HEADER VIRAL PROTEIN 19-JUN-25 9RN6 TITLE CRYSTAL STRUCTURE OF A PROTEIN MIMIC OF SARS-COV-2 SPIKE'S HR1 DOMAIN TITLE 2 IN COMPLEX WITH TWO NANOBODIES BOUND TO DIFFERENT EPITOPES COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S2',CHIMERIC PROTEIN MIMIC OF SARS-COV-2 COMPND 3 SPIKE HR1; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NANOBODY NB278; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: NANOBODY NB184; COMPND 12 CHAIN: C; COMPND 13 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 10 ORGANISM_TAXID: 30538; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 15 ORGANISM_TAXID: 30538; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NEUTRALIZING NANOBODIES; SARS-COV-2; SPIKE S2 SUBUNIT, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS,F.CONEJERO-LARA,D.POLO-MEGIAS,M.C.SALINAS-GARCIA, AUTHOR 2 J.A.GAVIRA REVDAT 1 21-JAN-26 9RN6 0 JRNL AUTH D.POLO-MEGIAS,M.CANO-MUNOZ,P.TROLESE,S.LESTANI,I.LA ROCCHIA, JRNL AUTH 2 A.PIERANGELINI,B.FONGARO,P.P.DE LAURETO,F.J.MORALES-YANEZ, JRNL AUTH 3 J.VANEYCK,A.VANDERPLASSCHEN,T.DECOVILLE,G.LAUMOND, JRNL AUTH 4 M.C.SALINAS-GARCIA,A.CAMARA-ARTIGAS,J.A.GAVIRA,C.MOOG, JRNL AUTH 5 M.DUMOULIN,F.CONEJERO-LARA JRNL TITL NEUTRALIZING NANOBODIES AGAINST SARS-COV-2 RECOGNIZING JRNL TITL 2 HIGHLY CONSERVED EPITOPES AT THE SPIKE'S S2 SUBUNIT. JRNL REF INT.J.BIOL.MACROMOL. V. 340 50022 2026 JRNL REFN ISSN 0141-8130 JRNL PMID 41506506 JRNL DOI 10.1016/J.IJBIOMAC.2025.150022 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.170 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 55779 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 2686 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 19.9900 - 6.3400 0.99 2804 119 0.1856 0.1949 REMARK 3 2 6.3300 - 5.0600 1.00 2805 131 0.2148 0.2274 REMARK 3 3 5.0600 - 4.4300 1.00 2805 150 0.1785 0.1754 REMARK 3 4 4.4300 - 4.0300 1.00 2771 147 0.1933 0.2022 REMARK 3 5 4.0300 - 3.7400 1.00 2763 143 0.2321 0.2748 REMARK 3 6 3.7400 - 3.5200 1.00 2853 131 0.2573 0.2699 REMARK 3 7 3.5200 - 3.3400 1.00 2787 138 0.2681 0.2515 REMARK 3 8 3.3400 - 3.2000 1.00 2786 153 0.2982 0.3289 REMARK 3 9 3.2000 - 3.0800 1.00 2812 141 0.3078 0.3383 REMARK 3 10 3.0800 - 2.9700 1.00 2780 119 0.3036 0.3417 REMARK 3 11 2.9700 - 2.8800 1.00 2886 121 0.3053 0.3461 REMARK 3 12 2.8800 - 2.8000 1.00 2692 150 0.3300 0.3383 REMARK 3 13 2.8000 - 2.7200 1.00 2865 127 0.3509 0.3135 REMARK 3 14 2.7200 - 2.6600 1.00 2694 194 0.3423 0.3739 REMARK 3 15 