HEADER IMMUNE SYSTEM 19-FEB-23 8CMH TITLE HUMAN LEUKOCYTE ANTIGEN CLASS II ALLOTYPE DR1 PRESENTING SARS-COV-2 TITLE 2 OMICRON (BA.1) SPIKE PEPTIDE S486-505 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MHC CLASS II ANTIGEN DRA; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HUMAN LEUKOCYTE ANTIGEN DR BETA CHAIN ALLOTYPE DR1 COMPND 8 (DRB1*0101); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: SPIKE PROTEIN S2'; COMPND 13 CHAIN: C; COMPND 14 SYNONYM: SARS-COV-2 OMICRON (BA.1) SPIKE EPITOPE S486-505; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HLA-DRA, HLA-DRA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 16 2; SOURCE 17 ORGANISM_TAXID: 2697049 KEYWDS HLA-II, HLA-DR, HLA-DR1, HUMAN LEUKOCYTE ANTIGEN, MAJOR KEYWDS 2 HISTOCOMPATIBILITY COMPLEX, MAJOR HISTOCOMPATIBILITY COMPLEX CLASS KEYWDS 3 2, SARS-COV-2, CORONAVIRUS, COVID-19, SPIKE, OMICRON, BA.1, VIRAL KEYWDS 4 VARIANT, IMMUNE ESCAPE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR B.J.MACLACHLAN,G.H.MASON,D.O.SOURFIELD,A.J.GODKIN,P.J.RIZKALLAH REVDAT 3 03-APR-24 8CMH 1 SSBOND LINK REVDAT 2 02-AUG-23 8CMH 1 JRNL REVDAT 1 26-JUL-23 8CMH 0 JRNL AUTH Y.CHEN,G.H.MASON,D.O.SCOURFIELD,A.GREENSHIELDS-WATSON, JRNL AUTH 2 T.A.HAIGH,A.K.SEWELL,H.M.LONG,A.M.GALLIMORE,P.RIZKALLAH, JRNL AUTH 3 B.J.MACLACHLAN,A.GODKIN JRNL TITL STRUCTURAL DEFINITION OF HLA CLASS II-PRESENTED SARS-COV-2 JRNL TITL 2 EPITOPES REVEALS A MECHANISM TO ESCAPE PRE-EXISTING CD4 + T JRNL TITL 3 CELL IMMUNITY. JRNL REF CELL REP V. 42 12827 2023 JRNL REFN ESSN 2211-1247 JRNL PMID 37471227 JRNL DOI 10.1016/J.CELREP.2023.112827 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2-4158 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 55337 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 2731 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 50.1500 - 4.4500 1.00 2883 152 0.1639 0.2011 REMARK 3 2 4.4500 - 3.5300 1.00 2735 134 0.1411 0.1455 REMARK 3 3 3.5300 - 3.0900 1.00 2704 141 0.1566 0.1785 REMARK 3 4 3.0900 - 2.8000 1.00 2679 143 0.1651 0.1873 REMARK 3 5 2.8000 - 2.6000 1.00 2632 139 0.1766 0.1930 REMARK 3 6 2.6000 - 2.4500 0.99 2659 131 0.1716 0.2071 REMARK 3 7 2.4500 - 2.3300 0.99 2651 137 0.1769 0.2195 REMARK 3 8 2.3300 - 2.2300 0.99 2600 149 0.1747 0.2073 REMARK 3 9 2.2300 - 2.1400 0.99 2589 149 0.1688 0.2237 REMARK 3 10 2.1400 - 2.0700 1.00 2642 129 0.1813 0.2153 REMARK 3 11 2.0700 - 2.0000 0.98 2589 137 0.1939 0.2501 REMARK 3 12 2.0000 - 1.9400 1.00 2615 131 0.2195 0.2493 REMARK 3 13 1.9400 - 1.8900 0.98 2608 130 0.2206 0.2485 REMARK 3 14 1.8900 - 1.8500 0.99 2550 142 0.2311 0.2442 REMARK 3 15 1.8500 - 1.8000 0.98 2601 134 0.2335 