HEADER IMMUNE SYSTEM 19-FEB-23 8CMC TITLE HUMAN LEUKOCYTE ANTIGEN CLASS II ALLOTYPE DR1 PRESENTING SARS-COV-2 TITLE 2 SPIKE PEPTIDE S511-530 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 SPIKE EPITOPE S511-530; 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, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR B.J.MACLACHLAN,G.H.MASON,D.O.SOURFIELD,A.J.GODKIN,P.J.RIZKALLAH REVDAT 2 02-AUG-23 8CMC 1 JRNL REVDAT 1 26-JUL-23 8CMC 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. 1.42 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 87968 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 4405 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 4.4100 - 3.5000 1.00 2974 145 0.1632 0.1901 REMARK 3 2 3.5000 - 3.0600 1.00 2924 142 0.1826 0.2065 REMARK 3 3 3.0600 - 2.7800 1.00 2866 146 0.1845 0.1839 REMARK 3 4 2.7800 - 2.5800 1.00 2852 159 0.1790 0.2097 REMARK 3 5 2.5800 - 2.4300 1.00 2780 161 0.1869 0.2239 REMARK 3 6 2.4300 - 2.3100 1.00 2858 134 0.1842 0.2020 REMARK 3 7 2.3100 - 2.2100 1.00 2805 140 0.1718 0.2151 REMARK 3 8 2.2100 - 2.1200 1.00 2811 141 0.1725 0.2150 REMARK 3 9 2.1200 - 2.0500 1.00 2773 139 0.1875 0.2119 REMARK 3 10 2.0500 - 1.9800 1.00 2771 154 0.1835 0.1993 REMARK 3 11 1.9800 - 1.9300 1.00 2767 149 0.1715 0.1890 REMARK 3 12 1.9300 - 1.8800 1.00 2770 143 0.1737 0.1972 REMARK 3 13 1.8800 - 1.8300 1.00 2761 142 0.1757 0.2300 REMARK 3 14 1.8300 - 1.7900 1.00 2745 146 0.1819 0.2088 REMARK 3 15 1.7900 - 1.7500 1.00 2767 148 0.1886 0.1981 REMARK 3 16 1.7500 - 1.7200 1.00 2760 138 0.1987 0.2343 REMARK 3 17 1.7200 - 1.6800 1.00 2696 157 0.2213 0.2730 REMARK 3 18 1.6800 - 1.6500 1.00 2769 157 0.2337 0.2749 REMARK 3 19 1.6500 - 1.6300 1.00 2741 150 0.2285 0.2571 REMARK 3 20 1.6300 - 1.6000 1.00 2687 153 0.2182 0.2664 REMARK 3 21 1.6000 - 1.5700 1.00 2782 134 0.2306 0.2282 REMARK 3 22 1.5700 - 1.5500 1.00 2699 129 0.2241 0.2422 REMARK 3 23 1.5500 - 1.5300 1.00 2772 139 0.2350 0.2510 REMARK 3 24 1.5300 - 1.5100 1.00 2681 146 0.2460 0.3240 REMARK 3 25 1.5100 - 1.4900 1.00 2747 165 0.2711 0.3065 REMARK 3 26 1.4900 - 1.4700 1.00 2666 153 0.2628 0.2896 REMARK 3 27 1.4700 - 1.4500 1.00 2722 141 0.2871 0.2678 REMARK 3 28 1.4500 - 1.4400 1.00 2705 147 0.3066 0.3278 REMARK 3 29 1.4400 - 1.4200 1.00 2713 137 0.3386 0.3656 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) : 0.171 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.043 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.06 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 : 0.015 3403 REMARK 3 ANGLE : 1.438 4616 REMARK 3 CHIRALITY : 0.117 492 REMARK 3 PLANARITY : 0.012 599 REMARK 3 DIHEDRAL : 12.870 475 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 90 THROUGH 190 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.6070 -11.1751 -10.7305 REMARK 3 T TENSOR REMARK 3 T11: 0.2097 T22: 0.1415 REMARK 3 T33: 0.1710 T12: 0.0412 REMARK 3 T13: -0.0266 T23: 0.0163 REMARK 3 L TENSOR REMARK 3 L11: 3.4107 L22: 3.2450 REMARK 3 L33: 2.2715 L12: -1.2637 REMARK 3 L13: 0.6469 L23: -0.6778 REMARK 3 S TENSOR REMARK 3 S11: -0.0544 S12: -0.0777 S13: -0.1476 REMARK 3 S21: 0.3370 S22: -0.0324 S23: -0.3032 REMARK 3 S31: 0.1461 S32: 0.2418 S33: 0.0816 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 2 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.4602 12.0373 -35.6978 REMARK 3 T TENSOR REMARK 3 T11: 0.3251 T22: 0.2333 REMARK 3 T33: 0.2780 T12: 0.1003 REMARK 3 T13: 0.0014 T23: 0.0269 REMARK 3 L TENSOR