HEADER VIRAL PROTEIN/IMMUNE SYSTEM 07-SEP-21 7S3N TITLE SARS-COV-2 S STEM HELIX PEPTIDE BOUND TO FAB22 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: STEM HELIX PEPTIDE (UNP RESIDUES 1146-1164); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: FAB22 HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: FAB22 LIGHT CHAIN; COMPND 12 CHAIN: L; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 4 2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 8 ORGANISM_COMMON: MOUSE; SOURCE 9 ORGANISM_TAXID: 10090; SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 11 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 15 ORGANISM_COMMON: MOUSE; SOURCE 16 ORGANISM_TAXID: 10090; SOURCE 17 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 18 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SPIKE, FUSION, ANTIBODY, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.A.GOLDSMITH,J.S.MCLELLAN REVDAT 5 18-OCT-23 7S3N 1 REMARK REVDAT 4 10-AUG-22 7S3N 1 COMPND SOURCE REMARK DBREF REVDAT 4 2 1 SEQRES HELIX SHEET SSBOND REVDAT 4 3 1 CRYST1 SCALE ATOM REVDAT 3 17-NOV-21 7S3N 1 JRNL REVDAT 2 10-NOV-21 7S3N 1 JRNL REVDAT 1 27-OCT-21 7S3N 0 JRNL AUTH C.L.HSIEH,A.P.WERNER,S.R.LEIST,L.J.STEVENS,E.FALCONER, JRNL AUTH 2 J.A.GOLDSMITH,C.W.CHOU,O.M.ABIONA,A.WEST,K.WESTENDORF, JRNL AUTH 3 K.MUTHURAMAN,E.J.FRITCH,K.H.DINNON 3RD,A.SCHAFER, JRNL AUTH 4 M.R.DENISON,J.D.CHAPPELL,R.S.BARIC,B.S.GRAHAM,K.S.CORBETT, JRNL AUTH 5 J.S.MCLELLAN JRNL TITL STABILIZED CORONAVIRUS SPIKE STEM ELICITS A BROADLY JRNL TITL 2 PROTECTIVE ANTIBODY. JRNL REF CELL REP V. 37 09929 2021 JRNL REFN ESSN 2211-1247 JRNL PMID 34710354 JRNL DOI 10.1016/J.CELREP.2021.109929 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 38918 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1937 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 43.7800 - 4.5800 0.98 2729 149 0.1828 0.2141 REMARK 3 2 4.5800 - 3.6300 0.99 2662 166 0.1628 0.2234 REMARK 3 3 3.6300 - 3.1700 0.99 2724 123 0.1910 0.2157 REMARK 3 4 3.1700 - 2.8800 0.99 2692 132 0.2160 0.2113 REMARK 3 5 2.8800 - 2.6800 0.99 2692 153 0.2164 0.2443 REMARK 3 6 2.6800 - 2.5200 0.99 2677 128 0.2275 0.2581 REMARK 3 7 2.5200 - 2.3900 0.97 2659 142 0.2384 0.2659 REMARK 3 8 2.3900 - 2.2900 0.99 2651 140 0.2346 0.2689 REMARK 3 9 2.2900 - 2.2000 0.99 2684 146 0.2252 0.2479 REMARK 3 10 2.2000 - 2.1300 0.98 2605 137 0.2317 0.2461 REMARK 3 11 2.1300 - 2.0600 0.96 2610 125 0.2317 0.2479 REMARK 3 12 2.0600 - 2.0000 0.92 2471 134 0.2426 0.2801 REMARK 3 13 2.0000 - 1.9500 0.96 2567 138 0.2523 0.2744 REMARK 3 14 1.9500 - 1.9000 0.94 2558 124 0.2676 0.2705 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) : 0.182 