HEADER IMMUNE SYSTEM 19-FEB-23 8CMB TITLE HUMAN LEUKOCYTE ANTIGEN CLASS II ALLOTYPE DR1 PRESENTING SARS-COV-2 TITLE 2 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 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, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR B.J.MACLACHLAN,G.H.MASON,A.J.GODKIN,P.J.RIZKALLAH REVDAT 3 03-APR-24 8CMB 1 SSBOND LINK REVDAT 2 02-AUG-23 8CMB 1 JRNL REVDAT 1 26-JUL-23 8CMB 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. 1.84 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 44523 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2182 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 41.1800 - 4.6300 1.00 2849 154 0.1538 0.2072 REMARK 3 2 4.6300 - 3.6800 1.00 2721 134 0.1497 0.1764 REMARK 3 3 3.6800 - 3.2200 1.00 2675 144 0.1897 0.2079 REMARK 3 4 3.2100 - 2.9200 1.00 2669 138 0.2026 0.2309 REMARK 3 5 2.9200 - 2.7100 1.00 2652 124 0.2125 0.2204 REMARK 3 6 2.7100 - 2.5500 1.00 2649 128 0.2077 0.2806 REMARK 3 7 2.5500 - 2.4200 1.00 2629 139 0.2008 0.2422 REMARK 3 8 2.4200 - 2.3200 1.00 2651 133 0.2083 0.2543 REMARK 3 9 2.3200 - 2.2300 1.00 2618 129 0.2221 0.3022 REMARK 3 10 2.2300 - 2.1500 1.00 2602 128 0.2364 0.2958 REMARK 3 11 2.1500 - 2.0800 1.00 2633 134 0.2414 0.2707 REMARK 3 12 2.0800 - 2.0300 1.00 2623 121 0.2380 0.2909 REMARK 3 13 2.0300 - 1.9700 1.00 2571 149 0.2589 0.3251 REMARK 3 14 1.9700 - 1.9200 1.00 2618 153 0.2996 0.3539 REMARK 3 15 1.9200 - 1.8800 1.00 2579 139 0.3394 0.3852 REMARK 3 16 1.8800 - 1.8400 1.00 2602 135 0.3972 0.4563 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) : 0.294 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.255 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.93 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 : 0.016 3339 REMARK 3 ANGLE : 1.365 4525 REMARK 3 CHIRALITY : 0.082 476 REMARK 3 PLANARITY : 0.012 594 REMARK 3 DIHEDRAL : 7.641 448 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): 14.7242 19.5099 3.4919 REMARK 3 T TENSOR REMARK 3 T11: 0.2745 T22: 0.2687 REMARK 3 T33: 0.1869 T12: 0.0016 REMARK 3 T13: -0.0011 T23: -0.0113 REMARK 3 L TENSOR REMARK 3 L11: 8.6424 L22: 5.2602 REMARK 3 L33: 1.9779 L12: 4.3064 REMARK 3 L13: -2.5729 L23: -1.2983 REMARK 3 S TENSOR REMARK 3 S11: -0.3517 S12: 0.0093 S13: -0.2318 REMARK 3 S21: -0.1535 S22: 0.1139 S23: -0.1091 REMARK 3 S31: 0.1021 S32: 0.1045 S33: 0.2155 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 55 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.1778 30.1116 -2.7897 REMARK 3 T TENSOR REMARK 3 T11: 0.2625 T22: 0.2789 REMARK 3 T33: 0.2593 T12: -0.0027 REMARK 3 T13: -0.0102 T23: 0.0201 REMARK 3 L TENSOR REMARK 3 L11: 4.6972 L22: 3.5948 REMARK 3 L33: 3.9250 L12: 1.8104 REMARK 3 L13: 0.1105 L23: 0.9345 REMARK 3 S TENSOR REMARK 3 S11: 0.0563 S12: 0.1528 S13: 0.2047 REMARK 3 S21: -0.2155 S22: -0.1030 S23: 0.1146 REMARK 3 S31: -0.0593 S32: -0.0279 S33: 0.0446 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 56 THROUGH 87 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.4584 8.1196 4.6285 REMARK 3 T TENSOR REMARK 3 T11: 0.2614 T22: 0.2712 REMARK 3 T33: 0.3409 T12: -0.0281 REMARK 3 T13: 0.0410 T23: -0.0123 REMARK 3 L TENSOR REMARK 3 L11: 1.4646 L22: 1.6171 REMARK 3 L33: 2.3986 L12: 0.6154 REMARK 3 L13: -1.2484 L23: -0.6072 REMARK 3 S TENSOR REMARK 3 S11: -0.2895 S12: 0.1359 S13: -0.3997 REMARK 3 S21: -0.1668 S22: 0.0890 S23: -0.0059 REMARK 3 S31: 0.4086 S32: -0.2249 S33: 0.2000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 88 THROUGH 101 