697049; SOURCE 11 EXPRESSION_SYSTEM: HEKISTOCARPA MINUTIFLORA; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 172253; 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 VIRUS, SARS-COV-2, RBD, SPIKE, ANTIBODY, IGG, NEUTRALIZING ANTIBODY, KEYWDS 2 COMPLEX, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.MORIYAMA,Y.ANRAKU,S.TAMINISHI,Y.ADACHI,D.KURODA,Y.HIGUCHI,R.KOTAKI, AUTHOR 2 K.TONOUCHI,K.YUMOTO,T.SUZUKI,S.KITA,T.SOMEYA,H.FUKUHARA,Y.KURODA, AUTHOR 3 T.YAMAMOTO,T.ONODERA,S.FUKUSHI,K.MAEDA,F.NAKAMURA-UCHIYAMA, AUTHOR 4 T.HASHIGUCHI,A.HOSHINO,K.MAENAKA,Y.TAKAHASHI REVDAT 1 08-NOV-23 8HES 0 JRNL AUTH S.MORIYAMA,Y.ANRAKU,S.TAMINISHI,Y.ADACHI,D.KURODA,S.KITA, JRNL AUTH 2 Y.HIGUCHI,Y.KIRITA,R.KOTAKI,K.TONOUCHI,K.YUMOTO,T.SUZUKI, JRNL AUTH 3 T.SOMEYA,H.FUKUHARA,Y.KURODA,T.YAMAMOTO,T.ONODERA,S.FUKUSHI, JRNL AUTH 4 K.MAEDA,F.NAKAMURA-UCHIYAMA,T.HASHIGUCHI,A.HOSHINO, JRNL AUTH 5 K.MAENAKA,Y.TAKAHASHI JRNL TITL STRUCTURAL DELINEATION AND COMPUTATIONAL DESIGN OF JRNL TITL 2 SARS-COV-2-NEUTRALIZING ANTIBODIES AGAINST OMICRON JRNL TITL 3 SUBVARIANTS. JRNL REF NAT COMMUN V. 14 4198 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37452031 JRNL DOI 10.1038/S41467-023-39890-8 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 36858 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1785 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.3100 - 5.1700 0.97 2856 155 0.1939 0.1976 REMARK 3 2 5.1700 - 4.1100 1.00 2809 127 0.1495 0.1907 REMARK 3 3 4.1000 - 3.5900 0.96 2663 131 0.1728 0.2258 REMARK 3 4 3.5900 - 3.2600 0.99 2741 119 0.1831 0.2140 REMARK 3 5 3.2600 - 3.0300 1.00 2763 128 0.2084 0.2671 REMARK 3 6 3.0200 - 2.8500 0.99 2707 144 0.2096 0.2493 REMARK 3 7 2.8500 - 2.7000 0.99 2699 139 0.2131 0.2483 REMARK 3 8 2.7000 - 2.5900 0.99 2671 141 0.2347 0.3080 REMARK 3 9 2.5900 - 2.4900 0.93 2502 137 0.2479 0.3723 REMARK 3 10 2.4900 - 2.4000 0.99 2677 142 0.2454 0.3000 REMARK 3 11 2.4000 - 2.3300 0.99 2695 144 0.2523 0.2731 REMARK 3 12 2.3300 - 2.2600 0.98 2648 142 0.2510 0.3264 REMARK 3 13 2.2600 - 2.2000 0.98 2642 136 0.2789 0.3159 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.299 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.851 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 4879 REMARK 3 ANGLE : 1.024 6647 REMARK 3 CHIRALITY : 0.063 729 REMARK 3 PLANARITY : 0.008 857 REMARK 3 DIHEDRAL : 13.479 1721 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 1 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.1139 -15.2735 -13.1791 REMARK 3 T TENSOR REMARK 3 T11: 0.2223 T22: 0.2525 REMARK 3 T33: 0.2329 T12: 0.0234 REMARK 3 T13: 0.0068 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 1.5583 L22: 1.4308 REMARK 3 L33: 1.9731 L12: 0.7944 REMARK 3 L13: 0.9321 L23: 0.3871 REMARK 3 S TENSOR REMARK 3 S11: 0.0200 S12: 0.0037 S13: -0.0349 REMARK 3 S21: -0.0140 S22: -0.0078 S23: -0.0359 REMARK 