0.2451 REMARK 3 16 1.8000 - 1.7700 0.98 2562 145 0.2569 0.2890 REMARK 3 17 1.7700 - 1.7300 0.98 2581 121 0.2786 0.2904 REMARK 3 18 1.7300 - 1.7000 0.99 2605 104 0.2968 0.3288 REMARK 3 19 1.7000 - 1.6700 0.96 2551 144 0.3128 0.3538 REMARK 3 20 1.6700 - 1.6400 0.99 2570 139 0.3362 0.3354 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.216 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.866 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.80 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 : 0.005 3428 REMARK 3 ANGLE : 0.801 4612 REMARK 3 CHIRALITY : 0.057 484 REMARK 3 PLANARITY : 0.006 598 REMARK 3 DIHEDRAL : 6.792 479 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.1030 14.6653 3.9166 REMARK 3 T TENSOR REMARK 3 T11: 0.0990 T22: 0.1159 REMARK 3 T33: 0.0739 T12: -0.0077 REMARK 3 T13: -0.0235 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 5.2688 L22: 4.0047 REMARK 3 L33: 2.0310 L12: 3.1971 REMARK 3 L13: -2.9026 L23: -0.8605 REMARK 3 S TENSOR REMARK 3 S11: 0.0063 S12: -0.0809 S13: -0.1997 REMARK 3 S21: 0.0606 S22: -0.0348 S23: -0.2015 REMARK 3 S31: -0.0468 S32: 0.1542 S33: -0.0259 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.2192 25.5419 -2.4477 REMARK 3 T TENSOR REMARK 3 T11: 0.0972 T22: 0.1072 REMARK 3 T33: 0.0988 T12: 0.0011 REMARK 3 T13: -0.0050 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 3.6274 L22: 4.4450 REMARK 3 L33: 4.2967 L12: 1.3022 REMARK 3 L13: -0.1385 L23: 0.1719 REMARK 3 S TENSOR REMARK 3 S11: 0.0150 S12: 0.1404 S13: 0.2870 REMARK 3 S21: -0.1258 S22: 0.0070 S23: 0.1395 REMARK 3 S31: -0.2584 S32: -0.0909 S33: -0.0238 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 56 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.8814 4.1986 4.9483 REMARK 3 T TENSOR REMARK 3 T11: 0.0942 T22: 0.1227 REMARK 3 T33: 0.1452 T12: 0.0065 REMARK 3 T13: -0.0038 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.6461 L22: 1.5204 REMARK 3 L33: 1.6091 L12: 0.7104 REMARK 3 L13: -0.4858 L23: -0.7247 REMARK 3 S TENSOR REMARK 3 S11: -0.0927 S12: 0.0803 S13: -0.0959 REMARK 3 S21: -0.1473 S22: 0.0442 S23: -0.0203 REMARK 3 S31: 0.1723 S32: -0.0829 S33: 0.0586 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2326 31.5675 18.2339 REMARK 3 T TENSOR REMARK 3 T11: 0.1303 T22: 0.1119 REMARK 3 T33: 0.1202 T12: -0.0035 REMARK 3 T13: -0.0035 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 1.5959 L22: 5.7326 REMARK 3 L33: 1.4167 L12: 0.6217 REMARK 3 L13: 0.0308 L23: 1.4037 REMARK 3 S TENSOR REMARK 3 S11: 0.0111 S12: -0.0378 S13: 0.2967 REMARK 3 S21: -0.0262 S22: -0.0330 S23: 0.0053 REMARK 3 S31: -0.2111 S32: -0.0104 S33: 0.0255 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 