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.1466 42.5182 21.0984 REMARK 3 T TENSOR REMARK 3 T11: 0.4131 T22: 0.3975 REMARK 3 T33: 0.4236 T12: -0.0444 REMARK 3 T13: 0.0429 T23: -0.0934 REMARK 3 L TENSOR REMARK 3 L11: 3.7221 L22: 4.5036 REMARK 3 L33: 3.0759 L12: 1.6087 REMARK 3 L13: -0.2391 L23: -0.4144 REMARK 3 S TENSOR REMARK 3 S11: 0.0035 S12: -0.2581 S13: 0.6652 REMARK 3 S21: -0.7894 S22: -0.0592 S23: 0.1256 REMARK 3 S31: -0.4198 S32: 0.1820 S33: 0.0596 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 102 THROUGH 134 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.5775 32.1932 16.6163 REMARK 3 T TENSOR REMARK 3 T11: 0.3038 T22: 0.3077 REMARK 3 T33: 0.3071 T12: 0.0243 REMARK 3 T13: -0.0330 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 2.1191 L22: 3.9969 REMARK 3 L33: 1.9003 L12: 1.8734 REMARK 3 L13: -1.0351 L23: 0.8597 REMARK 3 S TENSOR REMARK 3 S11: 0.0930 S12: 0.0168 S13: 0.4146 REMARK 3 S21: -0.2621 S22: -0.0563 S23: 0.3895 REMARK 3 S31: -0.2309 S32: -0.1676 S33: -0.0367 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 135 THROUGH 154 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.2850 27.3105 13.0205 REMARK 3 T TENSOR REMARK 3 T11: 0.2948 T22: 0.3373 REMARK 3 T33: 0.2697 T12: -0.0331 REMARK 3 T13: -0.0065 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 1.8811 L22: 6.7669 REMARK 3 L33: 2.1824 L12: -0.9216 REMARK 3 L13: -0.2095 L23: 0.4383 REMARK 3 S TENSOR REMARK 3 S11: 0.1288 S12: -0.0064 S13: 0.1363 REMARK 3 S21: -0.1613 S22: -0.1719 S23: -0.0551 REMARK 3 S31: 0.0052 S32: 0.1465 S33: 0.0403 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 155 THROUGH 182 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.3686 33.9181 24.8109 REMARK 3 T TENSOR REMARK 3 T11: 0.3203 T22: 0.3870 REMARK 3 T33: 0.3436 T12: -0.0210 REMARK 3 T13: 0.0549 T23: -0.0943 REMARK 3 L TENSOR REMARK 3 L11: 2.8682 L22: 8.8712 REMARK 3 L33: 2.8611 L12: 1.3445 REMARK 3 L13: -0.1967 L23: 1.8653 REMARK 3 S TENSOR REMARK 3 S11: 0.2389 S12: -0.4754 S13: 0.4429 REMARK 3 S21: 0.8137 S22: -0.2302 S23: 0.3790 REMARK 3 S31: -0.2074 S32: -0.0922 S33: 0.0340 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID -3 THROUGH 89 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.7077 11.4094 2.1369 REMARK 3 T TENSOR REMARK 3 T11: 0.2866 T22: 0.2997 REMARK 3 T33: 0.3376 T12: 0.0024 REMARK 3 T13: 0.0524 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 2.9894 L22: 2.2463 REMARK 3 L33: 1.4752 L12: 0.3530 REMARK 3 L13: -1.0127 L23: -0.5407 REMARK 3 S TENSOR REMARK 3 S11: -0.2978 S12: -0.0456 S13: -0.6354 REMARK 3 S21: -0.2207 S22: -0.0548 S23: -0.3899 REMARK 3 S31: 0.2442 S32: 0.2006 S33: 0.3604 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 90 THROUGH 190 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.7243 43.8660 24.1907 REMARK 3 T TENSOR REMARK 3 T11: 0.3070 T22: 0.3162 REMARK 3 T33: 0.2809 T12: -0.0281 REMARK 3 T13: -0.0001 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 1.9401 L22: 1.7985 REMARK 3 L33: 2.5300 L12: 0.7198 REMARK 3 L13: 0.5366 L23: 0.5819 REMARK 3 S TENSOR REMARK 3 S11: 0.0750 S12: -0.1847 S13: 0.1080 REMARK 3 S21: 0.1908 S22: -0.0071 S23: -0.0939 REMARK 3 S31: -0.1406 S32: -0.0173 S33: -0.0518 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6919 15.2386 -8.0087 REMARK 3 T TENSOR REMARK 3 T11: 0.4423 T22: 0.4356 REMARK 3 T33: 0.5170 T12: -0.0460 REMARK 3 T13: 0.0382 T23: -0.0412 REMARK 3 L TENSOR REMARK 3 L11: 5.4488 L22: 4.1992 REMARK 3 L33: 6.7312 L12: 2.7144 REMARK 3 L13: -2.2005 L23: -4.9894 REMARK 3 S TENSOR REMARK 3 S11: -0.7842 S12: 0.6586 S13: -0.8217 REMARK 3 S21: -1.7042 S22: 1.0262 S23: 0.8892 REMARK 3 S31: 0.8860 S32: -0.4740 S33: -0.3183 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 8CMB 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_1292127969. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-21 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84216 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 42.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.90 REMARK 200 R MERGE FOR SHELL (I) : 3.04600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 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 (%): 54.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.0, 20 % PEG1500, VAPOR REMARK 280 DIFFUSION, HANGING DROP, 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 44.64500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 68.06000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.64500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 68.06000 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: 9940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 ASN C 16 REMARK 465 GLY C 17 REMARK 465 VAL C 18 REMARK 465 GLY C 19 REMARK 465 TYR 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 OG SER B 37 O HOH B 301 2.09 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 O HOH B 308 O HOH B 326 4456 2.18 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 B 128 CB GLU B 128 CG -0.115 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 35 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 136 -175.05 -69.70 REMARK 500 ASP B 2 71.37 56.87 REMARK 500 ASN B 33 -112.17 60.83 REMARK 500 TYR B 78 -64.71 -120.00 REMARK 500 THR B 90 -74.61 -118.46 REMARK 500 ASN B 134 -128.29 51.71 REMARK 500 REMARK 500 REMARK: NULL DBREF 8CMB A 1 182 UNP P01903 DRA_HUMAN 26 207 DBREF 8CMB B -3 190 PDB 8CMB 8CMB -3 190 DBREF 8CMB C 1 20 UNP P0DTC2 SPIKE_SARS2 486 505 SEQADV 8CMB 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 PHE ASN CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN SEQRES 2 C 20 PRO THR ASN GLY VAL GLY TYR HET EDO A 201 4 HET EDO A 202 4 HET EDO A 203 4 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 DHL C 101 8 HETNAM EDO 1,2-ETHANEDIOL HETNAM DHL 2-AMINO-ETHANETHIOL HETSYN EDO ETHYLENE GLYCOL HETSYN DHL 2,3-DESHYDROLANTHIONINE FORMUL 4 EDO 10(C2 H6 O2) FORMUL 14 DHL C2 H7 N S FORMUL 15 HOH *196(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 GLN B 64 1 11 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 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 VAL A 128 0 SHEET 2 AA4 4 ASN A 118 ARG A 123 -1 N ARG A 123 O LYS A 126 SHEET 3 AA4 4 TYR A 161 GLU A 166 -1 O ARG A 164 N THR A 120 SHEET 4 AA4 4 LEU A 174 TRP A 178 -1 O LEU A 174 N VAL A 165 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 118 N THR B 100 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 118 N THR B 100 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 137 0 SHEET 2 AA7 4 GLU B 128 ARG B 133 -1 N ARG B 133 O GLN B 136 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 2.02 SSBOND 2 CYS B 15 CYS B 79 1555 1555 2.13 SSBOND 3 CYS B 117 CYS B 173 1555 1555 2.04 LINK SG ACYS C 3 SG ADHL C 101 1555 1555 2.10 LINK SG BCYS C 3 SG BDHL C 101 1555 1555 2.06 CISPEP 1 ASN A 15 PRO A 16 0 4.19 CISPEP 2 THR A 113 PRO A 114 0 1.38 CISPEP 3 TYR B 123 PRO B 124 0 2.27 CRYST1 89.290 136.120 41.180 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 0.011199 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024284 0.00000