HEADER VIRAL PROTEIN/IMMUNE SYSTEM 03-APR-22 7UL0 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 RBD IN COMPLEX WITH THE RIDGE-BINDING TITLE 2 NAB EH8 ISOLATED FROM A NONVACCINATED PEDIATRIC PATIENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN OF EH8; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: LIGHT CHAIN OF EH8; COMPND 11 CHAIN: L; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: S, 2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS PEDIATRIC NEUTRALIZING MAB, RBD-RIDGE-TARGETING, BIND TO BOTH CLOSED KEYWDS 2 AND OPEN SARS-COV-2 SPIKE, CLASS-2 RBD-BINDING ANTIBODY, VIRAL KEYWDS 3 PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHEN,W.D.TOLBERT,X.BAI,M.PAZGIER REVDAT 2 25-OCT-23 7UL0 1 REMARK REVDAT 1 08-MAR-23 7UL0 0 JRNL AUTH Y.CHEN,J.PREVOST,I.ULLAH,H.ROMERO,V.LISI,W.D.TOLBERT, JRNL AUTH 2 J.R.GROVER,S.DING,S.Y.GONG,G.BEAUDOIN-BUSSIERES,R.GASSER, JRNL AUTH 3 M.BENLARBI,D.VEZINA,S.P.ANAND,D.CHATTERJEE,G.GOYETTE, JRNL AUTH 4 M.W.GRUNST,Z.YANG,Y.BO,F.ZHOU,K.BELAND,X.BAI,A.R.ZEHER, JRNL AUTH 5 R.K.HUANG,D.N.NGUYEN,R.SHERBURN,D.WU,G.PISZCZEK,B.PARE, JRNL AUTH 6 D.MATTHIES,D.XIA,J.RICHARD,P.KUMAR,W.MOTHES,M.COTE, JRNL AUTH 7 P.D.UCHIL,V.P.LAVALLEE,M.A.SMITH,M.PAZGIER,E.HADDAD,A.FINZI JRNL TITL MOLECULAR BASIS FOR ANTIVIRAL ACTIVITY OF TWO PEDIATRIC JRNL TITL 2 NEUTRALIZING ANTIBODIES TARGETING SARS-COV-2 SPIKE RBD. JRNL REF ISCIENCE V. 26 05783 2023 JRNL REFN ESSN 2589-0042 JRNL PMID 36514310 JRNL DOI 10.1016/J.ISCI.2022.105783 REMARK 2 REMARK 2 RESOLUTION. 2.49 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 31070 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.460 REMARK 3 FREE R VALUE TEST SET COUNT : 2008 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 46.9100 - 6.0000 1.00 2245 156 0.1936 0.2133 REMARK 3 2 6.0000 - 4.7600 1.00 2141 144 0.1815 0.2185 REMARK 3 3 4.7600 - 4.1600 1.00 2122 154 0.1654 0.1692 REMARK 3 4 4.1600 - 3.7800 1.00 2104 138 0.2017 0.2294 REMARK 3 5 3.7800 - 3.5100 1.00 2085 144 0.2206 0.2369 REMARK 3 6 3.5100 - 3.3000 1.00 2078 149 0.2312 0.2935 REMARK 3 7 3.3000 - 3.1400 1.00 2082 144 0.2903 0.3559 REMARK 3 8 3.1400 - 3.0000 1.00 2080 140 0.2863 0.3271 REMARK 3 9 3.0000 - 2.8800 1.00 2051 147 0.2756 0.3239 REMARK 3 10 2.8800 - 2.7900 1.00 2064 146 0.2723 0.3445 REMARK 3 11 2.7900 - 2.7000 1.00 2084 142 0.2935 0.3400 REMARK 3 12 2.7000 - 2.6200 1.00 2055 135 0.3233 0.4049 REMARK 3 13 2.6200 - 2.5500 1.00 2068 140 0.3698 0.4219 REMARK 3 14 2.5500 - 2.4900 0.88 1803 129 0.4253 0.4203 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) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.59 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 334 THROUGH 358 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.5751 -49.2248 -10.6996 REMARK 3 T TENSOR REMARK 3 T11: 0.6171 T22: 0.4544 REMARK 3 T33: 0.4209 T12: 0.0847 REMARK 3 T13: -0.0449 T23: -0.1528 REMARK 3 L TENSOR REMARK 3 L11: 1.3233 L22: 0.4326 REMARK 3 L33: 0.9629 L12: -0.4694 REMARK 3 L13: -0.1934 L23: 0.3401 REMARK 3 S TENSOR REMARK 3 S11: 0.1394 S12: 0.4159 S13: -0.1545 REMARK 3 S21: -0.3847 S22: 0.1252 S23: -0.0188 REMARK 3 S31: 0.5440 S32: 0.0205 S33: 0.1215 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 359 THROUGH 393 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.1797 -56.0053 2.8684 REMARK 3 T TENSOR REMARK 3 T11: 0.7794 T22: 0.5307 REMARK 3 T33: 0.7837 T12: 0.0600 REMARK 3 T13: -0.0412 T23: 0.2724 REMARK 3 L TENSOR REMARK 3 L11: 0.8677 L22: 1.1874 REMARK 3 L33: 1.9746 L12: 0.0721 REMARK 3 L13: -0.9470 L23: 0.3900 REMARK 3 S TENSOR REMARK 3 S11: -0.1354 S12: -0.6758 S13: -0.7434 REMARK 3 S21: 0.1346 S22: 0.2038 S23: -0.1134 REMARK 3 S31: 1.1371 S32: 0.4310 S33: 0.2548 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 394 THROUGH 469 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.7600 -37.3145 -5.0104 REMARK 3 T TENSOR REMARK 3 T11: 0.3280 T22: 0.3985 REMARK 3 T33: 0.3027 T12: 0.0081 REMARK 3 T13: 0.0389 T23: -0.0356 REMARK 3 L TENSOR REMARK 3 L11: 1.7014 L22: 2.6047 REMARK 3 L33: 1.2293 L12: -0.1029 REMARK 3 L13: 0.9490 L23: -1.6300 REMARK 3 S TENSOR REMARK 3 S11: -0.0855 S12: 0.0058 S13: 0.1028 REMARK 3 S21: -0.1505 S22: 0.1373 S23: -0.0755 REMARK 3 S31: 0.0295 S32: 0.2718 S33: 0.0009 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 470 THROUGH 494 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.6726 -18.0578 -14.7233 REMARK 3 T TENSOR REMARK 3 T11: 0.5076 T22: 0.5035 REMARK 3 T33: 0.5699 T12: -0.0526 REMARK 3 T13: 0.0158 T23: 0.1084 REMARK 3 L TENSOR REMARK 3 L11: 0.1662 L22: 0.8298 REMARK 3 L33: 0.4269 L12: 0.3045 REMARK 3 L13: -0.4726 L23: -0.9054 REMARK 3 S TENSOR REMARK 3 S11: -0.0270 S12: 0.8152 S13: 0.5121 REMARK 3 S21: -0.3063 S22: 0.0519 S23: -0.1149 REMARK 3 S31: -0.1183 S32: 0.2641 S33: 0.0044 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 495 THROUGH 527 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.0794 -45.8964 -3.9748 REMARK 3 T TENSOR REMARK 3 T11: 0.3352 T22: 0.5274 REMARK 3 T33: 0.4293 T12: 0.0706 REMARK 3 T13: 0.0575 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 1.3309 L22: 1.9985 REMARK 3 L33: 1.3789 L12: -1.4834 REMARK 3 L13: 0.5674 L23: 0.1927 REMARK 3 S TENSOR REMARK 3 S11: 0.4127 S12: -0.6609 S13: 0.2373 REMARK 3 S21: 0.1902 S22: -0.3967 S23: 0.4858 REMARK 3 S31: -0.0781 S32: 0.2859 S33: 0.0005 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 1 THROUGH 119 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.9050 4.1575 -13.3434 REMARK 3 T TENSOR REMARK 3 T11: 0.5056 T22: 0.4610 REMARK 3 T33: 0.7295 T12: -0.0097 REMARK 3 T13: -0.0877 T23: 0.1091 REMARK 3 L TENSOR REMARK 3 L11: 0.2601 L22: 3.8642 REMARK 3 L33: 1.1476 L12: 2.6043 REMARK 3 L13: -0.6161 L23: -0.4534 REMARK 3 S TENSOR REMARK 3 S11: 0.0620 S12: -0.0753 S13: -0.1597 REMARK 3 S21: 0.7079 S22: -0.2534 S23: -0.6698 REMARK 3 S31: -0.0951 S32: 0.1020 S33: -0.0005 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 120 THROUGH 134 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.7714 42.4093 -30.1690 REMARK 3 T TENSOR REMARK 3 T11: 0.7814 T22: 0.5794 REMARK 3 T33: 0.4836 T12: 0.1799 REMARK 3 T13: -0.1299 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.2345 L22: 0.4708 REMARK 3 L33: 0.4753 L12: -0.1991 REMARK 3 L13: -0.3898 L23: 0.2965 REMARK 3 S TENSOR REMARK 3 S11: 0.1370 S12: 0.1543 S13: 0.3411 REMARK 3 S21: -0.0729 S22: -0.3857 S23: 1.1118 REMARK 3 S31: -0.3367 S32: -0.3865 S33: 0.0035 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 135 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.0406 