3 S31: 0.0901 S32: 0.0605 S33: -0.0261 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 132 THROUGH 187 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.8128 14.7864 -13.0409 REMARK 3 T TENSOR REMARK 3 T11: 0.3119 T22: 0.3889 REMARK 3 T33: 0.3333 T12: 0.0222 REMARK 3 T13: 0.0230 T23: 0.0618 REMARK 3 L TENSOR REMARK 3 L11: 3.2418 L22: 4.9342 REMARK 3 L33: 6.1019 L12: 0.4232 REMARK 3 L13: 0.7562 L23: -0.6060 REMARK 3 S TENSOR REMARK 3 S11: 0.0832 S12: 0.2279 S13: 0.3716 REMARK 3 S21: 0.0265 S22: -0.3497 S23: 0.1056 REMARK 3 S31: -0.4377 S32: -0.2276 S33: 0.2607 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 188 THROUGH 225 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3652 20.2262 -10.2248 REMARK 3 T TENSOR REMARK 3 T11: 0.5553 T22: 0.3686 REMARK 3 T33: 0.5195 T12: -0.0067 REMARK 3 T13: -0.0354 T23: 0.0499 REMARK 3 L TENSOR REMARK 3 L11: 5.4677 L22: 7.0321 REMARK 3 L33: 8.2558 L12: 0.9811 REMARK 3 L13: -1.3818 L23: -2.0759 REMARK 3 S TENSOR REMARK 3 S11: 0.2896 S12: -0.0694 S13: 1.0079 REMARK 3 S21: 0.4247 S22: -0.3856 S23: -0.0687 REMARK 3 S31: -1.6842 S32: -0.0152 S33: 0.1588 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 335 THROUGH 364 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.7575 -51.1977 -15.5955 REMARK 3 T TENSOR REMARK 3 T11: 0.4607 T22: 0.3430 REMARK 3 T33: 0.3117 T12: -0.0603 REMARK 3 T13: 0.0320 T23: -0.1189 REMARK 3 L TENSOR REMARK 3 L11: 6.8755 L22: 6.7269 REMARK 3 L33: 6.5654 L12: 1.6617 REMARK 3 L13: -1.7259 L23: -1.8761 REMARK 3 S TENSOR REMARK 3 S11: -0.4194 S12: 0.3756 S13: -0.8665 REMARK 3 S21: 0.0021 S22: 0.1048 S23: 0.0085 REMARK 3 S31: 1.0157 S32: -0.2194 S33: 0.2987 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 365 THROUGH 393 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.1025 -51.2286 -0.9858 REMARK 3 T TENSOR REMARK 3 T11: 0.4553 T22: 0.3219 REMARK 3 T33: 0.3467 T12: 0.0120 REMARK 3 T13: 0.0462 T23: 0.0407 REMARK 3 L TENSOR REMARK 3 L11: 7.9242 L22: 3.9841 REMARK 3 L33: 4.2617 L12: 1.2647 REMARK 3 L13: -2.1476 L23: 0.9088 REMARK 3 S TENSOR REMARK 3 S11: -0.3607 S12: 0.0340 S13: -0.8209 REMARK 3 S21: 0.3685 S22: 0.0496 S23: -0.0573 REMARK 3 S31: 0.8686 S32: -0.0433 S33: 0.3291 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 394 THROUGH 442 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.6877 -39.7280 -10.2602 REMARK 3 T TENSOR REMARK 3 T11: 0.2099 T22: 0.2151 REMARK 3 T33: 0.2253 T12: 0.0048 REMARK 3 T13: -0.0308 T23: -0.0073 REMARK 3 L TENSOR REMARK 3 L11: 6.5443 L22: 5.6137 REMARK 3 L33: 5.4064 L12: 0.5744 REMARK 3 L13: -2.5756 L23: -0.2753 REMARK 3 S TENSOR REMARK 3 S11: -0.0334 S12: -0.0623 S13: 0.0788 REMARK 3 S21: -0.0160 S22: 0.0316 S23: -0.0461 REMARK 3 S31: -0.0059 S32: 0.0698 S33: -0.0126 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 443 THROUGH 459 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.6592 -35.6193 -21.6356 REMARK 3 T TENSOR REMARK 3 T11: 0.3201 T22: 0.3780 REMARK 3 T33: 0.2650 T12: -0.0932 REMARK 3 T13: 0.0216 T23: 0.0106 REMARK 3 L TENSOR REMARK 3 L11: 4.7090 L22: 6.7194 REMARK 3 L33: 5.0407 L12: 0.1359 REMARK 3 L13: -4.7609 L23: 1.1916 REMARK 3 S TENSOR REMARK 3 S11: -0.0894 S12: 0.3544 S13: -0.2804 REMARK 3 S21: -0.9962 S22: -0.1430 S23: -0.4845 REMARK 3 S31: 0.0869 S32: 0.2708 S33: 0.1949 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 460 THROUGH 494 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.6526 -25.5002 -25.8634 REMARK 3 T TENSOR REMARK 3 T11: 0.3515 T22: 0.3790 REMARK 3 T33: 0.3290 T12: -0.0533 REMARK 3 T13: -0.0739 T23: 0.0188 REMARK 3 L TENSOR REMARK 3 L11: 4.9574 L22: 6.2798 REMARK 3 L33: 2.7989 L12: 5.4890 REMARK 3 L13: -3.8840 L23: -4.0986 REMARK 3 S TENSOR REMARK 3 S11: -0.3067 S12: 0.6076 S13: 0.4925 REMARK 3 S21: -0.5328 S22: 0.5701 S23: 0.6053 REMARK 3 S31: 0.2192 S32: -0.4730 S33: -0.3132 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 495 THROUGH 527 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.4250 -45.6595 -10.5595 REMARK 3 T TENSOR REMARK 3 T11: 0.3006 T22: 0.1933 REMARK 3 T33: 0.1949 T12: 0.0220 REMARK 3 T13: -0.0154 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 8.9729 L22: 4.9451 REMARK 3 L33: 4.9926 L12: 2.9624 REMARK 3 L13: -3.4169 L23: -0.5234 REMARK 3 S TENSOR REMARK 3 S11: -0.0834 S12: -0.3761 S13: -0.6000 REMARK 3 S21: 0.1287 S22: -0.1605 S23: -0.2187 REMARK 3 S31: 0.2121 S32: 0.0909 S33: 0.2387 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.8580 -7.7945 -34.9494 REMARK 3 T TENSOR REMARK 3 T11: 0.2519 T22: 0.3617 REMARK 3 T33: 0.2196 T12: 0.0303 REMARK 3 T13: 0.0150 T23: 0.0103 REMARK 3 L TENSOR REMARK 3 L11: 1.4141 L22: 3.0170 REMARK 3 L33: 2.7238 L12: 0.6495 REMARK 3 L13: -0.1650 L23: -0.4230 REMARK 3 S TENSOR REMARK 3 S11: -0.0148 S12: 0.2008 S13: 0.0726 REMARK 3 S21: -0.2580 S22: 0.0139 S23: -0.0648 REMARK 3 S31: 0.1029 S32: -0.0703 S33: -0.0026 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 84 THROUGH 121 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.5631 -3.7929 -29.5502 REMARK 3 T TENSOR REMARK 3 T11: 0.3280 T22: 0.4068 REMARK 3 T33: 0.2828 T12: 0.0651 REMARK 3 T13: 0.0089 T23: 0.0751 REMARK 3 L TENSOR REMARK 3 L11: 2.3889 L22: 0.6550 REMARK 3 L33: 1.0413 L12: 1.1982 REMARK 3 L13: 0.2633 L23: 1.0237 REMARK 3 S TENSOR REMARK 3 S11: 0.0264 S12: 0.2376 S13: -0.0614 REMARK 3 S21: 0.1436 S22: -0.1263 S23: -0.2617 REMARK 3 S31: 0.0905 S32: 0.1806 S33: 0.0962 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 122 THROUGH 212 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.6069 5.6758 -23.2939 REMARK 3 T TENSOR REMARK 3 T11: 0.2664 T22: 0.4790 REMARK 3 T33: 0.3621 T12: -0.0002 REMARK 3 T13: 0.0310 T23: 0.0493 REMARK 3 L TENSOR REMARK 3 L11: 3.8556 L22: 1.8557 REMARK 3 L33: 4.8143 L12: -0.0556 REMARK 3 L13: 1.0603 L23: -0.0879 REMARK 3 S TENSOR REMARK 3 S11: -0.0137 S12: 0.1756 S13: 0.0999 REMARK 3 S21: 0.0206 S22: -0.0419 S23: -0.1094 REMARK 3 S31: -0.0058 S32: 0.1154 S33: 0.0568 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8HES COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1300033429. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36935 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 47.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.15200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 7EAM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM NITRATE, 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 26.57350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.13250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.55650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.13250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.57350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.55650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, C, L 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 H 140 REMARK 465 LYS H 141 REMARK 465 SER H 142 REMARK 465 THR H 143 REMARK 465 SER H 144 REMARK 465 SER H 199 REMARK 465 SER H 200 REMARK 465 LEU H 201 REMARK 465 LYS H 226 REMARK 465 SER H 227 REMARK 465 CYS H 228 REMARK 465 ASP H 229 REMARK 465 LYS H 230 REMARK 465 GLY H 231 REMARK 465 SER H 232 REMARK 465 SER H 233 REMARK 465 LEU H 234 REMARK 465 GLU H 235 REMARK 465 VAL H 236 REMARK 465 LEU H 237 REMARK 465 PHE H 238 REMARK 465 GLN H 239 REMARK 465 GLY H 240 REMARK 465 PRO H 241 REMARK 465 LEU H 242 REMARK 465 GLY H 243 REMARK 465 HIS H 244 REMARK 465 HIS H 245 REMARK 465 HIS H 246 REMARK 465 HIS H 247 REMARK 465 HIS H 248 REMARK 465 HIS H 249 REMARK 465 PRO C 322 REMARK 465 THR C 323 REMARK 465 GLU C 324 REMARK 465 SER C 325 REMARK 465 ILE C 326 REMARK 465 VAL C 327 REMARK 465 ARG C 328 REMARK 465 PHE C 329 REMARK 465 PRO C 330 REMARK 465 ASN C 331 REMARK 465 ILE C 332 REMARK 465 THR C 333 REMARK 465 ASN C 334 REMARK 465 HIS C 519 REMARK 465 LYS C 528 REMARK 465 LYS C 529 REMARK 465 SER C 530 REMARK 465 THR C 531 REMARK 465 ASN C 532 REMARK 465 LEU C 533 REMARK 465 VAL C 534 REMARK 465 LYS C 535 REMARK 465 ASN C 536 REMARK 465 GLN L -1 REMARK 465 SER L 0 REMARK 465 GLU L 213 REMARK 465 CYS L 214 REMARK 465 SER L 215 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 GLU H 55 6.00 53.73 REMARK 500 ASP H 99 -148.21 72.54 REMARK 500 SER H 113 -74.11 -113.55 REMARK 500 THR H 128 135.97 -38.44 REMARK 500 ASP H 156 60.69 65.81 REMARK 500 SER C 373 71.70 -102.39 REMARK 500 ASN C 422 -52.26 -125.91 REMARK 500 PHE C 497 109.93 -52.06 REMARK 500 ASP L 26 -90.55 -159.25 REMARK 500 ASN L 31 46.50 -101.45 REMARK 500 VAL L 51 -44.03 71.72 REMARK 500 ASP L 154 -115.96 49.