HEADER VIRAL PROTEIN 21-JUN-21 7OWX TITLE STRUCTURE OF COILED-COIL TETRAMER FROM SARS-COV-2 SPIKE STALK REGION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 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_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 6 ORGANISM_TAXID: 2697049 KEYWDS SPIKE, SARS-COV-2, COILED-COIL, TETRAMER, VIRUS, CORONAVIRUS, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZIVIC,S.HADZI REVDAT 1 16-MAR-22 7OWX 0 JRNL AUTH Z.ZIVIC,Z.STRMSEK,M.NOVINEC,J.LAH,S.HADZI JRNL TITL STRUCTURAL POLYMORPHISM OF COILED-COILS FROM THE STALK JRNL TITL 2 DOMAIN OF SARS-COV-2 SPIKE PROTEIN. JRNL REF FASEB J. V. 36 22199 2022 JRNL REFN ESSN 1530-6860 JRNL PMID 35157347 JRNL DOI 10.1096/FJ.202101670R REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 7779 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 777 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 33.0040 - 3.5035 1.00 1252 130 0.1668 0.2208 REMARK 3 2 3.5035 - 2.7813 1.00 1188 136 0.1659 0.2164 REMARK 3 3 2.7813 - 2.4298 1.00 1172 124 0.1604 0.2232 REMARK 3 4 2.4298 - 2.2077 1.00 1151 135 0.1665 0.2450 REMARK 3 5 2.2077 - 2.0495 1.00 1151 128 0.1964 0.2767 REMARK 3 6 2.0495 - 1.9290 0.95 728 124 0.2473 0.3459 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.62 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 : 0.006 923 REMARK 3 ANGLE : 0.730 1238 REMARK 3 CHIRALITY : 0.041 148 REMARK 3 PLANARITY : 0.004 167 REMARK 3 DIHEDRAL : 7.623 704 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1177 THROUGH 1203) REMARK 3 ORIGIN FOR THE GROUP (A): 28.7598 -10.7792 20.5373 REMARK 3 T TENSOR REMARK 3 T11: 0.2539 T22: 0.2381 REMARK 3 T33: 0.2903 T12: 0.0039 REMARK 3 T13: 0.0082 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.0934 L22: 0.0035 REMARK 3 L33: 0.0129 L12: 0.0179 REMARK 3 L13: -0.0353 L23: -0.0070 REMARK 3 S TENSOR REMARK 3 S11: 0.0361 S12: -0.0149 S13: 0.1799 REMARK 3 S21: 0.1078 S22: 0.0988 S23: 0.2489 REMARK 3 S31: 0.0606 S32: -0.0716 S33: 0.0031 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1177 THROUGH 1203) REMARK 3 ORIGIN FOR THE GROUP (A): 29.1243 -15.2658 12.0883 REMARK 3 T TENSOR REMARK 3 T11: 0.2991 T22: 0.3271 REMARK 3 T33: 0.3034 T12: -0.0191 REMARK 3 T13: -0.0324 T23: -0.0313 REMARK 3 L TENSOR REMARK 3 L11: 0.0901 L22: 0.0678 REMARK 3 L33: 0.1387 L12: 0.0315 REMARK 3 L13: 0.1075 L23: 0.0620 REMARK 3 S TENSOR REMARK 3 S11: -0.1457 S12: 0.1953 S13: 0.1741 REMARK 3 S21: -0.0124 S22: 0.2733 S23: 0.3066 REMARK 3 S31: 0.1116 S32: -0.3729 S33: 0.0004 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 1177 THROUGH 1203) REMARK 3 ORIGIN FOR THE GROUP (A): 39.2877 -14.7208 12.6497 REMARK 3 T TENSOR REMARK 3 T11: 0.2623 T22: 0.2361 REMARK 3 T33: 0.2438 T12: 0.0044 REMARK 3 T13: 0.0195 T23: -0.0240 REMARK 3 L TENSOR REMARK 3 L11: 0.1326 L22: 0.0535 REMARK 3 L33: 0.0859 L12: 0.0232 REMARK 3 L13: -0.0339 L23: 0.0562 REMARK 3 S TENSOR REMARK 3 S11: 0.0133 S12: -0.0220 S13: -0.0188 REMARK 3 S21: -0.1485 S22: -0.0755 S23: -0.0535 REMARK 3 S31: 0.0193 S32: 0.0142 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 1177 THROUGH 1203) REMARK 3 ORIGIN FOR THE GROUP (A): 38.6409 -14.1288 21.7977 REMARK 3 T TENSOR REMARK 3 T11: 0.2377 T22: 0.2563 REMARK 3 T33: 0.2622 T12: 0.0156 REMARK 3 T13: 0.0217 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 0.2228 L22: 0.0181 REMARK 3 L33: 0.3216 L12: -0.0465 REMARK 3 L13: -0.0266 L23: 0.0570 REMARK 3 S TENSOR REMARK 3 S11: 0.0336 S12: -0.1072 S13: -0.0046 REMARK 3 S21: 0.2083 S22: -0.1195 S23: -0.2023 REMARK 3 S31: 0.0402 S32: 0.0471 S33: -0.0001 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 7OWX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1292116549. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978565 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7780 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.929 REMARK 200 RESOLUTION RANGE LOW (A) : 32.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 18.10 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: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.002 M ZINC CHLORIDE, 0.1 M TRIS PH REMARK 280 8, 20 % W/V PEG 6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.57000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.95000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.77000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.95000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.57000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.77000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 TYR A1177 N CA CB CG CD1 CD2 CE1 REMARK 470 TYR A1177 CE2 CZ OH REMARK 470 TYR D1177 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU D1203 CG CD1 CD2 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D1302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A1195 OE2 REMARK 620 2 ASP A1199 OD1 84.8 REMARK 620 3 ASP A1199 OD2 119.6 53.2 REMARK 620 4 GLU D1195 OE1 38.1 76.0 86.2 REMARK 620 5 ASP D1199 OD2 42.0 81.0 85.6 6.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C1184 OD2 REMARK 620 2 GLU C1195 OE1 70.0 REMARK 620 3 ASP C1199 OD1 66.8 4.5 REMARK 620 4 ASP C1199 OD2 71.1 5.6 4.8 REMARK 620 5 HOH C1418 O 104.7 38.7 40.3 35.5 REMARK 620 N 1 2 3 4 DBREF 7OWX A 1177 1203 UNP P0DTC2 SPIKE_SARS2 1177 1203 DBREF 7OWX B 1177 1203 UNP P0DTC2 SPIKE_SARS2 1177 1203 DBREF 7OWX C 1177 1203 UNP P0DTC2 SPIKE_SARS2 1177 1203 DBREF 7OWX D 1177 1203 UNP P0DTC2 SPIKE_SARS2 1177 1203 SEQADV 7OWX TYR A 1177 UNP P0DTC2 VAL 1177 ENGINEERED MUTATION SEQADV 7OWX TYR B 1177 UNP P0DTC2 VAL 1177 ENGINEERED MUTATION SEQADV 7OWX TYR C 1177 UNP P0DTC2 VAL 1177 ENGINEERED MUTATION SEQADV 7OWX TYR D 1177 UNP P0DTC2 VAL 1177 ENGINEERED MUTATION SEQRES 1 A 27 TYR ASN ILE GLN LYS GLU ILE ASP ARG LEU ASN GLU VAL SEQRES 2 A 27 ALA LYS ASN LEU ASN GLU SER LEU ILE ASP LEU GLN GLU SEQRES 3 A 27 LEU SEQRES 1 B 27 TYR ASN ILE GLN LYS GLU ILE ASP ARG LEU ASN GLU VAL SEQRES 2 B 27 ALA LYS ASN LEU ASN GLU SER LEU ILE ASP LEU GLN GLU SEQRES 3 B 27 LEU SEQRES 1 C 27 TYR ASN ILE GLN LYS GLU ILE ASP ARG LEU ASN GLU VAL SEQRES 2 C 27 ALA LYS ASN LEU ASN GLU SER LEU ILE ASP LEU GLN GLU SEQRES 3 C 27 LEU SEQRES 1 D 27 TYR ASN ILE GLN LYS GLU ILE ASP ARG LEU ASN GLU VAL SEQRES 2 D 27 ALA LYS ASN LEU ASN GLU SER LEU ILE ASP LEU GLN GLU SEQRES 3 D 27 LEU HET EDO A1301 4 HET EDO A1302 4 HET ZN C1301 1 HET EDO D1301 4 HET ZN D1302 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO 3(C2 H6 O2) FORMUL 7 ZN 2(ZN 2+) FORMUL 10 HOH *76(H2 O) HELIX 1 AA1 ILE A 1179 LEU A 1203 1 25 HELIX 2 AA2 ASN B 1178 GLU B 1202 1 25 HELIX 3 AA3 ASN C 1178 GLU C 1202 1 25 HELIX 4 AA4 ILE D 1179 GLN D 1201 1 23 LINK OE2 GLU A1195 ZN ZN D1302 1555 4446 1.91 LINK OD1 ASP A1199 ZN ZN D1302 1555 4446 2.66 LINK OD2 ASP A1199 ZN ZN D1302 1555 4446 2.00 LINK OD2 ASP C1184 ZN ZN C1301 1555 1555 1.95 LINK OE1 GLU C1195 ZN ZN C1301 1555 3745 2.07 LINK OD1 ASP C1199 ZN ZN C1301 1555 3745 2.64 LINK OD2 ASP C1199 ZN ZN C1301 1555 3745 2.10 LINK ZN ZN C1301 O HOH C1418 1555 3755 2.03 LINK OE1 GLU D1195 ZN ZN D1302 1555 1555 1.96 LINK OD2 ASP D1199 ZN ZN D1302 1555 1555 1.94 CRYST1 45.140 45.540 47.900 90.00 90.00 90.00 P 21 21 21 16 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 0.022153 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021959 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020877 0.00000