2.6600 - 2.6000 1.00 2804 167 0.3390 0.3530 REMARK 3 16 2.6000 - 2.5400 1.00 2788 160 0.3719 0.4190 REMARK 3 17 2.5400 - 2.4900 1.00 2748 145 0.3655 0.3942 REMARK 3 18 2.4900 - 2.4400 1.00 2869 144 0.4008 0.4512 REMARK 3 19 2.4400 - 2.4000 1.00 2781 106 0.3976 0.4374 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) : 0.334 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.754 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 80.50 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 : 0.005 3556 REMARK 3 ANGLE : 0.737 4797 REMARK 3 CHIRALITY : 0.043 534 REMARK 3 PLANARITY : 0.012 629 REMARK 3 DIHEDRAL : 18.307 1314 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 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.8921 -3.8794 64.5231 REMARK 3 T TENSOR REMARK 3 T11: 0.4142 T22: 0.9885 REMARK 3 T33: 0.6357 T12: -0.0627 REMARK 3 T13: 0.0228 T23: 0.0318 REMARK 3 L TENSOR REMARK 3 L11: 2.3621 L22: 1.4944 REMARK 3 L33: 2.0260 L12: 0.8023 REMARK 3 L13: 1.8488 L23: 1.9134 REMARK 3 S TENSOR REMARK 3 S11: 0.5362 S12: -1.0733 S13: -0.2086 REMARK 3 S21: 0.3036 S22: -0.0012 S23: -0.1424 REMARK 3 S31: 1.1683 S32: -1.9251 S33: -0.6053 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.9322 3.4699 68.2133 REMARK 3 T TENSOR REMARK 3 T11: 0.3828 T22: 0.9877 REMARK 3 T33: 0.6411 T12: 0.1035 REMARK 3 T13: -0.0377 T23: -0.0744 REMARK 3 L TENSOR REMARK 3 L11: 2.9201 L22: 0.8978 REMARK 3 L33: 9.6471 L12: 1.6864 REMARK 3 L13: 5.1557 L23: 2.2398 REMARK 3 S TENSOR REMARK 3 S11: -0.2368 S12: -0.0269 S13: 0.3687 REMARK 3 S21: 0.0774 S22: -0.0438 S23: 0.0780 REMARK 3 S31: -0.0281 S32: 0.3649 S33: 0.2290 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.9863 26.9333 103.9363 REMARK 3 T TENSOR REMARK 3 T11: 0.3807 T22: 0.9793 REMARK 3 T33: 0.5289 T12: 0.0835 REMARK 3 T13: -0.0076 T23: -0.0847 REMARK 3 L TENSOR REMARK 3 L11: 0.0394 L22: 2.9366 REMARK 3 L33: 7.0225 L12: -0.2727 REMARK 3 L13: -0.4498 L23: 4.5023 REMARK 3 S TENSOR REMARK 3 S11: -0.0999 S12: -0.1262 S13: -0.0944 REMARK 3 S21: -0.0738 S22: -0.3121 S23: 0.4986 REMARK 3 S31: -0.6355 S32: -1.3521 S33: 0.4742 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 18 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.0148 18.7532 93.8216 REMARK 3 T TENSOR REMARK 3 T11: 0.3524 T22: 1.1578 REMARK 3 T33: 0.6416 T12: 0.0000 REMARK 3 T13: 0.0074 T23: -0.0744 REMARK 3 L TENSOR REMARK 3 L11: 6.2442 L22: 6.4651 REMARK 3 L33: 8.2245 L12: -0.4934 REMARK 3 L13: 4.5992 L23: 