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.177 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.50 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 : 0.007 3511 REMARK 3 ANGLE : 0.952 4783 REMARK 3 CHIRALITY : 0.059 544 REMARK 3 PLANARITY : 0.007 611 REMARK 3 DIHEDRAL : 16.188 1277 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1147 THROUGH 1156 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.3327 26.2776 40.0526 REMARK 3 T TENSOR REMARK 3 T11: 0.9016 T22: 0.8458 REMARK 3 T33: 0.5115 T12: -0.0183 REMARK 3 T13: -0.4501 T23: -0.1011 REMARK 3 L TENSOR REMARK 3 L11: 6.3756 L22: 6.5019 REMARK 3 L33: 4.8875 L12: 2.3721 REMARK 3 L13: -0.9187 L23: 1.6795 REMARK 3 S TENSOR REMARK 3 S11: 0.3668 S12: -0.2850 S13: -0.9166 REMARK 3 S21: 0.8096 S22: 0.0239 S23: -1.4907 REMARK 3 S31: 0.5581 S32: 2.1041 S33: -0.5696 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 3 THROUGH 93 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.0844 31.9766 26.3472 REMARK 3 T TENSOR REMARK 3 T11: 0.5296 T22: 0.2754 REMARK 3 T33: 0.1927 T12: -0.0476 REMARK 3 T13: -0.0051 T23: -0.0633 REMARK 3 L TENSOR REMARK 3 L11: 1.6696 L22: 2.2036 REMARK 3 L33: 5.4931 L12: 0.0277 REMARK 3 L13: -0.3459 L23: -0.4060 REMARK 3 S TENSOR REMARK 3 S11: 0.1366 S12: -0.2696 S13: -0.0034 REMARK 3 S21: 0.9133 S22: -0.0429 S23: -0.0531 REMARK 3 S31: 0.0735 S32: 0.2951 S33: -0.0958 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 94 THROUGH 130 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.9193 25.9444 26.2336 REMARK 3 T TENSOR REMARK 3 T11: 0.6736 T22: 0.2553 REMARK 3 T33: 0.1286 T12: -0.0250 REMARK 3 T13: 0.0188 T23: -0.0295 REMARK 3 L TENSOR REMARK 3 L11: 1.7397 L22: 1.9086 REMARK 3 L33: 2.7777 L12: -0.0931 REMARK 3 L13: 0.1542 L23: -0.0368 REMARK 3 S TENSOR REMARK 3 S11: 0.1542 S12: -0.4076 S13: 0.0462 REMARK 3 S21: 1.1106 S22: 0.0979 S23: 0.1903 REMARK 3 S31: 0.1425 S32: 0.1886 S33: -0.1669 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 131 THROUGH 225 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.6804 19.2960 5.0934 REMARK 3 T TENSOR REMARK 3 T11: 0.2118 T22: 0.1548 REMARK 3 T33: 0.2294 T12: -0.0348 REMARK 3 T13: 0.0595 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 3.1571 L22: 3.3218 REMARK 3 L33: 1.9218 L12: 0.5329 REMARK 3 L13: -0.7941 L23: 0.1779 REMARK 3 S TENSOR REMARK 3 S11: -0.1089 S12: 0.0284 S13: -0.2007 REMARK 3 S21: 0.2588 S22: -0.0732 S23: 0.5927 REMARK 3 S31: 0.2000 S32: -0.2111 S33: 0.1703 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 3 THROUGH 98 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.0779 8.4541 32.7497 REMARK 3 T TENSOR REMARK 3 T11: 1.0513 T22: 0.3565 