154 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.8025 23.2447 13.1195 REMARK 3 T TENSOR REMARK 3 T11: 0.1259 T22: 0.1566 REMARK 3 T33: 0.1366 T12: -0.0331 REMARK 3 T13: -0.0121 T23: 0.0055 REMARK 3 L TENSOR REMARK 3 L11: 2.0714 L22: 6.9465 REMARK 3 L33: 1.5455 L12: -3.2561 REMARK 3 L13: -0.6170 L23: 0.9795 REMARK 3 S TENSOR REMARK 3 S11: 0.0676 S12: -0.0270 S13: 0.0848 REMARK 3 S21: -0.0938 S22: -0.0529 S23: -0.0700 REMARK 3 S31: -0.0496 S32: 0.0522 S33: -0.0172 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 155 THROUGH 166 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.2277 35.2108 23.4350 REMARK 3 T TENSOR REMARK 3 T11: 0.1811 T22: 0.1534 REMARK 3 T33: 0.2783 T12: 0.0038 REMARK 3 T13: 0.0496 T23: -0.0653 REMARK 3 L TENSOR REMARK 3 L11: 1.5755 L22: 0.8270 REMARK 3 L33: 1.9122 L12: 1.1453 REMARK 3 L13: 0.8758 L23: 0.6636 REMARK 3 S TENSOR REMARK 3 S11: 0.1258 S12: -0.1841 S13: 0.4320 REMARK 3 S21: 0.2971 S22: -0.2138 S23: 0.6162 REMARK 3 S31: -0.2581 S32: -0.1222 S33: 0.1101 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 167 THROUGH 182 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.2930 26.1862 25.9784 REMARK 3 T TENSOR REMARK 3 T11: 0.1523 T22: 0.1678 REMARK 3 T33: 0.1046 T12: 0.0083 REMARK 3 T13: -0.0160 T23: -0.0110 REMARK 3 L TENSOR REMARK 3 L11: 2.8970 L22: 6.6184 REMARK 3 L33: 3.5278 L12: 2.2007 REMARK 3 L13: 0.6825 L23: 3.0929 REMARK 3 S TENSOR REMARK 3 S11: 0.1247 S12: -0.2560 S13: 0.2063 REMARK 3 S21: 0.7351 S22: -0.1879 S23: 0.2135 REMARK 3 S31: 0.1329 S32: -0.0454 S33: 0.0609 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID -2 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.5862 6.0236 2.1219 REMARK 3 T TENSOR REMARK 3 T11: 0.1514 T22: 0.1604 REMARK 3 T33: 0.1771 T12: 0.0124 REMARK 3 T13: 0.0230 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 1.9174 L22: 1.6548 REMARK 3 L33: 1.3729 L12: 0.2547 REMARK 3 L13: -0.6927 L23: -0.5546 REMARK 3 S TENSOR REMARK 3 S11: -0.1434 S12: -0.0499 S13: -0.3680 REMARK 3 S21: -0.1944 S22: -0.0826 S23: -0.3273 REMARK 3 S31: 0.2372 S32: 0.2453 S33: 0.2166 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 90 THROUGH 190 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.2972 38.6561 24.1857 REMARK 3 T TENSOR REMARK 3 T11: 0.0997 T22: 0.1140 REMARK 3 T33: 0.1033 T12: 0.0050 REMARK 3 T13: -0.0045 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 1.4407 L22: 2.0741 REMARK 3 L33: 2.5740 L12: 0.9137 REMARK 3 L13: 0.6230 L23: 1.2422 REMARK 3 S TENSOR REMARK 3 S11: 0.0260 S12: -0.1127 S13: 0.0119 REMARK 3 S21: 0.1415 S22: 0.0101 S23: -0.0133 REMARK 3 S31: 0.0599 S32: -0.0286 S33: -0.0402 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.5255 9.8953 -7.9100 REMARK 3 T TENSOR REMARK 3 T11: 0.2498 T22: 0.2209 REMARK 3 T33: 0.2992 T12: -0.0508 REMARK 3 T13: 0.0458 T23: -0.0373 REMARK 3 L TENSOR REMARK 3 L11: 4.6211 L22: 7.0329 REMARK 3 L33: 4.6552 L12: 2.6048 REMARK 3 L13: -0.4238 L23: -1.9767 REMARK 3 S TENSOR REMARK 3 S11: -0.4480 S12: 0.3475 S13: -0.5552 REMARK 3 S21: -1.1284 S22: 0.4395 S23: 0.5504 REMARK 3 S31: 0.6398 S32: -0.1968 S33: -0.0463 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 8CMH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128570. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55347 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 50.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 13.60 REMARK 200 R MERGE (I) : 0.34100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 14.10 REMARK 200 R MERGE FOR SHELL (I) : 3.67800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.590 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE PH 6.0, 25 % REMARK 280 PEG4000, 0.2 M AMMONIUM SULPHATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 45.51700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 60.09300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.51700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 60.09300 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: 13830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 26.0 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 MET A 0 REMARK 465 ILE A 1 REMARK 465 LYS A 2 REMARK 465 THR C 15 REMARK 465 TYR C 16 REMARK 465 GLY C 17 REMARK 465 VAL C 18 REMARK 465 GLY C 19 REMARK 465 HIS C 20 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 HOH A 396 O HOH A 434 2.08 REMARK 500 O2 EDO A 201 O HOH A 301 2.11 REMARK 500 O HOH A 455 O HOH A 458 2.13 REMARK 500 O HOH A 428 O HOH A 443 2.16 REMARK 500 O HOH B 419 O HOH B 420 2.16 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 B 2 73.95 57.73 REMARK 500 ASN B 33 -106.37 55.48 REMARK 500 THR B 90 -72.77 -123.80 REMARK 500 PRO B 124 -168.96 -78.77 REMARK 500 ASN B 134 -124.24 57.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 469 DISTANCE = 5.99 ANGSTROMS DBREF 8CMH A 1 182 UNP P01903 DRA_HUMAN 26 207 DBREF 8CMH B -3 190 PDB 8CMH 8CMH -3 190 DBREF 8CMH C 1 20 UNP P0DTC2 SPIKE_SARS2 486 505 SEQADV 8CMH MET A 0 UNP P01903 INITIATING METHIONINE SEQADV 8CMH ARG C 8 UNP P0DTC2 GLN 493 VARIANT SEQADV 8CMH SER C 11 UNP P0DTC2 GLY 496 VARIANT SEQADV 8CMH ARG C 13 UNP P0DTC2 GLN 498 VARIANT SEQADV 8CMH TYR C 16 UNP P0DTC2 ASN 501 VARIANT SEQADV 8CMH HIS C 20 UNP P0DTC2 TYR 505 VARIANT SEQRES 1 A 183 MET ILE LYS GLU