REMARK 3 L11: 7.5717 L22: 4.1754 REMARK 3 L33: 5.4382 L12: 5.0203 REMARK 3 L13: 6.2636 L23: 4.2872 REMARK 3 S TENSOR REMARK 3 S11: -0.3357 S12: 0.0282 S13: 0.6804 REMARK 3 S21: -0.5571 S22: -0.2211 S23: 0.3969 REMARK 3 S31: -0.6932 S32: -0.1859 S33: 0.6270 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.3912 1.3996 -23.2196 REMARK 3 T TENSOR REMARK 3 T11: 0.1954 T22: 0.1337 REMARK 3 T33: 0.1947 T12: 0.0558 REMARK 3 T13: 0.0269 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 0.5737 L22: 0.5547 REMARK 3 L33: 1.6023 L12: -0.2391 REMARK 3 L13: 0.4787 L23: -0.4365 REMARK 3 S TENSOR REMARK 3 S11: 0.0751 S12: 0.0645 S13: 0.0212 REMARK 3 S21: 0.0548 S22: -0.0630 S23: 0.0529 REMARK 3 S31: -0.0170 S32: -0.0473 S33: -0.0013 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 113 THROUGH 182 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.1629 -9.5595 -10.5720 REMARK 3 T TENSOR REMARK 3 T11: 0.2742 T22: 0.1470 REMARK 3 T33: 0.2145 T12: 0.0133 REMARK 3 T13: 0.0281 T23: 0.0285 REMARK 3 L TENSOR REMARK 3 L11: 1.6571 L22: 0.9862 REMARK 3 L33: 6.7704 L12: 0.5453 REMARK 3 L13: 2.2278 L23: -0.0366 REMARK 3 S TENSOR REMARK 3 S11: 0.2191 S12: -0.3193 S13: -0.0520 REMARK 3 S21: 0.2589 S22: -0.1000 S23: 0.0471 REMARK 3 S31: 0.2481 S32: -0.4964 S33: -0.1155 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID -1 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.0562 2.5239 -39.7361 REMARK 3 T TENSOR REMARK 3 T11: 0.2272 T22: 0.1897 REMARK 3 T33: 0.1946 T12: 0.0977 REMARK 3 T13: 0.0195 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 0.8363 L22: 1.1270 REMARK 3 L33: 1.0695 L12: 0.3900 REMARK 3 L13: 0.2416 L23: -0.2079 REMARK 3 S TENSOR REMARK 3 S11: 0.0632 S12: 0.0715 S13: -0.0407 REMARK 3 S21: -0.1554 S22: -0.0890 S23: -0.0046 REMARK 3 S31: 0.0914 S32: 0.0944 S33: 0.0192 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 8CMC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128551. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : 88010 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 52.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 38.90 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 39.40 REMARK 200 R MERGE FOR SHELL (I) : 3.34100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.730 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 (%): 49.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 7.0, 25 % PEG8000, 0.2 M REMARK 280 (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 279.49667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 139.74833 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 209.62250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 69.87417 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 349.37083 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 279.49667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 139.74833 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 69.87417 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 209.62250 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 349.37083 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: 10700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 117 LIES ON A SPECIAL POSITION. 