5.1989 REMARK 3 S TENSOR REMARK 3 S11: -0.1741 S12: 0.3249 S13: 0.4323 REMARK 3 S21: -0.1343 S22: -0.8071 S23: 0.8594 REMARK 3 S31: 0.2025 S32: -1.4678 S33: 0.9394 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 34 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.4165 22.7277 100.0225 REMARK 3 T TENSOR REMARK 3 T11: 0.5248 T22: 0.8095 REMARK 3 T33: 0.3963 T12: -0.0296 REMARK 3 T13: -0.0346 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 8.6552 L22: 7.4714 REMARK 3 L33: 2.0247 L12: 1.8837 REMARK 3 L13: -0.3223 L23: 8.2810 REMARK 3 S TENSOR REMARK 3 S11: 0.0374 S12: 0.0624 S13: -0.0384 REMARK 3 S21: 0.2035 S22: 0.4682 S23: -0.5918 REMARK 3 S31: 0.2954 S32: 1.0004 S33: -0.4003 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 46 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.6639 13.4761 101.3411 REMARK 3 T TENSOR REMARK 3 T11: 0.4042 T22: 0.8999 REMARK 3 T33: 0.4080 T12: -0.0173 REMARK 3 T13: 0.0243 T23: -0.0566 REMARK 3 L TENSOR REMARK 3 L11: 1.9542 L22: 9.5911 REMARK 3 L33: 8.0629 L12: 0.9164 REMARK 3 L13: -1.7565 L23: 3.5630 REMARK 3 S TENSOR REMARK 3 S11: -0.1406 S12: 0.0578 S13: -0.0327 REMARK 3 S21: 0.4021 S22: 0.0281 S23: 0.7317 REMARK 3 S31: 0.5424 S32: -0.5175 S33: 0.1026 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 83 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.4754 21.7796 97.2204 REMARK 3 T TENSOR REMARK 3 T11: 0.3718 T22: 1.1058 REMARK 3 T33: 0.5285 T12: 0.0470 REMARK 3 T13: -0.0440 T23: -0.1006 REMARK 3 L TENSOR REMARK 3 L11: 1.3926 L22: 2.6780 REMARK 3 L33: 2.0183 L12: 0.6540 REMARK 3 L13: -2.8146 L23: 2.0783 REMARK 3 S TENSOR REMARK 3 S11: 0.1932 S12: 0.0280 S13: -0.0389 REMARK 3 S21: 0.0627 S22: 0.1429 S23: -0.1556 REMARK 3 S31: -0.3051 S32: -0.0054 S33: -0.3990 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 111 THROUGH 122 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.6545 30.3375 119.0332 REMARK 3 T TENSOR REMARK 3 T11: 0.5553 T22: 0.9195 REMARK 3 T33: 0.6268 T12: -0.0733 REMARK 3 T13: -0.0684 T23: -0.1427 REMARK 3 L TENSOR REMARK 3 L11: 4.6935 L22: 3.1415 REMARK 3 L33: 8.0251 L12: -0.3114 REMARK 3 L13: -3.1386 L23: 2.2353 REMARK 3 S TENSOR REMARK 3 S11: 0.0254 S12: -0.9125 S13: -0.4223 REMARK 3 S21: 0.4836 S22: 0.1032 S23: 0.0571 REMARK 3 S31: -0.3722 S32: 0.4436 S33: -0.1201 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 2 THROUGH 67 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.2919 -13.7202 44.0275 REMARK 3 T TENSOR REMARK 3 