HEADER VIRAL PROTEIN 19-AUG-23 8Q94 TITLE CRYSTAL STRUCTURE OF THE SARS-COV-2 BA.2.75 RBD WITH NEUTRALIZING-VHHS TITLE 2 RE32D03 AND MA3B12 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: NANOBODY MA3B12; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: NANOBODY RE32D03; 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 10 ORGANISM_TAXID: 30538; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 15 ORGANISM_TAXID: 30538; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NEUTRALIZING VHH, FOLD-PROMOTER, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.AKSU,T.GUTTLER,D.GORLICH REVDAT 2 27-DEC-23 8Q94 1 JRNL REVDAT 1 20-DEC-23 8Q94 0 JRNL AUTH M.AKSU,P.KUMAR,T.GUTTLER,W.TAXER,K.GREGOR,B.MUSSIL, JRNL AUTH 2 O.RYMARENKO,K.M.STEGMANN,A.DICKMANNS,S.GERBER,W.REINEKING, JRNL AUTH 3 C.SCHULZ,T.HENNECK,A.MOHAMED,G.POHLMANN,M.RAMAZANOGLU, JRNL AUTH 4 K.MESE,U.GROSS,T.BEN-YEDIDIA,O.OVADIA,D.W.FISCHER, JRNL AUTH 5 M.KAMENSKY,A.REICHMAN,W.BAUMGARTNER, JRNL AUTH 6 M.VON KOCKRITZ-BLICKWEDE,M.DOBBELSTEIN,D.GORLICH JRNL TITL NANOBODIES TO MULTIPLE SPIKE VARIANTS AND INHALATION OF JRNL TITL 2 NANOBODY-CONTAINING AEROSOLS NEUTRALIZE SARS-COV-2 IN CELL JRNL TITL 3 CULTURE AND HAMSTERS. JRNL REF ANTIVIRAL RES. V. 221 05778 2023 JRNL REFN ISSN 0166-3542 JRNL PMID 38065245 JRNL DOI 10.1016/J.ANTIVIRAL.2023.105778 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 18675 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 933 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 47.4900 - 4.7800 1.00 2736 145 0.1980 0.2562 REMARK 3 2 4.7800 - 3.8000 1.00 2574 136 0.1799 0.2117 REMARK 3 3 3.8000 - 3.3200 1.00 2535 133 0.2341 0.3100 REMARK 3 4 3.3200 - 3.0100 1.00 2495 131 0.2510 0.3395 REMARK 3 5 3.0100 - 2.8000 1.00 2467 129 0.2816 0.3596 REMARK 3 6 2.8000 - 2.6300 1.00 2500 132 0.2807 0.2995 REMARK 3 7 2.6300 - 2.5000 1.00 2435 127 0.2849 0.3576 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.002 3396 REMARK 3 ANGLE : 0.461 4621 REMARK 3 CHIRALITY : 0.042 486 REMARK 3 PLANARITY : 0.003 603 REMARK 3 DIHEDRAL : 9.949 1199 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 40 THROUGH 52 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.7178 -41.2915 -11.7369 REMARK 3 T TENSOR REMARK 3 T11: 0.6156 T22: 0.4758 REMARK 3 T33: 0.4256 T12: 0.0746 REMARK 3 T13: 0.0373 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 2.5144 L22: 6.9289 REMARK 3 L33: 2.7667 L12: -1.0822 REMARK 3 L13: 2.4553 L23: -2.6094 REMARK 3 S TENSOR REMARK 3 S11: -0.6972 S12: -0.3383 S13: 0.3063 REMARK 3 S21: 1.1046 S22: 0.5396 S23: -0.4954 REMARK 3 S31: -1.2573 S32: 0.2365 S33: 0.1705 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 53 THROUGH 67 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.2034 -46.3674 -22.1953 REMARK 3 T TENSOR REMARK 3 T11: 0.3323 T22: 0.4003 REMARK 3 T33: 0.4220 T12: -0.0733 REMARK 3 T13: 0.1235 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 4.9207 L22: 3.6568 REMARK 3 L33: 5.5783 L12: 2.4291 REMARK 3 L13: 4.5772 L23: 0.5286 REMARK 3 S TENSOR REMARK 3 