REMARK 3 T33: 0.2327 T12: 0.0930 REMARK 3 T13: -0.0913 T23: 0.0432 REMARK 3 L TENSOR REMARK 3 L11: 1.9062 L22: 2.0786 REMARK 3 L33: 3.0891 L12: -0.0290 REMARK 3 L13: 0.0483 L23: 0.0365 REMARK 3 S TENSOR REMARK 3 S11: 0.0969 S12: -0.2972 S13: -0.1746 REMARK 3 S21: 0.6796 S22: -0.0720 S23: -0.1414 REMARK 3 S31: 0.7523 S32: 0.1960 S33: -0.0517 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 99 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.1209 7.5954 23.4262 REMARK 3 T TENSOR REMARK 3 T11: 0.8497 T22: 0.2811 REMARK 3 T33: 0.1896 T12: 0.0600 REMARK 3 T13: -0.0297 T23: 0.1269 REMARK 3 L TENSOR REMARK 3 L11: 1.1124 L22: 1.2394 REMARK 3 L33: 2.6131 L12: 0.6538 REMARK 3 L13: 1.2381 L23: 1.0161 REMARK 3 S TENSOR REMARK 3 S11: 0.1401 S12: -0.2545 S13: -0.5143 REMARK 3 S21: 0.5976 S22: 0.3553 S23: -0.7698 REMARK 3 S31: 0.8513 S32: 0.5268 S33: -0.1301 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 121 THROUGH 170 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.1246 7.8635 -3.0425 REMARK 3 T TENSOR REMARK 3 T11: 0.2234 T22: 0.1467 REMARK 3 T33: 0.1451 T12: -0.0194 REMARK 3 T13: 0.0454 T23: 0.0200 REMARK 3 L TENSOR REMARK 3 L11: 2.5252 L22: 3.7716 REMARK 3 L33: 4.3133 L12: -0.0466 REMARK 3 L13: 0.8268 L23: 0.0751 REMARK 3 S TENSOR REMARK 3 S11: 0.0119 S12: 0.0756 S13: -0.0932 REMARK 3 S21: 0.2019 S22: -0.0392 S23: -0.0028 REMARK 3 S31: -0.1003 S32: 0.1655 S33: 0.0518 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 171 THROUGH 218 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.7458 5.9370 -3.4291 REMARK 3 T TENSOR REMARK 3 T11: 0.1930 T22: 0.1348 REMARK 3 T33: 0.1946 T12: 0.0106 REMARK 3 T13: 0.0619 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 2.3242 L22: 4.2266 REMARK 3 L33: 5.5512 L12: 0.2542 REMARK 3 L13: 0.9601 L23: -0.2824 REMARK 3 S TENSOR REMARK 3 S11: 0.0700 S12: 0.0383 S13: -0.1612 REMARK 3 S21: 0.1695 S22: 0.0103 S23: 0.1885 REMARK 3 S31: -0.1333 S32: 0.0585 S33: -0.0204 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 7S3N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000259569. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38944 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 87.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 7M53 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, PH 5.5, 23% REMARK 280 PEG8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 40.12300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.54000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.12300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.54000 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: 4870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 