T11: 0.2956 T22: 1.0439 REMARK 3 T33: 0.5077 T12: -0.0017 REMARK 3 T13: -0.0452 T23: 0.0532 REMARK 3 L TENSOR REMARK 3 L11: 3.0330 L22: 6.8197 REMARK 3 L33: 5.2975 L12: -0.3183 REMARK 3 L13: -1.9911 L23: -0.3744 REMARK 3 S TENSOR REMARK 3 S11: -0.0084 S12: -0.6295 S13: -0.0094 REMARK 3 S21: 0.0854 S22: -0.0646 S23: 0.0434 REMARK 3 S31: 0.1391 S32: -0.1498 S33: 0.0991 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 68 THROUGH 124 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.5187 -15.4709 43.9886 REMARK 3 T TENSOR REMARK 3 T11: 0.3692 T22: 0.9746 REMARK 3 T33: 0.5153 T12: 0.0192 REMARK 3 T13: -0.0100 T23: 0.0471 REMARK 3 L TENSOR REMARK 3 L11: 6.0560 L22: 6.0111 REMARK 3 L33: 4.9993 L12: 2.7107 REMARK 3 L13: -1.9212 L23: -0.1017 REMARK 3 S TENSOR REMARK 3 S11: 0.0008 S12: -1.3691 S13: 0.0829 REMARK 3 S21: 0.4075 S22: -0.2400 S23: 0.5924 REMARK 3 S31: 0.3245 S32: -0.1377 S33: 0.2379 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 9RN6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1292148759. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29937 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 19.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 1.12100 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M NACL, PEG 6000 50% (V/V), 0.1 M REMARK 280 TRIS/HCL, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.67000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 115.39000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.67000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 115.39000 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, 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 1 REMARK 465 ASP A 2 REMARK 465 LYS A 144 REMARK 465 GLN A 145 REMARK 465 ARG A 146 REMARK 465 GLU A 147 REMARK 465 TYR A 148 REMARK 465 LEU A 149 REMARK 465 VAL A 150 REMARK 465 ASN A 151 REMARK 465 LYS A 152 REMARK 465 GLY A 153 REMARK 465 SER A 154 REMARK 465 GLY A 155 REMARK 465 ASN A 156 REMARK 465 VAL A 157 REMARK 465 LEU A 158 REMARK 465 TYR A 159 REMARK 465 GLU A 160 REMARK 465 GLU A 230 REMARK 465 GLY A 231 REMARK 465 GLY A 232 REMARK 465 GLY A 233 REMARK 465 GLY A 234 REMARK 465 SER A 235 REMARK 465 HIS A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 REMARK 465 HIS A 241 REMARK 465 GLN B 1 REMARK 465 HIS B 123 REMARK 465 GLN C 1 REMARK 465 TYR C 125 REMARK 465 ASP C 126 REMARK 465 VAL C 127 REMARK 465 PRO C 128 REMARK 465 ASP C 129 REMARK 465 TYR C 130 REMARK 465 GLY C 131 REMARK 465 SER C 132 REMARK 465 HIS C 133 REMARK 465 HIS C 134 REMARK 465 HIS C 135 REMARK 465 HIS C 136 REMARK 465 HIS C 137 REMARK 465 HIS C 138 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 C 48 -75.60 -110.77 REMARK 500 VAL C 75 -68.85 -103.93 REMARK 500 ALA C 120 34.68 71.