33.0066 -22.3693 REMARK 3 T TENSOR REMARK 3 T11: 0.5975 T22: 0.5581 REMARK 3 T33: 0.2096 T12: 0.1036 REMARK 3 T13: 0.0763 T23: 0.0243 REMARK 3 L TENSOR REMARK 3 L11: 0.9766 L22: 2.4814 REMARK 3 L33: 1.3768 L12: 1.2409 REMARK 3 L13: 0.5630 L23: -0.7835 REMARK 3 S TENSOR REMARK 3 S11: 0.0652 S12: -0.5582 S13: -0.0371 REMARK 3 S21: 0.6682 S22: 0.1329 S23: 0.0804 REMARK 3 S31: -0.3265 S32: -0.2890 S33: 0.6049 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1 THROUGH 24 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.7456 3.6532 -38.9764 REMARK 3 T TENSOR REMARK 3 T11: 0.6885 T22: 0.6571 REMARK 3 T33: 0.5689 T12: -0.0765 REMARK 3 T13: 0.0640 T23: 0.1587 REMARK 3 L TENSOR REMARK 3 L11: 0.8469 L22: 0.8734 REMARK 3 L33: 0.7773 L12: 0.5284 REMARK 3 L13: -0.6509 L23: 0.2650 REMARK 3 S TENSOR REMARK 3 S11: -0.1001 S12: 0.1503 S13: -0.2892 REMARK 3 S21: -0.8921 S22: 0.2061 S23: 0.3442 REMARK 3 S31: 0.6942 S32: -0.2089 S33: -0.0002 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 25 THROUGH 61 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.1238 1.1252 -28.3046 REMARK 3 T TENSOR REMARK 3 T11: 0.4200 T22: 0.4452 REMARK 3 T33: 0.6806 T12: -0.1174 REMARK 3 T13: -0.0349 T23: 0.0934 REMARK 3 L TENSOR REMARK 3 L11: 1.0863 L22: 1.2111 REMARK 3 L33: 1.9582 L12: 0.7766 REMARK 3 L13: -0.4782 L23: -1.4572 REMARK 3 S TENSOR REMARK 3 S11: 0.0160 S12: 0.1511 S13: 0.1144 REMARK 3 S21: 0.1436 S22: 0.0166 S23: 0.2637 REMARK 3 S31: 0.0242 S32: -0.2308 S33: 0.0000 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 62 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.5458 5.3374 -34.5153 REMARK 3 T TENSOR REMARK 3 T11: 0.4027 T22: 0.3875 REMARK 3 T33: 0.4924 T12: -0.0680 REMARK 3 T13: -0.0281 T23: 0.1595 REMARK 3 L TENSOR REMARK 3 L11: -0.8281 L22: 0.4855 REMARK 3 L33: 0.8862 L12: -0.3250 REMARK 3 L13: -0.3731 L23: -0.6616 REMARK 3 S TENSOR REMARK 3 S11: -0.1561 S12: 0.1794 S13: 0.0229 REMARK 3 S21: -0.4871 S22: 0.1868 S23: 0.0609 REMARK 3 S31: 0.3411 S32: -0.1510 S33: -0.0005 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 113 THROUGH 173 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.8694 32.7801 -36.2572 REMARK 3 T TENSOR REMARK 3 T11: 0.4666 T22: 0.4629 REMARK 3 T33: 0.2715 T12: 0.0513 REMARK 3 T13: 0.0297 T23: 0.0212 REMARK 3 L TENSOR REMARK 3 L11: 1.5014 L22: 2.0982 REMARK 3 L33: 0.8240 L12: -0.3350 REMARK 3 L13: -0.0843 L23: -0.9756 REMARK 3 S TENSOR REMARK 3 S11: 0.0205 S12: -0.0710 S13: -0.1169 REMARK 3 S21: 0.3232 S22: 0.0665 S23: -0.1144 REMARK 3 S31: -0.1586 S32: -0.0713 S33: 0.0005 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 174 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.6122 40.4317 -38.9474 REMARK 3 T TENSOR REMARK 3 T11: 0.4752 T22: 0.4321 REMARK 3 T33: 0.3833 T12: 0.0158 REMARK 3 T13: -0.0060 T23: -0.0283 REMARK 3 L TENSOR REMARK 3 L11: 1.2353 L22: 0.3931 REMARK 3 L33: 1.0704 L12: 0.9893 REMARK 3 L13: -0.5984 L23: -0.3223 REMARK 3 S TENSOR REMARK 3 S11: 0.1248 S12: 0.0756 S13: 0.1274 REMARK 3 S21: 0.0103 S22: 0.0781 S23: -0.1570 REMARK 3 S31: -0.2951 S32: 0.2966 S33: 0.0004 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 7UL0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000264359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.0-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31070 