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33823 RELATED DB: EMDB DBREF 8HES H 1 249 PDB 8HES 8HES 1 249 DBREF 8HES C 322 536 UNP P0DTC2 SPIKE_SARS2 322 536 DBREF 8HES L -1 215 PDB 8HES 8HES -1 215 SEQRES 1 H 249 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 249 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 249 PHE THR PHE TYR SER TYR TRP MET THR TRP VAL ARG GLN SEQRES 4 H 249 ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA ASN ILE LYS SEQRES 5 H 249 HIS ASP GLU SER GLU SER HIS TYR VAL ASP SER VAL ARG SEQRES 6 H 249 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SER SEQRES 7 H 249 VAL TYR LEU GLN MET LYS GLY LEU ARG ALA GLU ASP THR SEQRES 8 H 249 ALA VAL TYR TYR CYS ALA ARG ASP GLY GLY TYR ASN ILE SEQRES 9 H 249 LEU THR ALA TYR TYR HIS ALA PRO SER TYR TRP GLY GLN SEQRES 10 H 249 GLY THR LEU VAL THR VAL SER SER ALA SER THR LYS GLY SEQRES 11 H 249 PRO SER VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SEQRES 12 H 249 SER GLY GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP SEQRES 13 H 249 TYR PHE PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY SEQRES 14 H 249 ALA LEU THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU SEQRES 15 H 249 GLN SER SER GLY LEU TYR SER LEU SER SER VAL VAL THR SEQRES 16 H 249 VAL PRO SER SER SER LEU GLY THR GLN THR TYR ILE CYS SEQRES 17 H 249 ASN VAL ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS SEQRES 18 H 249 ARG VAL GLU PRO LYS SER CYS ASP LYS GLY SER SER LEU SEQRES 19 H 249 GLU VAL LEU PHE GLN GLY PRO LEU GLY HIS HIS HIS HIS SEQRES 20 H 249 HIS HIS SEQRES 1 C 215 PRO THR GLU SER ILE VAL ARG PHE PRO ASN ILE THR ASN SEQRES 2 C 215 LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG PHE SEQRES 3 C 215 ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER ASN SEQRES 4 C 215 CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SER SEQRES 5 C 215 PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR LYS SEQRES 6 C 215 LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SER SEQRES 7 C 215 PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA PRO SEQRES 8 C 215 GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS LEU SEQRES 9 C 215 PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SER SEQRES 10 C 215 ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN TYR SEQRES 11 C 215 LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO PHE SEQRES 12 C 215 GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SER SEQRES 13 C 215 THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR PHE SEQRES 14 C 215 PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY VAL SEQRES 15 C 215 GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE GLU SEQRES 16 C 215 LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO LYS LYS SEQRES 17 C 215 SER THR ASN LEU VAL LYS ASN SEQRES 1 L 217 GLN SER ALA LEU THR GLN PRO ALA SER VAL SER GLY SER SEQRES 2 L 217 PRO GLY GLN SER ILE THR ILE SER CYS THR GLY THR SER SEQRES 3 L 217 