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 123 0.09 SIDE CHAIN REMARK 500 ARG C 72 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9RN6 A 3 76 UNP P0DTC2 SPIKE_SARS2 915 988 DBREF 9RN6 A 157 230 UNP P0DTC2 SPIKE_SARS2 915 988 DBREF 9RN6 B 1 123 PDB 9RN6 9RN6 1 123 DBREF 9RN6 C 1 138 PDB 9RN6 9RN6 1 138 SEQADV 9RN6 MET A 1 UNP P0DTC2 INITIATING METHIONINE SEQADV 9RN6 ASP A 2 UNP P0DTC2 EXPRESSION TAG SEQADV 9RN6 LYS A 14 UNP P0DTC2 GLN 926 ENGINEERED MUTATION SEQADV 9RN6 GLU A 32 UNP P0DTC2 ALA 944 ENGINEERED MUTATION SEQADV 9RN6 GLU A 39 UNP P0DTC2 VAL 951 ENGINEERED MUTATION SEQADV 9RN6 ASP A 46 UNP P0DTC2 ALA 958 ENGINEERED MUTATION SEQADV 9RN6 ARG A 60 UNP P0DTC2 ALA 972 ENGINEERED MUTATION SEQADV 9RN6 GLU A 64 UNP P0DTC2 VAL 976 ENGINEERED MUTATION SEQADV 9RN6 GLY A 75 UNP P0DTC2 VAL 987 ENGINEERED MUTATION SEQADV 9RN6 PRO A 77 UNP P0DTC2 LINKER SEQADV 9RN6 ALA A 78 UNP P0DTC2 LINKER SEQADV 9RN6 LYS A 79 UNP P0DTC2 LINKER SEQADV 9RN6 ASP A 80 UNP P0DTC2 LINKER SEQADV 9RN6 LEU A 81 UNP P0DTC2 LINKER SEQADV 9RN6 ARG A 82 UNP P0DTC2 LINKER SEQADV 9RN6 SER A 83 UNP P0DTC2 LINKER SEQADV 9RN6 ASP A 84 UNP P0DTC2 LINKER SEQADV 9RN6 ILE A 85 UNP P0DTC2 LINKER SEQADV 9RN6 ASP A 86 UNP P0DTC2 LINKER SEQADV 9RN6 ASN A 87 UNP P0DTC2 LINKER SEQADV 9RN6 LEU A 88 UNP P0DTC2 LINKER SEQADV 9RN6 GLU A 89 UNP P0DTC2 LINKER SEQADV 9RN6 SER A 90 UNP P0DTC2 LINKER SEQADV 9RN6 LYS A 91 UNP P0DTC2 LINKER SEQADV 9RN6 ILE A 92 UNP P0DTC2 LINKER SEQADV 9RN6 ALA A 93 UNP P0DTC2 LINKER SEQADV 9RN6 GLY A 94 UNP P0DTC2 LINKER SEQADV 9RN6 PHE A 95 UNP P0DTC2 LINKER SEQADV 9RN6 ASN A 96 UNP P0DTC2 LINKER SEQADV 9RN6 SER A 97 UNP P0DTC2 LINKER SEQADV 9RN6 SER A 98 UNP P0DTC2 LINKER SEQADV 9RN6 LEU A 99 UNP P0DTC2 LINKER SEQADV 9RN6 GLN A 100 UNP P0DTC2 LINKER SEQADV 9RN6 LYS A 101 UNP P0DTC2 LINKER SEQADV 9RN6 VAL A 102 UNP P0DTC2 LINKER SEQADV 9RN6 LEU A 103 UNP P0DTC2 LINKER SEQADV 9RN6 THR A 104 UNP P0DTC2 LINKER SEQADV 9RN6 ASN A 105 UNP P0DTC2 LINKER SEQADV 9RN6 LEU A 106 UNP P0DTC2 LINKER SEQADV 9RN6 ALA A 107 UNP P0DTC2 LINKER SEQADV 9RN6 GLN A 108 UNP P0DTC2 LINKER SEQADV 9RN6 LYS A 109 UNP P0DTC2 LINKER SEQADV 9RN6 ASN A 110 UNP P0DTC2 