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 18.80 REMARK 200 R MERGE (I) : 0.14400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 16.60 REMARK 200 R MERGE FOR SHELL (I) : 1.03700 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: 7S4S, 7NAB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M NA HEPES REMARK 280 PH 7.5, 12% W/V PEG 8000, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.88550 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.00950 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.88550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.00950 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 APPLY THE FOLLOWING TO CHAINS: A, H, L, B 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 ARG A 319 REMARK 465 VAL A 320 REMARK 465 GLN A 321 REMARK 465 PRO A 322 REMARK 465 THR A 323 REMARK 465 GLU A 324 REMARK 465 SER A 325 REMARK 465 ILE A 326 REMARK 465 VAL A 327 REMARK 465 ARG A 328 REMARK 465 PHE A 329 REMARK 465 PRO A 330 REMARK 465 ASN A 331 REMARK 465 ILE A 332 REMARK 465 THR A 333 REMARK 465 LYS A 528 REMARK 465 LYS A 529 REMARK 465 SER A 530 REMARK 465 THR A 531 REMARK 465 ASN A 532 REMARK 465 LEU A 533 REMARK 465 VAL A 534 REMARK 465 LYS A 535 REMARK 465 ASN A 536 REMARK 465 LYS A 537 REMARK 465 CYS H 216 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER L 113 CA CB OG 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 ALA A 352 51.38 -108.24 REMARK 500 PHE A 377 81.11 -150.85 REMARK 500 ASN A 422 -54.16 -127.72 REMARK 500 PHE A 486 -119.73 57.47 REMARK 500 LEU A 517 68.89 -111.53 REMARK 500 GLU H 97 -128.79 54.70 REMARK 500 ASP L 27B -83.84 -127.50 REMARK 500 ALA L 84 -178.33 -172.66 REMARK 500 REMARK 500 REMARK: NULL DBREF 7UL0 A 319 537 UNP P0DTC2 SPIKE_SARS2 319 537 DBREF 7UL0 H 1 216 PDB 7UL0 7UL0 1 216 DBREF 7UL0 L 1 213 PDB 7UL0 7UL0 1 213 SEQRES 1 A 219 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2 A 219 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3 A 219 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4 A 219 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5 A 219 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6 A 219 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7 A 219 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8 A 219 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9 A 219 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10 A 219 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11 A 219 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12 A 219 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13 A 219 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14 A 219 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15 A 219 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16 A 219 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17 A 219 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS SEQRES 1 H 222 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 H 222 PRO GLY ALA SER VAL LYS VAL SER CYS LYS ALA SER GLY SEQRES 3 H 222 TYR THR PHE SER SER TYR GLY ILE SER TRP VAL ARG GLN SEQRES 4 H 222 ALA PRO GLY GLN GLY LEU GLU TRP MET GLY TRP ILE SER SEQRES 5 H 222 PRO TYR ASN GLY ASN THR