GLU HIS VAL ILE ILE GLN ALA GLU PHE SEQRES 2 A 183 TYR LEU ASN PRO ASP GLN SER GLY GLU PHE MET PHE ASP SEQRES 3 A 183 PHE ASP GLY ASP GLU ILE PHE HIS VAL ASP MET ALA LYS SEQRES 4 A 183 LYS GLU THR VAL TRP ARG LEU GLU GLU PHE GLY ARG PHE SEQRES 5 A 183 ALA SER PHE GLU ALA GLN GLY ALA LEU ALA ASN ILE ALA SEQRES 6 A 183 VAL ASP LYS ALA ASN LEU GLU ILE MET THR LYS ARG SER SEQRES 7 A 183 ASN TYR THR PRO ILE THR ASN VAL PRO PRO GLU VAL THR SEQRES 8 A 183 VAL LEU THR ASN SER PRO VAL GLU LEU ARG GLU PRO ASN SEQRES 9 A 183 VAL LEU ILE CYS PHE ILE ASP LYS PHE THR PRO PRO VAL SEQRES 10 A 183 VAL ASN VAL THR TRP LEU ARG ASN GLY LYS PRO VAL THR SEQRES 11 A 183 THR GLY VAL SER GLU THR VAL PHE LEU PRO ARG GLU ASP SEQRES 12 A 183 HIS LEU PHE ARG LYS PHE HIS TYR LEU PRO PHE LEU PRO SEQRES 13 A 183 SER THR GLU ASP VAL TYR ASP CYS ARG VAL GLU HIS TRP SEQRES 14 A 183 GLY LEU ASP GLU PRO LEU LEU LYS HIS TRP GLU PHE ASP SEQRES 15 A 183 ALA SEQRES 1 B 194 MET GLY SER MET GLY ASP THR ARG PRO ARG PHE LEU TRP SEQRES 2 B 194 GLN LEU LYS PHE GLU CYS HIS PHE PHE ASN GLY THR GLU SEQRES 3 B 194 ARG VAL ARG LEU LEU GLU ARG CYS ILE TYR ASN GLN GLU SEQRES 4 B 194 GLU SER VAL ARG PHE ASP SER ASP VAL GLY GLU TYR ARG SEQRES 5 B 194 ALA VAL THR GLU LEU GLY ARG PRO ASP ALA GLU TYR TRP SEQRES 6 B 194 ASN SER GLN LYS ASP LEU LEU GLU GLN ARG ARG ALA ALA SEQRES 7 B 194 VAL ASP THR TYR CYS ARG HIS ASN TYR GLY VAL GLY GLU SEQRES 8 B 194 SER PHE THR VAL GLN ARG ARG VAL GLU PRO LYS VAL THR SEQRES 9 B 194 VAL TYR PRO SER LYS THR GLN PRO LEU GLN HIS HIS ASN SEQRES 10 B 194 LEU LEU VAL CYS SER VAL SER GLY PHE TYR PRO GLY SER SEQRES 11 B 194 ILE GLU VAL ARG TRP PHE ARG ASN GLY GLN GLU GLU LYS SEQRES 12 B 194 ALA GLY VAL VAL SER THR GLY LEU ILE GLN ASN GLY ASP SEQRES 13 B 194 TRP THR PHE GLN THR LEU VAL MET LEU GLU THR VAL PRO SEQRES 14 B 194 ARG SER GLY GLU VAL TYR THR CYS GLN VAL GLU HIS PRO SEQRES 15 B 194 SER VAL THR SER PRO LEU THR VAL GLU TRP ARG ALA SEQRES 1 C 20 PHE ASN CYS TYR PHE PRO LEU ARG SER TYR SER PHE ARG SEQRES 2 C 20 PRO THR TYR GLY VAL GLY HIS HET EDO A 201 4 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HET EDO A 205 4 HET EDO A 206 4 HET EDO A 207 4 HET EDO A 208 4 HET EDO A 209 4 HET EDO A 210 4 HET EDO A 211 4 HET EDO A 212 4 HET EDO A 213 4 HET EDO A 214 4 HET EDO A 215 4 HET EDO A 216 4 HET EDO A 217 4 HET SO4 A 218 5 HET EDO B 201 4 HET EDO B 202 4 HET EDO B 203 4 HET EDO B 204 4 HET EDO B 205 4 HET EDO B 206 4 HET EDO B 207 4 HET EDO B 208 4 HET EDO B 209 4 HET EDO B 210 4 HET EDO B 211 4 HET EDO B 212 4 HET EDO B 213 4 HET DHL C 101 8 HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM DHL 2-AMINO-ETHANETHIOL HETSYN