LINKER SEQADV 9RN6 GLN A 111 UNP P0DTC2 LINKER SEQADV 9RN6 ASN A 112 UNP P0DTC2 LINKER SEQADV 9RN6 VAL A 113 UNP P0DTC2 LINKER SEQADV 9RN6 GLU A 114 UNP P0DTC2 LINKER SEQADV 9RN6 ASP A 115 UNP P0DTC2 LINKER SEQADV 9RN6 LYS A 116 UNP P0DTC2 LINKER SEQADV 9RN6 LEU A 117 UNP P0DTC2 LINKER SEQADV 9RN6 LYS A 118 UNP P0DTC2 LINKER SEQADV 9RN6 GLY A 119 UNP P0DTC2 LINKER SEQADV 9RN6 LEU A 120 UNP P0DTC2 LINKER SEQADV 9RN6 GLU A 121 UNP P0DTC2 LINKER SEQADV 9RN6 SER A 122 UNP P0DTC2 LINKER SEQADV 9RN6 ARG A 123 UNP P0DTC2 LINKER SEQADV 9RN6 THR A 124 UNP P0DTC2 LINKER SEQADV 9RN6 SER A 125 UNP P0DTC2 LINKER SEQADV 9RN6 SER A 126 UNP P0DTC2 LINKER SEQADV 9RN6 LEU A 127 UNP P0DTC2 LINKER SEQADV 9RN6 GLU A 128 UNP P0DTC2 LINKER SEQADV 9RN6 LYS A 129 UNP P0DTC2 LINKER SEQADV 9RN6 GLN A 130 UNP P0DTC2 LINKER SEQADV 9RN6 ILE A 131 UNP P0DTC2 LINKER SEQADV 9RN6 LYS A 132 UNP P0DTC2 LINKER SEQADV 9RN6 GLY A 133 UNP P0DTC2 LINKER SEQADV 9RN6 ILE A 134 UNP P0DTC2 LINKER SEQADV 9RN6 ALA A 135 UNP P0DTC2 LINKER SEQADV 9RN6 SER A 136 UNP P0DTC2 LINKER SEQADV 9RN6 ASN A 137 UNP P0DTC2 LINKER SEQADV 9RN6 PHE A 138 UNP P0DTC2 LINKER SEQADV 9RN6 GLN A 139 UNP P0DTC2 LINKER SEQADV 9RN6 ASN A 140 UNP P0DTC2 LINKER SEQADV 9RN6 GLU A 141 UNP P0DTC2 LINKER SEQADV 9RN6 ILE A 142 UNP P0DTC2 LINKER SEQADV 9RN6 LEU A 143 UNP P0DTC2 LINKER SEQADV 9RN6 LYS A 144 UNP P0DTC2 LINKER SEQADV 9RN6 GLN A 145 UNP P0DTC2 LINKER SEQADV 9RN6 ARG A 146 UNP P0DTC2 LINKER SEQADV 9RN6 GLU A 147 UNP P0DTC2 LINKER SEQADV 9RN6 TYR A 148 UNP P0DTC2 LINKER SEQADV 9RN6 LEU A 149 UNP P0DTC2 LINKER SEQADV 9RN6 VAL A 150 UNP P0DTC2 LINKER SEQADV 9RN6 ASN A 151 UNP P0DTC2 LINKER SEQADV 9RN6 LYS A 152 UNP P0DTC2 LINKER SEQADV 9RN6 GLY A 153 UNP P0DTC2 LINKER SEQADV 9RN6 SER A 154 UNP P0DTC2 LINKER SEQADV 9RN6 GLY A 155 UNP P0DTC2 LINKER SEQADV 9RN6 ASN A 156 UNP P0DTC2 LINKER SEQADV 9RN6 GLU A 166 UNP P0DTC2 ALA 924 ENGINEERED MUTATION SEQADV 9RN6 LYS A 184 UNP P0DTC2 ALA 942 ENGINEERED MUTATION SEQADV 9RN6 LYS A 191 UNP P0DTC2 GLN 949 ENGINEERED MUTATION SEQADV 9RN6 LYS A 198 UNP P0DTC2 ALA 956 ENGINEERED MUTATION SEQADV 9RN6 LYS A 223 UNP P0DTC2 LEU 981 ENGINEERED MUTATION SEQADV 9RN6 GLY A 231 UNP P0DTC2 EXPRESSION TAG SEQADV 9RN6 GLY A 232 UNP P0DTC2 EXPRESSION TAG SEQADV 9RN6 GLY A 233 UNP P0DTC2 EXPRESSION TAG SEQADV 9RN6 GLY A 234 UNP P0DTC2 EXPRESSION TAG SEQADV 9RN6 SER A 235 UNP P0DTC2 EXPRESSION TAG SEQADV 9RN6 HIS A 236 UNP P0DTC2 EXPRESSION TAG SEQADV 9RN6 HIS A 237 