1146 REMARK 465 LYS A 1157 REMARK 465 ASN A 1158 REMARK 465 HIS A 1159 REMARK 465 THR A 1160 REMARK 465 SER A 1161 REMARK 465 PRO A 1162 REMARK 465 ASP A 1163 REMARK 465 VAL A 1164 REMARK 465 SER H 138 REMARK 465 SER H 139 REMARK 465 LYS H 140 REMARK 465 SER H 141 REMARK 465 THR H 142 REMARK 465 SER H 143 REMARK 465 ASP L 36 REMARK 465 GLY L 37 REMARK 465 CYS L 219 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 GLN H 7 CG CD OE1 NE2 REMARK 470 LYS L 133 CG CD CE NZ 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 H 344 O HOH H 412 1.82 REMARK 500 O HOH L 421 O HOH L 428 1.83 REMARK 500 O HOH H 465 O HOH H 483 1.87 REMARK 500 OE2 GLU H 91 O HOH H 301 1.89 REMARK 500 O HOH H 452 O HOH L 351 1.90 REMARK 500 O HOH H 460 O HOH L 413 1.91 REMARK 500 O LEU L 91 O HOH L 301 1.99 REMARK 500 O HOH L 404 O HOH L 427 2.00 REMARK 500 OE1 GLU L 112 O HOH L 302 2.01 REMARK 500 O HOH H 374 O HOH H 469 2.02 REMARK 500 O HOH H 426 O HOH H 450 2.02 REMARK 500 O HOH L 365 O HOH L 429 2.03 REMARK 500 O HOH H 458 O HOH L 405 2.04 REMARK 500 O HOH H 394 O HOH H 478 2.04 REMARK 500 O HOH H 452 O HOH L 422 2.05 REMARK 500 OH TYR L 95 O HOH L 303 2.10 REMARK 500 O HOH L 423 O HOH L 431 2.10 REMARK 500 NZ LYS H 128 O HOH H 302 2.10 REMARK 500 O HOH L 376 O HOH L 416 2.14 REMARK 500 O ALA H 136 O HOH H 303 2.15 REMARK 500 OE2 GLU L 87 O HOH L 304 2.16 REMARK 500 O HOH H 478 O HOH H 481 2.17 REMARK 500 O HOH H 428 O HOH H 448 2.19 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 H 469 O HOH H 469 2555 1.86 REMARK 500 O HOH H 421 O HOH H 471 3555 1.87 REMARK 500 O HOH H 334 O HOH H 334 2455 2.17 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 LYS H 45 -75.23 -124.45 REMARK 500 ASP H 105 -113.37 65.99 REMARK 500 VAL L 59 -43.36 75.71 REMARK 500 TYR L 101 -162.42 -117.52 REMARK 500 ASN L 145 71.16 51.50 REMARK 500 REMARK 500 REMARK: NULL DBREF 7S3N A 1146 1164 UNP P0DTC2 SPIKE_SARS2 1146 1164 DBREF 7S3N H 3 225 PDB 7S3N 7S3N 3 225 DBREF 7S3N L 3 219 PDB 7S3N 7S3N 3 219 SEQRES 1 A 19 ASP SER PHE LYS GLU GLU LEU ASP LYS TYR PHE LYS ASN SEQRES 2 A 19 HIS THR SER PRO ASP VAL SEQRES 1 H 223 GLU VAL GLN LEU GLN GLN PRO GLY PRO VAL LEU VAL LYS SEQRES 2 H 223 PRO GLY ALA SER VAL ARG MET SER CYS LYS ALA SER GLY SEQRES 3 H 223 TYR ARG ILE THR ASP ASN PHE MET ASN TRP VAL LYS GLN SEQRES 4 H 223 SER HIS GLY LYS SER LEU GLU TRP ILE GLY ILE ILE ASN SEQRES 5 H 223 PRO TYR ASN GLY GLY THR LYS TYR ASN GLN LYS PHE LYS SEQRES 6 H 223 GLY LYS ALA THR LEU THR VAL ASP THR SER SER SER THR SEQRES 7 H 223 ALA TYR MET GLU LEU ASN SER LEU THR SER GLU ASP SER SEQRES 8 H 223 ALA VAL TYR TYR CYS THR ARG VAL ARG GLY ASN ASP TYR SEQRES 9 H 223 