HEADER VIRAL PROTEIN 04-FEB-20 6LVN TITLE STRUCTURE OF THE 2019-NCOV HR2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S2'; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: HR2 DOMAIN; COMPND 5 SYNONYM: SPIKE PROTEIN S2; COMPND 6 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; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 2019-NCOV, HR2 DOMAIN, VIRUS, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHU,F.SUN REVDAT 5 29-NOV-23 6LVN 1 REMARK REVDAT 4 10-MAR-21 6LVN 1 COMPND REVDAT 3 06-MAY-20 6LVN 1 COMPND SOURCE DBREF REVDAT 2 01-APR-20 6LVN 1 COMPND SOURCE REVDAT 1 26-FEB-20 6LVN 0 JRNL AUTH Y.ZHU,F.SUN JRNL TITL CRYSTAL STRUCTURE OF HR2 DOMAIN OF 2019-NCOV S2 SUBUNIT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 4862 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.51 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 1052 REMARK 3 ANGLE : 0.726 1416 REMARK 3 CHIRALITY : 0.049 180 REMARK 3 PLANARITY : 0.004 188 REMARK 3 DIHEDRAL : 16.733 672 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 35 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.5967 32.9173 28.9788 REMARK 3 T TENSOR REMARK 3 T11: 0.2902 T22: 0.2319 REMARK 3 T33: 0.2466 T12: 0.0031 REMARK 3 T13: -0.0378 T23: -0.0366 REMARK 3 L TENSOR REMARK 3 L11: 0.9035 L22: 0.3116 REMARK 3 L33: -0.0340 L12: 0.0203 REMARK 3 L13: -0.8222 L23: -0.8207 REMARK 3 S TENSOR REMARK 3 S11: 0.0187 S12: 0.2239 S13: -0.1741 REMARK 3 S21: -0.2627 S22: -0.0740 S23: 0.3357 REMARK 3 S31: 0.1329 S32: -0.0070 S33: 0.0012 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2854 37.5468 61.3536 REMARK 3 T TENSOR REMARK 3 T11: 0.2307 T22: 0.2620 REMARK 3 T33: 0.2892 T12: 0.0183 REMARK 3 T13: 0.0200 T23: -0.0234 REMARK 3 L TENSOR REMARK 3 L11: 0.1257 L22: 0.2222 REMARK 3 L33: 0.2215 L12: 0.8827 REMARK 3 L13: 0.8011 L23: 0.3979 REMARK 3 S TENSOR REMARK 3 S11: 0.2256 S12: -0.2823 S13: -0.0537 REMARK 3 S21: 0.3470 S22: -0.2752 S23: -0.1352 REMARK 3 S31: 0.0564 S32: 0.0139 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 3 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1064 28.7719 40.3969 REMARK 3 T TENSOR REMARK 3 T11: 0.2857 T22: 0.2438 REMARK 3 T33: 0.2467 T12: -0.0445 REMARK 3 T13: -0.0116 T23: -0.0553 REMARK 3 L TENSOR REMARK 3 L11: 0.0338 L22: 0.0240 REMARK 3 L33: 0.6601 L12: -0.3453 REMARK 3 L13: -0.3059 L23: -0.4514 REMARK 3 S TENSOR REMARK 3 S11: -0.0711 S12: -0.2600 S13: -0.1189 REMARK 3 S21: -0.1480 S22: 0.1617 S23: -0.0126 REMARK 3 S31: 0.0541 S32: 0.0642 S33: 0.0002 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 27 THROUGH 35 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.2961 45.4966 34.2446 REMARK 3 T TENSOR REMARK 3 T11: 0.2677 T22: 0.5010 REMARK 3 T33: 0.5372 T12: -0.0222 REMARK 3 T13: 0.1894 T23: 0.1522 REMARK 3 L TENSOR REMARK 3 L11: 1.2147 L22: 0.7126 REMARK 3 L33: 1.5444 L12: 0.0969 REMARK 3 L13: 1.0466 L23: 0.7622 REMARK 3 S TENSOR REMARK 3 S11: 0.3677 S12: -0.1234 S13: 0.3179 REMARK 3 S21: 0.6541 S22: 1.1766 S23: 0.5614 REMARK 3 S31: -0.2469 S32: -0.3769 S33: 0.4708 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 2 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.3920 30.0079 51.4449 REMARK 3 T TENSOR REMARK 3 T11: 0.2999 T22: 0.2176 REMARK 3 T33: 0.2710 T12: -0.0147 REMARK 3 T13: 0.0336 T23: -0.0176 REMARK 3 L TENSOR REMARK 3 L11: 0.2895 L22: 0.2373 REMARK 3 L33: 1.0068 L12: 0.0694 REMARK 