UNP P0DTC2 EXPRESSION TAG SEQADV 9RN6 HIS A 238 UNP P0DTC2 EXPRESSION TAG SEQADV 9RN6 HIS A 239 UNP P0DTC2 EXPRESSION TAG SEQADV 9RN6 HIS A 240 UNP P0DTC2 EXPRESSION TAG SEQADV 9RN6 HIS A 241 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 241 MET ASP VAL LEU TYR GLU ASN GLN LYS LEU ILE ALA ASN SEQRES 2 A 241 LYS PHE ASN SER ALA ILE GLY LYS ILE GLN ASP SER LEU SEQRES 3 A 241 SER SER THR ALA SER GLU LEU GLY LYS LEU GLN ASP GLU SEQRES 4 A 241 VAL ASN GLN ASN ALA GLN ASP LEU ASN THR LEU VAL LYS SEQRES 5 A 241 GLN LEU SER SER ASN PHE GLY ARG ILE SER SER GLU LEU SEQRES 6 A 241 ASN ASP ILE LEU SER ARG LEU ASP LYS GLY GLU PRO ALA SEQRES 7 A 241 LYS ASP LEU ARG SER ASP ILE ASP ASN LEU GLU SER LYS SEQRES 8 A 241 ILE ALA GLY PHE ASN SER SER LEU GLN LYS VAL LEU THR SEQRES 9 A 241 ASN LEU ALA GLN LYS ASN GLN ASN VAL GLU ASP LYS LEU SEQRES 10 A 241 LYS GLY LEU GLU SER ARG THR SER SER LEU GLU LYS GLN SEQRES 11 A 241 ILE LYS GLY ILE ALA SER ASN PHE GLN ASN GLU ILE LEU SEQRES 12 A 241 LYS GLN ARG GLU TYR LEU VAL ASN LYS GLY SER GLY ASN SEQRES 13 A 241 VAL LEU TYR GLU ASN GLN LYS LEU ILE GLU ASN GLN PHE SEQRES 14 A 241 ASN SER ALA ILE GLY LYS ILE GLN ASP SER LEU SER SER SEQRES 15 A 241 THR LYS SER ALA LEU GLY LYS LEU LYS ASP VAL VAL ASN SEQRES 16 A 241 GLN ASN LYS GLN ALA LEU ASN THR LEU VAL LYS GLN LEU SEQRES 17 A 241 SER SER ASN PHE GLY ALA ILE SER SER VAL LEU ASN ASP SEQRES 18 A 241 ILE LYS SER ARG LEU ASP LYS VAL GLU GLY GLY GLY GLY SEQRES 19 A 241 SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 123 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 123 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 123 ILE ALA PHE SER ASN ASN ALA MET GLY TRP TYR ARG GLN SEQRES 4 B 123 ALA PRO GLY LYS GLN ARG GLU LEU VAL ALA ASN ILE ILE SEQRES 5 B 123 THR PHE GLY ASN THR TYR TYR THR ASP SER VAL LYS GLY SEQRES 6 B 123 ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR VAL SEQRES 7 B 123 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 B 123 VAL TYR TYR CYS HIS THR TYR GLY ASP SER PRO GLU ARG SEQRES 9 B 123 GLY TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 10 B 123 HIS HIS HIS HIS HIS HIS SEQRES 1 C 138 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL HIS SEQRES 2 C 138 PRO GLY GLN SER LEU THR LEU SER CYS ALA PRO SER GLY SEQRES 3 C 138 ARG THR PHE SER ASN TYR ASP ILE GLY TRP PHE ARG GLN SEQRES 4 C 138 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ASP ILE ARG SEQRES 5 C 138 LEU ASN SER GLY SER THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 C 138 GLY ARG PHE THR ILE SER ARG ASP ASN VAL LYS ASN THR SEQRES 7 C 138 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 C 138 ALA VAL TYR TYR CYS ALA ALA ARG SER PRO GLY GLY ILE SEQRES 9 C 138 LEU TYR ASP TYR TRP GLY GLN GLY THR GLN VAL THR VAL SEQRES 10 C 138 SER SER ALA ALA ALA TYR PRO TYR ASP VAL PRO ASP TYR SEQRES 11 C 138 GLY SER HIS HIS HIS HIS HIS HIS HELIX 1 AA1 VAL A 3 PHE A 15 1 13 HELIX 2 AA2 PHE A 15 LYS A 74 1 60 HELIX 3 AA3 PRO A 77 ILE A 142 1 66 HELIX 4 AA4 LYS A 163 LYS A 228 1 66 HELIX 5 AA5 ASP B 61 LYS B 64 5 4 HELIX 6 AA6 LYS B 86 THR B 90 5 5 HELIX 7 AA7 LYS C 87 THR C 91 5 5 SHEET 1 AA1 4 GLN B 3 GLY B 8 0 SHEET 2 AA1 4 LEU B 18 SER B 25 -1 O ALA B 23 N GLN B 5 SHEET 3 AA1 4 THR B 77 MET B 82 -1 O LEU B 80 N LEU B 20 SHEET 4 AA1 4 PHE B 67 ASP B 72 -1 N THR B 68 O GLN B 81 SHEET 1 AA2 6 LEU B 11 GLN B 13 0 SHEET 2 AA2 6 THR B 111 SER B 116 1 O THR B 114 N VAL B 12 SHEET 3 AA2 6 ALA B 91 THR B 97 -1 N TYR B 93 O THR B 111 SHEET 4 AA2 6 MET B 34 GLN B 39 -1 N TYR B 37 O TYR B 94 SHEET 5 AA2 6 GLU B 46 ILE B 51 -1 O ILE B 51 N MET B 34 SHEET 6 AA2 6 THR B 57 TYR B 59 -1 O TYR B 58 N ASN B 50 SHEET 1 AA3 4 LEU B 11 GLN B 13 0 SHEET 2 AA3 4 THR B 111 SER B 116 1 O THR B 114 N VAL B 12 SHEET 3 AA3 4 ALA B 91 THR B 97 -1 N TYR B 93 O THR B 111 SHEET 4 AA3 4 TYR B 106 TRP B 107 -1 O TYR B 106 N THR B 97 SHEET 1 AA4 4 GLN C 3 SER C 7 0 SHEET 2 AA4 4 LEU C 18 SER C 25 -1 O SER C 21 N SER C 7 SHEET 3 AA4 4 VAL C 79 MET C 83 -1 O MET C 83 N LEU C 18 SHEET 4 AA4 4 PHE C 68 ARG C 72 -1 N THR C 69 O GLN C 82 SHEET 1 AA5 6 LEU C 11 VAL C 12 0 SHEET 2 AA5 6 THR C 113 VAL C 117 1 O THR C 116 N VAL C 12 SHEET 3 AA5 6 ALA C 92 ARG C 99 -1 N TYR C 94 O THR C 113 SHEET 4 AA5 6 ASP C 33 GLN C 39 -1 N PHE C 37 O TYR C 95 SHEET 5 AA5 6 GLU C 46 ARG C 52 -1 O VAL C 48 N TRP C 36 SHEET 6 AA5 6 THR C 58 TYR C 60 -1 O TYR C 59 N ASP C 50 SHEET 1 AA6 4 LEU C 11 VAL C 12 0 SHEET 2 AA6 4 THR C 113 VAL C 117 1 O THR C 116 N VAL C 12 SHEET 3 AA6 4 ALA C 92 ARG C 99 -1 N TYR C 94 O THR C 113 SHEET 4 AA6 4 TYR C 108 TRP C 109 -1 O TYR C 108 N ALA C 98 SSBOND 1 CYS B 22 CYS B 95 1555 1555 2.05 SSBOND 2 CYS C 22 CYS C 96 1555 1555 2.02 CRYST1 47.560 67.340 230.780 90.00 90.00 90.00 P 2 21 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 0.021026 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014850 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004333 0.00000