LYS TYR PRO GLN LYS PHE GLN SEQRES 6 H 222 GLY ARG VAL THR MET THR THR ASP THR SER THR ASN THR SEQRES 7 H 222 ALA TYR MET GLU LEU ARG SER LEU ARG SER ASP ASP THR SEQRES 8 H 222 ALA VAL TYR TYR CYS ALA ARG ASP LEU GLU LEU GLY GLY SEQRES 9 H 222 GLY PHE ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 10 H 222 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 H 222 ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA SEQRES 12 H 222 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 H 222 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 H 222 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 H 222 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 H 222 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 17 H 222 SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER SEQRES 18 H 222 CYS SEQRES 1 L 217 GLN SER ALA LEU THR GLN PRO ALA SER VAL SER GLY SER SEQRES 2 L 217 PRO GLY GLN SER ILE THR ILE SER CYS THR GLY THR SER SEQRES 3 L 217 SER ASP VAL GLY SER TYR ASN LEU VAL SER TRP TYR GLN SEQRES 4 L 217 GLN HIS PRO ASP LYS ALA PRO LYS PHE MET ILE TYR GLU SEQRES 5 L 217 GLY THR LYS ARG PRO SER GLY VAL SER ASN ARG PHE SER SEQRES 6 L 217 GLY SER LYS SER GLY ASN THR ALA SER LEU THR ILE SER SEQRES 7 L 217 GLY LEU GLN ALA GLU ASP GLU ALA ASP TYR TYR CYS CYS SEQRES 8 L 217 SER TYR ALA GLY ASN SER THR TRP VAL PHE GLY GLY GLY SEQRES 9 L 217 THR LYS LEU THR VAL LEU ARG THR VAL ALA ALA PRO SER SEQRES 10 L 217 VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER SEQRES 11 L 217 GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR SEQRES 12 L 217 PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA SEQRES 13 L 217 LEU GLN SER GLY ASN SER GLN GLU SER VAL THR GLU GLN SEQRES 14 L 217 ASP SER LYS ASP SER THR TYR SER LEU SER SER THR LEU SEQRES 15 L 217 THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR SEQRES 16 L 217 ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL SEQRES 17 L 217 THR LYS SER PHE ASN ARG GLY GLU CYS HET NAG B 1 14 HET NAG B 2 14 HET NAG L 301 14 HET NA L 302 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NA SODIUM ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 NAG 3(C8 H15 N O6) FORMUL 6 NA NA 1+ FORMUL 7 HOH *102(H2 O) HELIX 1 AA1 PHE A 338 ASN A 343 1 6 HELIX 2 AA2 SER A 349 TRP A 353 5 5 HELIX 3 AA3 ASP A 364 SER A 371 1 8 HELIX 4 AA4 ASP A 405 ILE A 410 5 6 HELIX 5 AA5 GLY A 416 ASN A 422 1 7 HELIX 6 AA6 SER A 438 SER A 443 1 6 HELIX 7 AA7 GLY A 502 TYR A 505 5 4 HELIX 8 AA8 THR H 28 TYR H 32 5 5 HELIX 9 AA9 PRO H 60 GLN H 64 5 5 HELIX 10 AB1 ARG H 83 THR H 87 5 5 HELIX 11 AB2 GLU H 97 GLY H 100 5 4 HELIX 12 AB3 SER H 187 LEU H 189 5 3 HELIX 13 AB4 LYS H 201 ASN H 204 5 4 HELIX 14 AB5 GLN L 79 GLU L 83 5 5 HELIX 15 AB6 SER L 120 SER L 126 1 7 HELIX 16 AB7 LYS L 182 LYS L 187 1 6 SHEET 1 AA1 5 ASN A 354 ILE A 358 0 SHEET 2 AA1 5 ASN A 394 ARG A 403 -1 O VAL A 395 N ILE A 358 SHEET 3 AA1 5 PRO A 507 GLU A 516 -1 O VAL A 512 N ASP A 398 SHEET 4 AA1 5 GLY A 431 ASN A 437 -1 N ILE A 434 O VAL A 511 SHEET 5 AA1 5 THR A 376 TYR A 380 -1 N TYR A 380 O GLY A 431 SHEET 1 AA2 2 CYS A 361 VAL A 362 0 SHEET 2 AA2 2 VAL A 524 CYS A 525 1 O CYS A 525 N CYS A 361 SHEET 1 AA3 2 LEU A 452 ARG A 454 0 SHEET 2 AA3 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA4 