HEADER VIRAL PROTEIN 26-FEB-20 6M1V TITLE CRYSTAL STRUCTURE OF POST FUSION CORE OF 2019-NCOV S2 SUBUNIT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S2,SPIKE PROTEIN S2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: K-12 KEYWDS 2019-NCOV, SPIKE PROTEIN, FUSION CORE, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.SUN,H.SONG,Q.WANG REVDAT 3 29-NOV-23 6M1V 1 REMARK REVDAT 2 03-FEB-21 6M1V 1 COMPND SOURCE JRNL REMARK REVDAT 2 2 1 DBREF SEQADV REVDAT 1 03-JUN-20 6M1V 0 JRNL AUTH H.SUN,Y.LI,P.LIU,C.QIAO,X.WANG,L.WU,K.LIU,Y.HU,C.SU,S.TAN, JRNL AUTH 2 S.ZOU,G.WU,J.YAN,G.F.GAO,J.QI,Q.WANG JRNL TITL STRUCTURAL BASIS OF HCOV-19 FUSION CORE AND AN EFFECTIVE JRNL TITL 2 INHIBITION PEPTIDE AGAINST VIRUS ENTRY. JRNL REF EMERG MICROBES INFECT V. 9 1238 2020 JRNL REFN ESSN 2222-1751 JRNL PMID 32482145 JRNL DOI 10.1080/22221751.2020.1770631 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 17786 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 836 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 21.6200 - 2.7200 1.00 3171 157 0.1951 0.2027 REMARK 3 2 2.7200 - 2.1600 1.00 2984 144 0.1947 0.1874 REMARK 3 3 2.1600 - 1.8900 1.00 2971 157 0.2019 0.2320 REMARK 3 4 1.8900 - 1.7200 1.00 2938 138 0.2212 0.2241 REMARK 3 5 1.7200 - 1.5900 0.98 2868 154 0.2388 0.2618 REMARK 3 6 1.5900 - 1.5000 0.68 2018 86 0.2313 0.2574 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) : 0.152 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.857 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.72 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.64 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 : 0.005 715 REMARK 3 ANGLE : 0.701 970 REMARK 3 CHIRALITY : 0.060 121 REMARK 3 PLANARITY : 0.004 129 REMARK 3 DIHEDRAL : 20.046 271 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -6.7429 26.8171 134.4335 REMARK 3 T TENSOR REMARK 3 T11: 0.0471 T22: 0.0944 REMARK 3 T33: 0.1337 T12: 0.0071 REMARK 3 T13: -0.0016 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.5130 L22: 0.4984 REMARK 3 L33: 2.5226 L12: 0.0670 REMARK 3 L13: -0.0816 L23: 0.1618 REMARK 3 S TENSOR REMARK 3 S11: -0.0058 S12: 0.0724 S13: 0.0200 REMARK 3 S21: -0.0468 S22: -0.0396 S23: 0.0784 REMARK 3 S31: -0.0502 S32: -0.5746 S33: 0.0638 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 6M1V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-APR-20. REMARK 100 THE DEPOSITION ID IS D_1300015870. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18825 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: 1WNC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH 6.5, AND 25% REMARK 280 (WT/VOL) POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: 8120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 21.33300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 36.94984 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -21.33300 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 36.94984 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1358 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1409 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1410 LIES ON A SPECIAL POSITION. 