S11: -0.3420 S12: 1.2192 S13: 0.1995 REMARK 3 S21: -0.3731 S22: 0.3786 S23: -0.0377 REMARK 3 S31: -0.4596 S32: 0.5489 S33: -0.0158 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 68 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.5503 -50.9520 -12.8331 REMARK 3 T TENSOR REMARK 3 T11: 0.4900 T22: 0.4105 REMARK 3 T33: 0.3676 T12: -0.0402 REMARK 3 T13: 0.0466 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 7.3870 L22: 4.6282 REMARK 3 L33: 2.8564 L12: 0.2067 REMARK 3 L13: -1.1402 L23: -1.2177 REMARK 3 S TENSOR REMARK 3 S11: -0.2407 S12: 0.0233 S13: 0.1174 REMARK 3 S21: 0.2072 S22: 0.1657 S23: -0.3866 REMARK 3 S31: 0.1744 S32: 0.4875 S33: 0.1238 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 101 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.9649 -41.8977 -23.0945 REMARK 3 T TENSOR REMARK 3 T11: 0.5217 T22: 0.4633 REMARK 3 T33: 0.4423 T12: 0.0279 REMARK 3 T13: -0.1148 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 6.2538 L22: 5.6556 REMARK 3 L33: 8.1219 L12: 4.6461 REMARK 3 L13: 3.2960 L23: 6.1996 REMARK 3 S TENSOR REMARK 3 S11: 0.4516 S12: 0.7007 S13: 0.2045 REMARK 3 S21: 0.1233 S22: -0.3323 S23: 0.3270 REMARK 3 S31: 1.2117 S32: 0.2836 S33: -0.3197 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 111 THROUGH 127 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.0734 -45.1851 -7.2859 REMARK 3 T TENSOR REMARK 3 T11: 0.5517 T22: 0.3292 REMARK 3 T33: 0.3099 T12: -0.0119 REMARK 3 T13: -0.0626 T23: -0.0579 REMARK 3 L TENSOR REMARK 3 L11: 9.9047 L22: 2.9948 REMARK 3 L33: 5.8652 L12: -2.4039 REMARK 3 L13: 2.4251 L23: -2.2757 REMARK 3 S TENSOR REMARK 3 S11: 0.4053 S12: -0.1500 S13: -0.4889 REMARK 3 S21: 0.0962 S22: -0.2918 S23: 0.2300 REMARK 3 S31: 0.5511 S32: -0.3742 S33: -0.1492 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 336 THROUGH 393 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.9802 -29.1545 -22.1362 REMARK 3 T TENSOR REMARK 3 T11: 0.5182 T22: 0.6256 REMARK 3 T33: 0.4868 T12: -0.0290 REMARK 3 T13: 0.0065 T23: 0.0991 REMARK 3 L TENSOR REMARK 3 L11: 6.6084 L22: 1.9536 REMARK 3 L33: 8.6985 L12: -1.2838 REMARK 3 L13: -0.2874 L23: 1.3524 REMARK 3 S TENSOR REMARK 3 S11: -0.1001 S12: 0.3096 S13: -0.0147 REMARK 3 S21: 0.0235 S22: 0.1204 S23: 0.3445 REMARK 3 S31: -0.0607 S32: -1.2501 S33: 0.0048 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 394 THROUGH 517 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.1150 -32.9162 -19.7351 REMARK 3 T TENSOR REMARK 3 T11: 0.5767 T22: 0.4988 REMARK 3 T33: 0.3678 T12: -0.0442 REMARK 3 T13: -0.0360 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 2.6951 L22: 1.3239 REMARK 3 L33: 1.2877 L12: -0.6317 REMARK 3 L13: -0.7660 L23: -0.0070 REMARK 3 S TENSOR REMARK 3 S11: -0.0348 S12: 0.1311 S13: 0.0779 REMARK 3 S21: 0.0222 S22: 0.0759 S23: 0.0510 REMARK 3 S31: -0.1175 S32: -0.2157 S33: -0.0304 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 39 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.5464 -29.3842 9.4954 REMARK 3 T TENSOR REMARK 3 T11: 0.4544 T22: 0.5976 REMARK 3 