SER ASP VAL GLY GLY TYR ASN PHE VAL SER TRP TYR ARG SEQRES 4 L 217 GLN TYR PRO GLY LYS ALA PRO GLN LEU MET ILE TYR ASP SEQRES 5 L 217 VAL SER ARG ARG PRO SER GLY ASP SER ASP ARG PHE SER SEQRES 6 L 217 GLY SER LYS SER GLY ASN THR ALA SER LEU THR ILE SER SEQRES 7 L 217 GLY LEU GLN ALA GLU ASP GLU ALA GLU TYR HIS CYS SER SEQRES 8 L 217 SER TYR THR GLY ARG SER PRO TYR VAL VAL PHE GLY GLY SEQRES 9 L 217 GLY THR LYS VAL THR VAL LEU GLY GLN PRO LYS ALA ALA SEQRES 10 L 217 PRO SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU SEQRES 11 L 217 GLN ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP SEQRES 12 L 217 PHE TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SEQRES 13 L 217 SER SER PRO VAL LYS ALA GLY VAL GLU THR THR THR PRO SEQRES 14 L 217 SER LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR SEQRES 15 L 217 LEU SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER SEQRES 16 L 217 TYR SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU SEQRES 17 L 217 LYS THR VAL ALA PRO THR GLU CYS SER HET NAG C 601 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 NAG C8 H15 N O6 FORMUL 5 HOH *236(H2 O) HELIX 1 AA1 THR H 28 TYR H 32 5 5 HELIX 2 AA2 ASP H 62 ARG H 65 5 4 HELIX 3 AA3 ASN H 74 LYS H 76 5 3 HELIX 4 AA4 ARG H 87 THR H 91 5 5 HELIX 5 AA5 SER H 168 ALA H 170 5 3 HELIX 6 AA6 LYS H 213 ASN H 216 5 4 HELIX 7 AA7 PHE C 338 ASN C 343 1 6 HELIX 8 AA8 SER C 349 TRP C 353 5 5 HELIX 9 AA9 ASP C 364 ALA C 372 1 9 HELIX 10 AB1 SER C 383 ASP C 389 5 7 HELIX 11 AB2 ASP C 405 ILE C 410 5 6 HELIX 12 AB3 GLY C 416 ASN C 422 1 7 HELIX 13 AB4 SER C 438 SER C 443 1 6 HELIX 14 AB5 GLY C 502 TYR C 505 5 4 HELIX 15 AB6 SER L 56 ASP L 60 5 5 HELIX 16 AB7 GLN L 79 GLU L 83 5 5 HELIX 17 AB8 SER L 124 ALA L 130 1 7 HELIX 18 AB9 THR L 184 HIS L 191 1 8 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 LEU H 18 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 AA1 4 SER H 78 MET H 83 -1 O MET H 83 N LEU H 18 SHEET 4 AA1 4 PHE H 68 ASP H 73 -1 N THR H 69 O GLN H 82 SHEET 1 AA2 6 GLY H 10 VAL H 12 0 SHEET 2 AA2 6 THR H 119 VAL H 123 1 O THR H 122 N GLY H 10 SHEET 3 AA2 6 ALA H 92 ARG H 98 -1 N TYR H 94 O THR H 119 SHEET 4 AA2 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 AA2 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA2 6 SER H 58 TYR H 60 -1 O HIS H 59 N ASN H 50 SHEET 1 AA3 2 GLY H 101 ASN H 103 0 SHEET 2 AA3 2 TYR H 108 HIS H 110 -1 O TYR H 108 N ASN H 103 SHEET 1 AA4 4 SER H 132 LEU H 136 0 SHEET 2 AA4 4 THR H 147 TYR H 157 -1 O GLY H 151 N LEU H 136 SHEET 3 AA4 4 TYR H 188 PRO H 197 -1 O VAL H 196 N ALA H 148 SHEET 4 AA4 4 VAL H 175 THR H 177 -1 N HIS H 176 O VAL H 193 SHEET 1 AA5 4 SER H 132 LEU H 136 0 SHEET 2 AA5 4 THR H 147 TYR H 157 -1 O GLY H 151 N LEU H 136 SHEET 3 AA5 4 TYR H 188 PRO H 197 -1 O VAL H 196 N ALA H 148 SHEET 4 AA5 4 VAL H 181 LEU H 182 -1 N VAL H 181 O SER H 189 SHEET 1 