2 TYR A 473 GLN A 474 0 SHEET 2 AA4 2 CYS A 488 TYR A 489 -1 O TYR A 489 N TYR A 473 SHEET 1 AA5 4 GLN H 3 GLN H 6 0 SHEET 2 AA5 4 VAL H 18 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 AA5 4 THR H 77 LEU H 82 -1 O ALA H 78 N CYS H 22 SHEET 4 AA5 4 VAL H 67 ASP H 72 -1 N ASP H 72 O THR H 77 SHEET 1 AA6 6 GLU H 10 LYS H 12 0 SHEET 2 AA6 6 THR H 107 VAL H 111 1 O THR H 110 N LYS H 12 SHEET 3 AA6 6 ALA H 88 ASP H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 AA6 6 GLY H 33 GLN H 39 -1 N GLY H 33 O ASP H 95 SHEET 5 AA6 6 LEU H 45 ILE H 51 -1 O MET H 48 N TRP H 36 SHEET 6 AA6 6 THR H 57 LYS H 58 -1 O LYS H 58 N TRP H 50 SHEET 1 AA7 4 GLU H 10 LYS H 12 0 SHEET 2 AA7 4 THR H 107 VAL H 111 1 O THR H 110 N LYS H 12 SHEET 3 AA7 4 ALA H 88 ASP H 95 -1 N ALA H 88 O VAL H 109 SHEET 4 AA7 4 PHE H 100B TRP H 103 -1 O TYR H 102 N ARG H 94 SHEET 1 AA8 4 SER H 120 LEU H 124 0 SHEET 2 AA8 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AA8 4 TYR H 176 PRO H 185 -1 O VAL H 184 N ALA H 136 SHEET 4 AA8 4 VAL H 163 THR H 165 -1 N HIS H 164 O VAL H 181 SHEET 1 AA9 4 SER H 120 LEU H 124 0 SHEET 2 AA9 4 THR H 135 TYR H 145 -1 O LEU H 141 N PHE H 122 SHEET 3 AA9 4 TYR H 176 PRO H 185 -1 O VAL H 184 N ALA H 136 SHEET 4 AA9 4 VAL H 169 LEU H 170 -1 N VAL H 169 O SER H 177 SHEET 1 AB1 3 THR H 151 TRP H 154 0 SHEET 2 AB1 3 ILE H 195 HIS H 200 -1 O ASN H 197 N SER H 153 SHEET 3 AB1 3 THR H 205 LYS H 210 -1 O VAL H 207 N VAL H 198 SHEET 1 AB2 5 SER L 9 GLY L 13 0 SHEET 2 AB2 5 THR L 102 VAL L 106 1 O LYS L 103 N VAL L 11 SHEET 3 AB2 5 ASP L 85 TYR L 91 -1 N TYR L 86 O THR L 102 SHEET 4 AB2 5 SER L 34 GLN L 38 -1 N GLN L 38 O ASP L 85 SHEET 5 AB2 5 LYS L 45 ILE L 48 -1 O MET L 47 N TRP L 35 SHEET 1 AB3 4 SER L 9 GLY L 13 0 SHEET 2 AB3 4 THR L 102 VAL L 106 1 O LYS L 103 N VAL L 11 SHEET 3 AB3 4 ASP L 85 TYR L 91 -1 N TYR L 86 O THR L 102 SHEET 4 AB3 4 TRP L 96 PHE L 98 -1 O VAL L 97 N SER L 90 SHEET 1 AB4 3 ILE L 19 THR L 24 0 SHEET 2 AB4 3 THR L 70 ILE L 75 -1 O ALA L 71 N CYS L 23 SHEET 3 AB4 3 PHE L 62 SER L 67 -1 N SER L 65 O SER L 72 SHEET 1 AB5 4 SER L 113 PHE L 117 0 SHEET 2 AB5 4 THR L 128 PHE L 138 -1 O VAL L 132 N PHE L 117 SHEET 3 AB5 4 TYR L 172 SER L 181 -1 O LEU L 178 N VAL L 131 SHEET 4 AB5 4 SER L 158 VAL L 162 -1 N GLN L 159 O THR L 177 SHEET 1 AB6 4 ALA L 152 GLN L 154 0 SHEET 2 AB6 4 LYS L 144 VAL L 149 -1 N TRP L 147 O GLN L 154 SHEET 3 AB6 4 VAL L 190 THR L 196 -1 O THR L 196 N LYS L 144 SHEET 4 AB6 4 VAL L 204 ASN L 209 -1 O LYS L 206 N CYS L 193 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.04 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.01 SSBOND 5 CYS H 22 CYS H 92 1555 1555 2.03 SSBOND 6 CYS H 140 CYS H 196 1555 1555 2.04 SSBOND 7 CYS L 23 CYS L 88 1555 1555 2.03 SSBOND 8 CYS L 133 CYS L 193 1555 1555 2.02 LINK ND2 ASN A 343 C1 NAG B 1 1555 1555 1.44 LINK ND2 ASN L 94 C1 NAG L 301 1555 1555 1.41 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 CISPEP 1 GLU H 148 PRO H 149 0 29.10 CISPEP 2 TYR L 139 PRO L 140 0 5.38 CRYST1 81.771 100.709 106.019 90.00 90.00 90.00 P 21 2 21 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 0.012229 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009930 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009432 0.00000