EDO ETHYLENE GLYCOL HETSYN DHL 2,3-DESHYDROLANTHIONINE FORMUL 4 EDO 30(C2 H6 O2) FORMUL 21 SO4 O4 S 2- FORMUL 35 DHL C2 H7 N S FORMUL 36 HOH *325(H2 O) HELIX 1 AA1 GLU A 47 ALA A 52 1 6 HELIX 2 AA2 GLU A 55 SER A 77 1 23 HELIX 3 AA3 THR B 51 LEU B 53 5 3 HELIX 4 AA4 GLY B 54 SER B 63 1 10 HELIX 5 AA5 GLN B 64 TYR B 78 1 15 HELIX 6 AA6 TYR B 78 GLU B 87 1 10 HELIX 7 AA7 SER B 88 THR B 90 5 3 SHEET 1 AA1 8 GLU A 40 TRP A 43 0 SHEET 2 AA1 8 ASP A 29 ASP A 35 -1 N HIS A 33 O VAL A 42 SHEET 3 AA1 8 SER A 19 PHE A 26 -1 N PHE A 26 O ASP A 29 SHEET 4 AA1 8 HIS A 5 ASN A 15 -1 N ALA A 10 O MET A 23 SHEET 5 AA1 8 PHE B 7 PHE B 18 -1 O CYS B 15 N ILE A 7 SHEET 6 AA1 8 ARG B 23 TYR B 32 -1 O LEU B 27 N GLU B 14 SHEET 7 AA1 8 GLU B 35 ASP B 41 -1 O SER B 37 N CYS B 30 SHEET 8 AA1 8 TYR B 47 ALA B 49 -1 O ARG B 48 N ARG B 39 SHEET 1 AA2 4 GLU A 88 THR A 93 0 SHEET 2 AA2 4 ASN A 103 PHE A 112 -1 O ILE A 106 N LEU A 92 SHEET 3 AA2 4 PHE A 145 PHE A 153 -1 O HIS A 149 N CYS A 107 SHEET 4 AA2 4 SER A 133 GLU A 134 -1 N SER A 133 O TYR A 150 SHEET 1 AA3 4 GLU A 88 THR A 93 0 SHEET 2 AA3 4 ASN A 103 PHE A 112 -1 O ILE A 106 N LEU A 92 SHEET 3 AA3 4 PHE A 145 PHE A 153 -1 O HIS A 149 N CYS A 107 SHEET 4 AA3 4 LEU A 138 PRO A 139 -1 N LEU A 138 O ARG A 146 SHEET 1 AA4 4 LYS A 126 PRO A 127 0 SHEET 2 AA4 4 ASN A 118 ARG A 123 -1 N ARG A 123 O LYS A 126 SHEET 3 AA4 4 VAL A 160 GLU A 166 -1 O ARG A 164 N THR A 120 SHEET 4 AA4 4 LEU A 174 GLU A 179 -1 O TRP A 178 N TYR A 161 SHEET 1 AA5 4 LYS B 98 PRO B 103 0 SHEET 2 AA5 4 ASN B 113 PHE B 122 -1 O SER B 120 N LYS B 98 SHEET 3 AA5 4 PHE B 155 THR B 163 -1 O LEU B 161 N LEU B 115 SHEET 4 AA5 4 VAL B 142 SER B 144 -1 N VAL B 143 O MET B 160 SHEET 1 AA6 4 LYS B 98 PRO B 103 0 SHEET 2 AA6 4 ASN B 113 PHE B 122 -1 O SER B 120 N LYS B 98 SHEET 3 AA6 4 PHE B 155 THR B 163 -1 O LEU B 161 N LEU B 115 SHEET 4 AA6 4 ILE B 148 GLN B 149 -1 N ILE B 148 O GLN B 156 SHEET 1 AA7 4 GLN B 136 GLU B 138 0 SHEET 2 AA7 4 GLU B 128 ARG B 133 -1 N TRP B 131 O GLU B 138 SHEET 3 AA7 4 VAL B 170 GLU B 176 -1 O GLN B 174 N ARG B 130 SHEET 4 AA7 4 LEU B 184 ARG B 189 -1 O TRP B 188 N TYR B 171 SSBOND 1 CYS A 107 CYS A 163 1555 1555 2.04 SSBOND 2 CYS B 15 CYS B 79 1555 1555 2.07 SSBOND 3 CYS B 117 CYS B 173 1555 1555 2.03 LINK SG ACYS C 3 SG ADHL C 101 1555 1555 2.03 LINK SG BCYS C 3 SG BDHL C 101 1555 1555 2.03 CISPEP 1 ASN A 15 PRO A 16 0 5.21 CISPEP 2 THR A 113 PRO A 114 0 -1.66 CISPEP 3 TYR B 123 PRO B 124 0 -1.12 CRYST1 91.034 120.186 40.879 90.00 90.00 90.00 P 21 21 2 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 0.010985 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024462 0.00000