T33: 0.3718 T12: 0.0918 REMARK 3 T13: -0.0128 T23: 0.0147 REMARK 3 L TENSOR REMARK 3 L11: 5.2220 L22: 4.2024 REMARK 3 L33: 1.5142 L12: 1.7022 REMARK 3 L13: -0.4383 L23: -0.3831 REMARK 3 S TENSOR REMARK 3 S11: 0.2099 S12: -0.3536 S13: 0.1317 REMARK 3 S21: 0.4684 S22: -0.3249 S23: 0.0113 REMARK 3 S31: -0.3969 S32: -0.1262 S33: 0.0944 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 40 THROUGH 60 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.4900 -33.0321 1.0941 REMARK 3 T TENSOR REMARK 3 T11: 0.5703 T22: 0.7770 REMARK 3 T33: 0.3990 T12: 0.0863 REMARK 3 T13: 0.1779 T23: 0.0364 REMARK 3 L TENSOR REMARK 3 L11: 3.1089 L22: 5.9304 REMARK 3 L33: 4.3817 L12: -1.5775 REMARK 3 L13: 3.5107 L23: -2.7072 REMARK 3 S TENSOR REMARK 3 S11: 0.2608 S12: -0.1791 S13: -0.4663 REMARK 3 S21: -0.5760 S22: -0.1167 S23: 0.6472 REMARK 3 S31: 0.1718 S32: -0.5043 S33: -0.0634 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 61 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.6663 -32.8734 7.9925 REMARK 3 T TENSOR REMARK 3 T11: 0.5019 T22: 0.6704 REMARK 3 T33: 0.4235 T12: -0.0548 REMARK 3 T13: 0.1020 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.9966 L22: 4.0620 REMARK 3 L33: 4.0308 L12: -1.5936 REMARK 3 L13: 0.2479 L23: 0.9986 REMARK 3 S TENSOR REMARK 3 S11: 0.1616 S12: -0.1003 S13: 0.2879 REMARK 3 S21: 0.4883 S22: -0.0450 S23: 0.5181 REMARK 3 S31: -0.0017 S32: -1.0951 S33: -0.0711 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 74 THROUGH 128 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.9698 -33.1777 5.4722 REMARK 3 T TENSOR REMARK 3 T11: 0.5906 T22: 0.6409 REMARK 3 T33: 0.4455 T12: 0.0054 REMARK 3 T13: 0.0220 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 2.8144 L22: 2.6576 REMARK 3 L33: 0.6749 L12: -0.0101 REMARK 3 L13: 0.1904 L23: 0.3519 REMARK 3 S TENSOR REMARK 3 S11: 0.0741 S12: 0.0181 S13: -0.0137 REMARK 3 S21: -0.0357 S22: -0.0221 S23: 0.0602 REMARK 3 S31: -0.1682 S32: -0.2703 S33: -0.0055 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.3200 -53.0592 -5.7992 REMARK 3 T TENSOR REMARK 3 T11: 0.6588 T22: 0.5107 REMARK 3 T33: 0.3455 T12: -0.0087 REMARK 3 T13: -0.0673 T23: -0.0399 REMARK 3 L TENSOR REMARK 3 L11: 3.9635 L22: 2.8546 REMARK 3 L33: 1.5109 L12: -0.2094 REMARK 3 L13: 2.2530 L23: -0.9311 REMARK 3 S TENSOR REMARK 3 S11: -0.0504 S12: -0.7267 S13: 0.0743 REMARK 3 S21: 0.1506 S22: -0.0098 S23: -0.1361 REMARK 3 S31: 0.1165 S32: -0.2440 S33: 0.0288 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 18 THROUGH 39 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.9861 -51.4073 -13.9844 REMARK 3 T TENSOR REMARK 3 T11: 0.3983 T22: 0.4564 REMARK 3 T33: 0.3051 T12: 0.0203 REMARK 3 T13: 0.0667 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 5.9832 L22: 5.7334 REMARK 3 L33: 1.4978 L12: -0.5732 REMARK 3 L13: 1.6014 L23: -1.5787 REMARK 3 S TENSOR REMARK 3 S11: 0.0148 S12: -0.2019 S13: -0.1189 REMARK 3 S21: 0.6015 S22: -0.0472 S23: 0.2407 REMARK 3 S31: -0.0613 S32: -0.1856 S33: 0.0404 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 8Q94 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292127690. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : POINTLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 485338 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 47.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 26.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 27.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.130 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.0, 18% PEG 12000, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 112.44850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.57950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.57950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 168.67275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.57950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.57950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.22425 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.57950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.57950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 168.67275 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.57950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.57950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 56.22425 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 112.44850 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: 3180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL 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 GLU A 331 REMARK 465 GLY A 332 REMARK 465 SER A 333 REMARK 465 ASN A 334 REMARK 465 LEU A 335 REMARK 465 ALA A 363 REMARK 465 ASP A 364 REMARK 465 TYR A 365 REMARK 465 SER A 366 REMARK 465 VAL A 367 REMARK 465 LEU A 368 REMARK 465 TYR A 369 REMARK 465 ASN A 370 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 SER B 129 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 SER C 128 REMARK 465 THR C 129 REMARK 465 SER C 130 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 ASP A 339 CG OD1 OD2 REMARK 470 GLU A 340 CG CD OE1 OE2 REMARK 470 ARG A 346 NE CZ NH1 NH2 REMARK 470 PHE A 374 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 386 CG CD CE NZ REMARK 470 ASP A 389 CG OD1 OD2 REMARK 470 LEU A 390 CG CD1 CD2 REMARK 470 SER A 391 OG REMARK 470 LYS A 458 CG CD CE NZ REMARK 470 LYS A 478 CG CD CE NZ REMARK 470 LEU A 517 CG CD1 CD2 REMARK 470 GLN B 1 CG CD OE1 NE2 REMARK 470 LYS B 87 CD CE NZ REMARK 470 LYS B 106 CD CE NZ REMARK 470 THR B 128 OG1 CG2 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 67.50 -69.11 REMARK 500 ALA A 352 54.88 -114.02 REMARK 500 ASN A 360 72.55 56.76 REMARK 500 CYS A 361 -159.62 -160.47 REMARK 500 ASP A 389 59.82 -115.28 REMARK 500 ASN A 422 -61.75 -130.23 REMARK 500 ASP A 428 35.99 -96.74 REMARK 500 REMARK 500 REMARK: NULL DBREF 8Q94 A 334 517 UNP P0DTC2 SPIKE_SARS2 334 517 DBREF 8Q94 B -1 129 PDB 8Q94 8Q94 -1 129 DBREF 8Q94 C -1 130 PDB 8Q94 8Q94 -1 130 SEQADV 8Q94 GLU A 331 UNP P0DTC2 EXPRESSION TAG SEQADV 8Q94 GLY A 332 UNP P0DTC2 EXPRESSION TAG SEQADV 