HIS GLY ARG ALA MET ASP TYR TRP GLY GLN GLY THR SER SEQRES 10 H 223 VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER VAL SEQRES 11 H 223 PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY GLY SEQRES 12 H 223 THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO SEQRES 13 H 223 GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SEQRES 14 H 223 SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER SEQRES 15 H 223 GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SER SEQRES 16 H 223 SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN SEQRES 17 H 223 HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU SEQRES 18 H 223 PRO LYS SEQRES 1 L 216 ASP VAL VAL LEU THR GLN THR PRO LEU SER LEU PRO VAL SEQRES 2 L 216 ASN ILE GLY ASP GLN ALA SER ILE SER CYS LYS SER THR SEQRES 3 L 216 LYS SER LEU LEU ASN ARG ASP GLY PHE THR PHE LEU ASP SEQRES 4 L 216 TRP TYR LEU GLN LYS PRO GLY GLN SER PRO GLN LEU LEU SEQRES 5 L 216 ILE TYR LEU VAL SER ASN ARG PHE SER GLY VAL PRO ASP SEQRES 6 L 216 ARG PHE SER GLY SER GLY SER GLY THR ASP PHE THR LEU SEQRES 7 L 216 LYS ILE SER ARG VAL GLU ALA GLU ASP LEU GLY VAL TYR SEQRES 8 L 216 TYR CYS PHE GLN SER ASN TYR LEU PHE THR PHE GLY SER SEQRES 9 L 216 GLY THR LYS LEU GLU ILE LYS ARG THR VAL ALA ALA PRO SEQRES 10 L 216 SER VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SEQRES 11 L 216 SER GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE SEQRES 12 L 216 TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN SEQRES 13 L 216 ALA LEU GLN SER GLY ASN SER GLN GLU SER VAL THR GLU SEQRES 14 L 216 GLN ASP SER LYS ASP SER THR TYR SER LEU SER SER THR SEQRES 15 L 216 LEU THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL SEQRES 16 L 216 TYR ALA CYS GLU VAL THR GLN GLY THR THR SER VAL THR SEQRES 17 L 216 LYS SER PHE ASN ARG GLY GLU CYS FORMUL 4 HOH *325(H2 O) HELIX 1 AA1 SER A 1147 PHE A 1156 1 10 HELIX 2 AA2 ARG H 30 ASN H 34 5 5 HELIX 3 AA3 GLN H 64 LYS H 67 5 4 HELIX 4 AA4 THR H 76 SER H 78 5 3 HELIX 5 AA5 THR H 89 SER H 93 5 5 HELIX 6 AA6 ASN H 104 GLY H 108 5 5 HELIX 7 AA7 SER H 167 ALA H 169 5 3 HELIX 8 AA8 SER H 198 LEU H 200 5 3 HELIX 9 AA9 LYS H 212 ASN H 215 5 4 HELIX 10 AB1 GLU L 87 LEU L 91 5 5 HELIX 11 AB2 SER L 128 LYS L 133 1 6 HELIX 12 AB3 LYS L 190 GLU L 194 1 5 SHEET 1 AA1 4 GLN H 5 GLN H 7 0 SHEET 2 AA1 4 VAL H 20 SER H 27 -1 O LYS H 25 N GLN H 7 SHEET 3 AA1 4 THR H 80 LEU H 85 -1 O MET H 83 N MET H 22 SHEET 4 AA1 4 ALA H 70 ASP H 75 -1 N THR H 73 O TYR H 82 SHEET 1 AA2 6 VAL H 12 VAL H 14 0 SHEET 2 AA2 6 THR H 118 VAL H 122 1 O THR H 121 N VAL H 12 SHEET 3 AA2 6 ALA H 94 VAL H 101 -1 N ALA H 94 O VAL H 120 SHEET 4 AA2 6 PHE H 35 SER H 42 -1 N VAL