3 L13: 0.0034 L23: -0.2536 REMARK 3 S TENSOR REMARK 3 S11: -0.0206 S12: 0.3528 S13: -0.0519 REMARK 3 S21: 0.3981 S22: 0.2229 S23: 0.1058 REMARK 3 S31: 0.0946 S32: -0.2714 S33: 0.0232 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 27 THROUGH 35 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4818 48.6463 52.0183 REMARK 3 T TENSOR REMARK 3 T11: 0.3151 T22: 0.4072 REMARK 3 T33: 0.5068 T12: 0.0223 REMARK 3 T13: 0.1238 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 1.3353 L22: 0.3347 REMARK 3 L33: 1.8105 L12: 0.3080 REMARK 3 L13: 1.4775 L23: 0.4236 REMARK 3 S TENSOR REMARK 3 S11: 0.1732 S12: 0.0832 S13: 0.4272 REMARK 3 S21: -1.0324 S22: 0.1259 S23: -0.4064 REMARK 3 S31: 0.1102 S32: -0.4344 S33: 1.3651 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 6LVN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1300015571. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4862 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.469 REMARK 200 RESOLUTION RANGE LOW (A) : 26.894 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.13240 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 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: 1WYY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS HCL, PH 8.5, 25% PEG3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 14.09750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.78800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.86450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.78800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.09750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.86450 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: 5670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 14.09750 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 74.59350 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 89.57600 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 1 REMARK 465 LEU A 36 REMARK 465 ASP B 1 REMARK 465 ASP C 1 REMARK 465 ILE C 2 REMARK 465 LEU C 36 REMARK 465 ASP D 1 REMARK 465 LEU D 36 DBREF 6LVN A 1 36 UNP P0DTC2 SPIKE_SARS2 1168 1203 DBREF 6LVN B 1 36 UNP P0DTC2 SPIKE_SARS2 1168 1203 DBREF 6LVN C 1 36 UNP P0DTC2 SPIKE_SARS2 1168 1203 DBREF 6LVN D 1 36 UNP P0DTC2 SPIKE_SARS2 1168 1203 SEQRES 1 A 36 ASP ILE SER GLY ILE ASN ALA SER VAL VAL ASN ILE GLN SEQRES 2 A 36 LYS GLU ILE ASP ARG LEU ASN GLU VAL ALA LYS ASN LEU SEQRES 3 A 36 ASN GLU SER LEU ILE ASP LEU GLN GLU LEU SEQRES 1 B 36 ASP ILE SER GLY ILE ASN ALA SER VAL VAL ASN ILE GLN SEQRES 2 B 36 LYS GLU ILE ASP ARG LEU ASN GLU VAL ALA LYS ASN LEU SEQRES 3 B 36 ASN GLU SER LEU ILE ASP LEU GLN GLU LEU SEQRES 1 C 36 ASP ILE SER GLY ILE ASN ALA SER VAL VAL ASN ILE GLN SEQRES 2 C 36 LYS GLU ILE ASP ARG LEU ASN GLU VAL ALA LYS ASN LEU SEQRES 3 C 36 ASN GLU SER LEU ILE ASP LEU GLN GLU LEU SEQRES 1 D 36 ASP ILE SER GLY ILE ASN ALA SER VAL VAL ASN ILE GLN SEQRES 2 D 36 LYS GLU ILE ASP ARG LEU ASN GLU VAL ALA LYS ASN LEU SEQRES 3 D 36 ASN GLU SER LEU ILE ASP LEU GLN GLU LEU FORMUL 5 HOH *22(H2 O) HELIX 1 AA1 ILE A 2 GLU A 35 1 34 HELIX 2 AA2 SER B 3 GLU B 35 1 33 HELIX 3 AA3 GLY C 4 GLU C 35 1 32 HELIX 4 AA4 SER D 3 GLU D 35 1 33 CRYST1 28.195 49.729 89.576 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 0.035467 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020109 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011164 0.00000