8Q94 SER A 333 UNP P0DTC2 EXPRESSION TAG SEQADV 8Q94 ASP A 339 UNP P0DTC2 GLY 339 VARIANT SEQADV 8Q94 ASP A 343 UNP P0DTC2 ASN 343 CONFLICT SEQADV 8Q94 LEU A 371 UNP P0DTC2 SER 371 VARIANT SEQADV 8Q94 PRO A 373 UNP P0DTC2 SER 373 VARIANT SEQADV 8Q94 PHE A 375 UNP P0DTC2 SER 375 VARIANT SEQADV 8Q94 SER A 391 UNP P0DTC2 CYS 391 CONFLICT SEQADV 8Q94 ASN A 417 UNP P0DTC2 LYS 417 VARIANT SEQADV 8Q94 LYS A 440 UNP P0DTC2 ASN 440 VARIANT SEQADV 8Q94 SER A 446 UNP P0DTC2 GLY 446 VARIANT SEQADV 8Q94 ASN A 477 UNP P0DTC2 SER 477 VARIANT SEQADV 8Q94 LYS A 478 UNP P0DTC2 THR 478 VARIANT SEQADV 8Q94 ALA A 484 UNP P0DTC2 GLU 484 VARIANT SEQADV 8Q94 ARG A 498 UNP P0DTC2 GLN 498 VARIANT SEQADV 8Q94 TYR A 501 UNP P0DTC2 ASN 501 VARIANT SEQADV 8Q94 HIS A 505 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 A 187 GLU GLY SER ASN LEU CYS PRO PHE ASP GLU VAL PHE ASP SEQRES 2 A 187 ALA THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS SEQRES 3 A 187 ARG ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR SEQRES 4 A 187 ASN LEU ALA PRO PHE PHE THR PHE LYS CYS TYR GLY VAL SEQRES 5 A 187 SER PRO THR LYS LEU ASN ASP LEU SER PHE THR ASN VAL SEQRES 6 A 187 TYR ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG SEQRES 7 A 187 GLN ILE ALA PRO GLY GLN THR GLY ASN ILE ALA ASP TYR SEQRES 8 A 187 ASN TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE SEQRES 9 A 187 ALA TRP ASN SER ASN LYS LEU ASP SER LYS VAL SER GLY SEQRES 10 A 187 ASN TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN SEQRES 11 A 187 LEU LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR SEQRES 12 A 187 GLN ALA GLY ASN LYS PRO CYS ASN GLY VAL ALA GLY PHE SEQRES 13 A 187 ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE ARG PRO SEQRES 14 A 187 THR TYR GLY VAL GLY HIS GLN PRO TYR ARG VAL VAL VAL SEQRES 15 A 187 LEU SER PHE GLU LEU SEQRES 1 B 131 GLY SER GLN VAL GLN LEU VAL GLU THR GLY GLY ASP LEU SEQRES 2 B 131 VAL GLN SER GLY GLY SER LEU ARG LEU ALA CYS VAL LEU SEQRES 3 B 131 SER GLY VAL THR LEU ASP SER TYR SER ILE GLY TRP PHE SEQRES 4 B 131 ARG GLN ALA PRO GLY LYS GLU ARG GLU GLY ILE SER TYR SEQRES 5 B 131 SER GLU LYS SER SER GLY PRO THR TYR TYR VAL ASP SER SEQRES 6 B 131 VAL LYS GLY ARG PHE THR VAL SER ARG ASP ASN ALA LYS SEQRES 7 B 131 ASN THR ALA TYR LEU GLN MET ASN SER LEU LYS PRO GLU SEQRES 8 B 131 ASP SER GLY ILE TYR TYR CYS ALA ALA ASP GLU ALA TYR SEQRES 9 B 131 TYR HIS GLU LYS GLY TRP GLN SER PRO LEU GLY TRP PRO SEQRES 10 B 131 TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER THR SEQRES 11 B 131 SER SEQRES 1 C 132 GLY SER GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU SEQRES 2 C 132 VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA ILE SEQRES 3 C 132 SER GLY ILE THR LEU ASP TYR TYR ALA VAL GLY TRP PHE SEQRES 4 C 132 LEU GLN ALA PRO GLY LYS GLU ARG GLU GLY ILE SER CYS SEQRES 5 C 132 MET ARG ASN TRP ASP GLY ARG THR VAL TYR ALA PRO SER SEQRES 6 C 132 VAL LYS GLY ARG PHE THR ILE SER SER ASP ASN ALA LYS SEQRES 7 C 132 LYS MET VAL TYR LEU GLU MET ASP ASN LEU LYS SER GLU SEQRES 8 C 