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 GLY A 1145 REMARK 465 SER A 1146 REMARK 465 GLY A 1147 REMARK 465 GLY A 1148 REMARK 465 SER A 1149 REMARK 465 GLY A 1150 REMARK 465 GLY A 1151 REMARK 465 SER A 1152 REMARK 465 GLY A 1153 REMARK 465 GLY A 1154 REMARK 465 LEU A 1155 REMARK 465 GLU A 1156 REMARK 465 VAL A 1157 REMARK 465 LEU A 1158 REMARK 465 PHE A 1159 REMARK 465 GLN A 1160 REMARK 465 GLY A 1161 REMARK 465 PRO A 1162 REMARK 465 ASP A 1163 REMARK 465 VAL A 1164 REMARK 465 ASP A 1165 REMARK 465 LEU A 1166 REMARK 465 GLY A 1167 REMARK 465 ASP A 1168 REMARK 465 HIS A 1206 REMARK 465 HIS A 1207 REMARK 465 HIS A 1208 REMARK 465 HIS A 1209 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 ARG A 970 CG CD NE CZ NH1 NH2 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1412 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A1413 DISTANCE = 6.58 ANGSTROMS DBREF 6M1V A 918 966 UNP P0DTC2 SPIKE_SARS2 918 966 DBREF 6M1V A 1162 1203 UNP P0DTC2 SPIKE_SARS2 1162 1203 SEQADV 6M1V MET A 917 UNP P0DTC2 EXPRESSION TAG SEQADV 6M1V LEU A 967 UNP P0DTC2 LINKER SEQADV 6M1V VAL A 968 UNP P0DTC2 LINKER SEQADV 6M1V PRO A 969 UNP P0DTC2 LINKER SEQADV 6M1V ARG A 970 UNP P0DTC2 LINKER SEQADV 6M1V GLY A 1145 UNP P0DTC2 LINKER SEQADV 6M1V SER A 1146 UNP P0DTC2 LINKER SEQADV 6M1V GLY A 1147 UNP P0DTC2 LINKER SEQADV 6M1V GLY A 1148 UNP P0DTC2 LINKER SEQADV 6M1V SER A 1149 UNP P0DTC2 LINKER SEQADV 6M1V GLY A 1150 UNP P0DTC2 LINKER SEQADV 6M1V GLY A 1151 UNP P0DTC2 LINKER SEQADV 6M1V SER A 1152 UNP P0DTC2 LINKER SEQADV 6M1V GLY A 1153 UNP P0DTC2 LINKER SEQADV 6M1V GLY A 1154 UNP P0DTC2 LINKER SEQADV 6M1V LEU A 1155 UNP P0DTC2 LINKER SEQADV 6M1V GLU A 1156 UNP P0DTC2 LINKER SEQADV 6M1V VAL A 1157 UNP P0DTC2 LINKER SEQADV 6M1V LEU A 1158 UNP P0DTC2 LINKER SEQADV 6M1V PHE A 1159 UNP P0DTC2 LINKER SEQADV 6M1V GLN A 1160 UNP P0DTC2 LINKER SEQADV 6M1V GLY A 1161 UNP P0DTC2 LINKER SEQADV 6M1V HIS A 1204 UNP P0DTC2 EXPRESSION TAG SEQADV 6M1V HIS A 1205 UNP P0DTC2 EXPRESSION TAG SEQADV 6M1V HIS A 1206 UNP P0DTC2 EXPRESSION TAG SEQADV 6M1V HIS A 1207 UNP P0DTC2 EXPRESSION TAG SEQADV 6M1V HIS A 1208 UNP P0DTC2 EXPRESSION TAG SEQADV 6M1V HIS A 1209 UNP P0DTC2 EXPRESSION TAG SEQRES 1 A 119 MET GLU ASN GLN LYS LEU ILE ALA ASN GLN PHE ASN SER SEQRES 2 A 119 ALA ILE GLY LYS ILE GLN ASP SER LEU SER SER THR ALA SEQRES 3 A 119 SER ALA LEU GLY LYS LEU GLN ASP VAL VAL ASN GLN ASN SEQRES 4 A 119 ALA GLN ALA LEU ASN THR LEU VAL LYS GLN LEU LEU VAL SEQRES 5 A 119 PRO ARG GLY SER GLY GLY SER GLY GLY SER GLY GLY LEU SEQRES 6 A 119 GLU VAL LEU PHE GLN GLY PRO ASP VAL ASP LEU GLY ASP SEQRES 7 A 119 ILE SER GLY ILE ASN ALA SER VAL VAL ASN ILE GLN LYS SEQRES 8 A 119 GLU ILE ASP ARG LEU ASN GLU VAL ALA LYS ASN LEU ASN SEQRES 9 A 119 GLU SER LEU ILE ASP LEU GLN GLU LEU HIS HIS HIS HIS SEQRES 10 A 119 HIS HIS FORMUL 2 HOH *113(H2 O) HELIX 1 AA1 GLU A 918 VAL A 968 1 51 HELIX 2 AA2 ILE A 1179 LEU A 1193 1 15 HELIX 3 AA3 ASN A 1194 LEU A 1197 5 4 HELIX 4 AA4 ASP A 1199 LEU A 1203 5 5 CRYST1 42.666 42.666 106.648 90.00 90.00 120.00 P 3 2 1 6 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 0.023438 0.013532 0.000000 0.00000 SCALE2 0.000000 0.027064 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009377 0.00000