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 MET B -3 REMARK 465 GLY B -2 REMARK 465 VAL C 1 REMARK 465 GLY C 16 REMARK 465 PRO C 17 REMARK 465 LYS C 18 REMARK 465 LYS C 19 REMARK 465 SER 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 405 O HOH A 411 1.79 REMARK 500 NZ LYS B 98 O HOH B 301 1.93 REMARK 500 NE2 HIS B 111 O1 EDO B 208 2.16 REMARK 500 O HOH B 403 O HOH B 413 2.17 REMARK 500 NZ LYS A 126 O3 SO4 A 209 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 ND1 HIS A 177 C1 EDO B 208 8445 1.42 REMARK 500 OD1 ASP A 162 O1 EDO B 208 8445 1.97 REMARK 500 ND1 HIS A 177 O1 EDO B 208 8445 2.06 REMARK 500 O HOH A 305 O HOH A 426 8555 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 4 CB GLU A 4 CG 0.119 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 VAL A 136 -177.29 -68.53 REMARK 500 ASN B 33 -108.61 63.41 REMARK 500 THR B 90 -74.65 -126.15 REMARK 500 GLN B 110 11.98 83.41 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 B 426 DISTANCE = 5.89 ANGSTROMS DBREF 8CMC A 1 182 UNP P01903 DRA_HUMAN 26 207 DBREF 8CMC B -3 190 PDB 8CMC 8CMC -3 190 DBREF 8CMC C 1 20 UNP P0DTC2 SPIKE_SARS2 511 530 SEQADV 8CMC MET A 0 UNP P01903 INITIATING METHIONINE 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 VAL VAL LEU SER PHE GLU LEU LEU HIS ALA PRO ALA THR SEQRES 2 C 20 VAL CYS GLY PRO LYS LYS SER 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 SO4 A 208 5 HET SO4 A 209 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 MES B 209 12 HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 4 EDO 15(C2 H6 O2) FORMUL 11 SO4 2(O4 S 2-) FORMUL 21 MES C6 H13 N O4 S FORMUL 22 HOH *287(H2 O) HELIX 1 AA1 GLU A 47 PHE A 51 1 5 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 GLU A 4 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 ARG B 25 N HIS B 16 SHEET 7 AA1 8 GLU B 35 ASP B 41 -1 O PHE B 40 N GLU B 28 SHEET 8 AA1 8 TYR B 47 ALA B 49 -1 O ARG B 48 N ARG B 39 SHEET 1 AA2 2 ALA A 52 SER A 53 0 SHEET 2 AA2 2 LEU C 3 SER C 4 1 O LEU C 3 N SER A 53 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 LEU A 151 N LEU A 105 SHEET 4 AA3 4 SER A 133 GLU A 134 -1 N SER A 133 O TYR A 150 SHEET 1 AA4 4 GLU A 88 THR A 93 0 SHEET 2 AA4 4 ASN A 103 PHE A 112 -1 O ILE A 106 N LEU A 92 SHEET 3 AA4 4 PHE A 145 PHE A 153 -1 O LEU A 151 N LEU A 105 SHEET 4 AA4 4 LEU A 138 PRO A 139 -1 N LEU A 138 O ARG A 146 SHEET 1 AA5 4 LYS A 126 VAL A 128 0 SHEET 2 AA5 4 ASN A 118 ARG A 123 -1 N ARG A 123 O LYS A 126 SHEET 3 AA5 4 VAL A 160 GLU A 166 -1 O ARG A 164 N THR A 120 SHEET 4 AA5 4 LEU A 174 GLU A 179 -1 O TRP A 178 N TYR A 161 SHEET 1 AA6 4 LYS B 98 PRO B 103 0 SHEET 2 AA6 4 ASN B 113 PHE B 122 -1 O VAL B 116 N TYR B 102 SHEET 3 AA6 4 PHE B 155 THR B 163 -1 O LEU B 161 N LEU B 115 SHEET 4 AA6 4 VAL B 142 SER B 144 -1 N VAL B 143 O MET B 160 SHEET 1 AA7 4 LYS B 98 PRO B 103 0 SHEET 2 AA7 4 ASN B 113 PHE B 122 -1 O VAL B 116 N TYR B 102 SHEET 3 AA7 4 PHE B 155 THR B 163 -1 O LEU B 161 N LEU B 115 SHEET 4 AA7 4 ILE B 148 GLN B 149 -1 N ILE B 148 O GLN B 156 SHEET 1 AA8 4 GLN B 136 GLU B 138 0 SHEET 2 AA8 4 GLU B 128 ARG B 133 -1 N ARG B 133 O GLN B 136 SHEET 3 AA8 4 VAL B 170 GLU B 176 -1 O GLN B 174 N ARG B 130 SHEET 4 AA8 4 LEU B 184 ARG B 189 -1 O LEU B 184 N VAL B 175 SSBOND 1 CYS A 107 CYS A 163 1555 1555 2.06 SSBOND 2 CYS B 15 CYS B 79 1555 1555 2.20 SSBOND 3 CYS B 117 CYS B 173 1555 1555 2.03 CISPEP 1 ASN A 15 PRO A 16 0 2.90 CISPEP 2 THR A 113 PRO A 114 0 2.67 CISPEP 3 TYR B 123 PRO B 124 0 2.60 CRYST1 60.576 60.576 419.245 90.00 90.00 120.00 P 65 2 2 12 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 0.016508 0.009531 0.000000 0.00000 SCALE2 0.000000 0.019062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002385 0.00000