132 ASP THR GLY VAL TYR TYR CYS ALA ALA GLY PRO LEU PRO SEQRES 9 C 132 PRO GLY ILE SER CYS ARG ILE PRO THR PRO LEU GLY TYR SEQRES 10 C 132 ASP ASP TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 11 C 132 THR SER FORMUL 4 HOH *28(H2 O) HELIX 1 AA1 PHE A 338 ASP A 343 1 6 HELIX 2 AA2 SER A 383 ASN A 388 1 6 HELIX 3 AA3 ASP A 405 ILE A 410 5 6 HELIX 4 AA4 GLY A 416 ASN A 422 1 7 HELIX 5 AA5 GLY A 502 HIS A 505 5 4 HELIX 6 AA6 THR B 28 TYR B 32 5 5 HELIX 7 AA7 LYS B 87 SER B 91 5 5 HELIX 8 AA8 SER B 110 TRP B 114 5 5 HELIX 9 AA9 LYS C 87 THR C 91 5 5 SHEET 1 AA1 6 ASN A 354 SER A 359 0 SHEET 2 AA1 6 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 6 PRO A 507 GLU A 516 -1 O VAL A 512 N ASP A 398 SHEET 4 AA1 6 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 6 PHE A 375 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 6 AA1 6 TYR B 102 TYR B 103 -1 O TYR B 102 N CYS A 379 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 TYR A 473 GLN A 474 0 SHEET 2 AA3 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA4 4 GLN B 3 THR B 7 0 SHEET 2 AA4 4 LEU B 18 SER B 25 -1 O ALA B 21 N THR B 7 SHEET 3 AA4 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA4 4 PHE B 68 ASP B 73 -1 N THR B 69 O GLN B 82 SHEET 1 AA5 6 LEU B 11 GLN B 13 0 SHEET 2 AA5 6 THR B 121 SER B 126 1 O THR B 124 N VAL B 12 SHEET 3 AA5 6 GLY B 92 ASP B 99 -1 N TYR B 94 O THR B 121 SHEET 4 AA5 6 SER B 33 GLN B 39 -1 N SER B 33 O ASP B 99 SHEET 5 AA5 6 ARG B 45 SER B 51 -1 O SER B 51 N ILE B 34 SHEET 6 AA5 6 THR B 58 TYR B 60 -1 O TYR B 59 N TYR B 50 SHEET 1 AA6 4 LEU B 11 GLN B 13 0 SHEET 2 AA6 4 THR B 121 SER B 126 1 O THR B 124 N VAL B 12 SHEET 3 AA6 4 GLY B 92 ASP B 99 -1 N TYR B 94 O THR B 121 SHEET 4 AA6 4 TYR B 116 TRP B 117 -1 O TYR B 116 N ALA B 98 SHEET 1 AA7 4 GLN C 3 SER C 7 0 SHEET 2 AA7 4 LEU C 18 SER C 25 -1 O ALA C 23 N VAL C 5 SHEET 3 AA7 4 MET C 78 MET C 83 -1 O MET C 83 N LEU C 18 SHEET 4 AA7 4 PHE C 68 SER C 72 -1 N THR C 69 O GLU C 82 SHEET 1 AA8 6 GLY C 10 VAL C 12 0 SHEET 2 AA8 6 THR C 122 VAL C 126 1 O THR C 125 N GLY C 10 SHEET 3 AA8 6 GLY C 92 PRO C 100 -1 N TYR C 94 O THR C 122 SHEET 4 AA8 6 TYR C 32 GLN C 39 -1 N GLN C 39 O VAL C 93 SHEET 5 AA8 6 ARG C 45 ARG C 52 -1 O SER C 49 N TRP C 36 SHEET 6 AA8 6 THR C 58 TYR C 60 -1 O VAL C 59 N CYS C 50 SHEET 1 AA9 4 GLY C 10 VAL C 12 0 SHEET 2 AA9 4 THR C 122 VAL C 126 1 O THR C 125 N GLY C 10 SHEET 3 AA9 4 GLY C 92 PRO C 100 -1 N TYR C 94 O THR C 122 SHEET 4 AA9 4 ASP C 117 TRP C 118 -1 O ASP C 117 N ALA C 98 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.04 SSBOND 3 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 4 CYS B 22 CYS B 96 1555 1555 2.04 SSBOND 5 CYS C 22 CYS C 96 1555 1555 2.03 SSBOND 6 CYS C 50 CYS C 107 1555 1555 2.04 CISPEP 1 ILE C 109 PRO C 110 0 3.03 CRYST1 67.159 67.159 224.897 90.00 90.00 90.00 P 43 21 2 8 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 0.014890 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014890 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004446 0.00000