H 39 O TYR H 97 SHEET 5 AA2 6 SER H 46 ILE H 53 -1 O GLU H 48 N LYS H 40 SHEET 6 AA2 6 THR H 60 TYR H 62 -1 O LYS H 61 N ILE H 52 SHEET 1 AA3 4 VAL H 12 VAL H 14 0 SHEET 2 AA3 4 THR H 118 VAL H 122 1 O THR H 121 N VAL H 12 SHEET 3 AA3 4 ALA H 94 VAL H 101 -1 N ALA H 94 O VAL H 120 SHEET 4 AA3 4 MET H 111 TRP H 114 -1 O TYR H 113 N ARG H 100 SHEET 1 AA4 4 SER H 131 LEU H 135 0 SHEET 2 AA4 4 THR H 146 TYR H 156 -1 O LEU H 152 N PHE H 133 SHEET 3 AA4 4 TYR H 187 PRO H 196 -1 O LEU H 189 N VAL H 153 SHEET 4 AA4 4 VAL H 174 THR H 176 -1 N HIS H 175 O VAL H 192 SHEET 1 AA5 4 SER H 131 LEU H 135 0 SHEET 2 AA5 4 THR H 146 TYR H 156 -1 O LEU H 152 N PHE H 133 SHEET 3 AA5 4 TYR H 187 PRO H 196 -1 O LEU H 189 N VAL H 153 SHEET 4 AA5 4 VAL H 180 LEU H 181 -1 N VAL H 180 O SER H 188 SHEET 1 AA6 3 THR H 162 TRP H 165 0 SHEET 2 AA6 3 ILE H 206 HIS H 211 -1 O ASN H 208 N SER H 164 SHEET 3 AA6 3 THR H 216 LYS H 221 -1 O VAL H 218 N VAL H 209 SHEET 1 AA7 4 LEU L 6 THR L 9 0 SHEET 2 AA7 4 ALA L 21 SER L 27 -1 O SER L 24 N THR L 9 SHEET 3 AA7 4 ASP L 78 ILE L 83 -1 O PHE L 79 N CYS L 25 SHEET 4 AA7 4 PHE L 70 SER L 75 -1 N SER L 73 O THR L 80 SHEET 1 AA8 6 SER L 12 VAL L 15 0 SHEET 2 AA8 6 THR L 109 ILE L 113 1 O LYS L 110 N LEU L 13 SHEET 3 AA8 6 GLY L 92 GLN L 98 -1 N GLY L 92 O LEU L 111 SHEET 4 AA8 6 LEU L 41 GLN L 46 -1 N ASP L 42 O PHE L 97 SHEET 5 AA8 6 GLN L 53 TYR L 57 -1 O ILE L 56 N TRP L 43 SHEET 6 AA8 6 ASN L 61 ARG L 62 -1 O ASN L 61 N TYR L 57 SHEET 1 AA9 4 SER L 12 VAL L 15 0 SHEET 2 AA9 4 THR L 109 ILE L 113 1 O LYS L 110 N LEU L 13 SHEET 3 AA9 4 GLY L 92 GLN L 98 -1 N GLY L 92 O LEU L 111 SHEET 4 AA9 4 THR L 104 PHE L 105 -1 O THR L 104 N GLN L 98 SHEET 1 AB1 4 SER L 121 PHE L 125 0 SHEET 2 AB1 4 THR L 136 PHE L 146 -1 O LEU L 142 N PHE L 123 SHEET 3 AB1 4 TYR L 180 SER L 189 -1 O LEU L 182 N LEU L 143 SHEET 4 AB1 4 SER L 166 VAL L 170 -1 N GLN L 167 O THR L 185 SHEET 1 AB2 4 ALA L 160 LEU L 161 0 SHEET 2 AB2 4 LYS L 152 VAL L 157 -1 N VAL L 157 O ALA L 160 SHEET 3 AB2 4 VAL L 198 GLN L 205 -1 O GLU L 202 N GLN L 154 SHEET 4 AB2 4 THR L 208 ASN L 215 -1 O VAL L 210 N VAL L 203 SSBOND 1 CYS H 24 CYS H 98 1555 1555 2.03 SSBOND 2 CYS H 151 CYS H 207 1555 1555 2.03 SSBOND 3 CYS L 25 CYS L 96 1555 1555 2.05 SSBOND 4 CYS L 141 CYS L 201 1555 1555 2.04 CISPEP 1 PHE H 157 PRO H 158 0 -10.89 CISPEP 2 GLU H 159 PRO H 160 0 -1.31 CISPEP 3 THR L 9 PRO L 10 0 -3.03 CISPEP 4 TYR L 147 PRO L 148 0 -2.44 CRYST1 80.246 73.080 89.043 90.00 100.50 90.00 C 1 2 1 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 0.012462 0.000000 0.002310 0.00000 SCALE2 0.000000 0.013684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011422 0.00000