AA6 3 THR H 163 TRP H 166 0 SHEET 2 AA6 3 TYR H 206 HIS H 212 -1 O ASN H 209 N SER H 165 SHEET 3 AA6 3 THR H 217 VAL H 223 -1 O VAL H 219 N VAL H 210 SHEET 1 AA7 5 ASN C 354 ILE C 358 0 SHEET 2 AA7 5 ASN C 394 ARG C 403 -1 O VAL C 395 N ILE C 358 SHEET 3 AA7 5 PRO C 507 GLU C 516 -1 O SER C 514 N TYR C 396 SHEET 4 AA7 5 GLY C 431 ASN C 437 -1 N ILE C 434 O VAL C 511 SHEET 5 AA7 5 THR C 376 TYR C 380 -1 N LYS C 378 O VAL C 433 SHEET 1 AA8 3 CYS C 361 VAL C 362 0 SHEET 2 AA8 3 VAL C 524 CYS C 525 1 O CYS C 525 N CYS C 361 SHEET 3 AA8 3 CYS C 391 PHE C 392 -1 N PHE C 392 O VAL C 524 SHEET 1 AA9 2 LEU C 452 ARG C 454 0 SHEET 2 AA9 2 LEU C 492 SER C 494 -1 O GLN C 493 N TYR C 453 SHEET 1 AB1 2 TYR C 473 GLN C 474 0 SHEET 2 AB1 2 CYS C 488 TYR C 489 -1 O TYR C 489 N TYR C 473 SHEET 1 AB2 5 SER L 7 GLY L 10 0 SHEET 2 AB2 5 THR L 104 VAL L 108 1 O THR L 107 N VAL L 8 SHEET 3 AB2 5 ALA L 84 TYR L 91 -1 N ALA L 84 O VAL L 106 SHEET 4 AB2 5 VAL L 33 GLN L 38 -1 N TYR L 36 O HIS L 87 SHEET 5 AB2 5 GLN L 45 ILE L 48 -1 O MET L 47 N TRP L 35 SHEET 1 AB3 4 SER L 7 GLY L 10 0 SHEET 2 AB3 4 THR L 104 VAL L 108 1 O THR L 107 N VAL L 8 SHEET 3 AB3 4 ALA L 84 TYR L 91 -1 N ALA L 84 O VAL L 106 SHEET 4 AB3 4 VAL L 98 PHE L 100 -1 O VAL L 99 N SER L 90 SHEET 1 AB4 3 ILE L 16 THR L 21 0 SHEET 2 AB4 3 THR L 70 ILE L 75 -1 O ALA L 71 N CYS L 20 SHEET 3 AB4 3 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 AB5 4 SER L 117 PHE L 121 0 SHEET 2 AB5 4 ALA L 133 PHE L 142 -1 O VAL L 136 N PHE L 121 SHEET 3 AB5 4 TYR L 175 LEU L 183 -1 O ALA L 177 N ILE L 139 SHEET 4 AB5 4 VAL L 162 THR L 164 -1 N GLU L 163 O TYR L 180 SHEET 1 AB6 4 SER L 117 PHE L 121 0 SHEET 2 AB6 4 ALA L 133 PHE L 142 -1 O VAL L 136 N PHE L 121 SHEET 3 AB6 4 TYR L 175 LEU L 183 -1 O ALA L 177 N ILE L 139 SHEET 4 AB6 4 SER L 168 LYS L 169 -1 N SER L 168 O ALA L 176 SHEET 1 AB7 4 SER L 156 VAL L 158 0 SHEET 2 AB7 4 THR L 148 ALA L 153 -1 N ALA L 153 O SER L 156 SHEET 3 AB7 4 TYR L 194 HIS L 200 -1 O THR L 199 N THR L 148 SHEET 4 AB7 4 SER L 203 VAL L 209 -1 O VAL L 205 N VAL L 198 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.00 SSBOND 2 CYS H 152 CYS H 208 1555 1555 2.04 SSBOND 3 CYS C 336 CYS C 361 1555 1555 2.04 SSBOND 4 CYS C 379 CYS C 432 1555 1555 2.06 SSBOND 5 CYS C 391 CYS C 525 1555 1555 2.06 SSBOND 6 CYS C 480 CYS C 488 1555 1555 2.06 SSBOND 7 CYS L 20 CYS L 88 1555 1555 2.06 SSBOND 8 CYS L 137 CYS L 196 1555 1555 2.04 LINK ND2 ASN C 343 C1 NAG C 601 1555 1555 1.44 CISPEP 1 PHE H 158 PRO H 159 0 -8.31 CISPEP 2 GLU H 160 PRO H 161 0 -2.17 CISPEP 3 SER L 95 PRO L 96 0 -29.40 CISPEP 4 TYR L 143 PRO L 144 0 -2.67 CRYST1 53.147 101.113 134.265 90.00 90.00 90.00 P 21 21 21 4 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 0.018816 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009890 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007448 0.00000