HEADER VIRAL PROTEIN 31-AUG-21 7VBF TITLE 1.3 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF SARS-COV-2 NUCLEOCAPSID TITLE 2 DIMERIZATION DOMAIN, PH 8.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DIMERIZATION DOMAIN; COMPND 5 SYNONYM: NUCLEOCAPSID PROTEIN,PROTEIN N; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SARS-COV-2, NUCLEOCAPSID DIMERIZATION DOMAIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.L.ZHOU,F.L.ZHONG,J.LI,J.ZHANG REVDAT 2 29-NOV-23 7VBF 1 REMARK REVDAT 1 06-JUL-22 7VBF 0 JRNL AUTH X.L.ZHOU,F.L.ZHONG,J.LI,J.ZHANG JRNL TITL 1.3 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF SARS-COV-2 JRNL TITL 2 NUCLEOCAPSID DIMERIZATION DOMAIN, PH 8.5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 112547 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.312 REMARK 3 FREE R VALUE TEST SET COUNT : 3727 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 18.1400 - 3.8877 1.00 4140 135 0.1626 0.1957 REMARK 3 2 3.8877 - 3.0907 1.00 4129 140 0.1762 0.1640 REMARK 3 3 3.0907 - 2.7015 1.00 4107 144 0.1888 0.2511 REMARK 3 4 2.7015 - 2.4551 1.00 4123 141 0.1987 0.2083 REMARK 3 5 2.4551 - 2.2795 1.00 4134 145 0.1923 0.2194 REMARK 3 6 2.2795 - 2.1453 1.00 4142 139 0.1809 0.1836 REMARK 3 7 2.1453 - 2.0380 1.00 4110 148 0.1791 0.2180 REMARK 3 8 2.0380 - 1.9494 1.00 4117 141 0.1829 0.1861 REMARK 3 9 1.9494 - 1.8745 1.00 4121 141 0.0000 0.1674 REMARK 3 10 1.8745 - 1.8098 1.00 4129 146 0.1808 0.2061 REMARK 3 11 1.8098 - 1.7533 1.00 4093 142 0.1854 0.1887 REMARK 3 12 1.7533 - 1.7032 1.00 4126 145 0.1873 0.2012 REMARK 3 13 1.7032 - 1.6584 1.00 4195 146 0.1834 0.1981 REMARK 3 14 1.6584 - 1.6180 1.00 4091 138 0.1826 0.2013 REMARK 3 15 1.6180 - 1.5812 1.00 4109 146 0.1754 0.1954 REMARK 3 16 1.5812 - 1.5476 1.00 4151 141 0.1836 0.2162 REMARK 3 17 1.5476 - 1.5166 1.00 4081 140 0.1805 0.1974 REMARK 3 18 1.5166 - 1.4880 1.00 4168 142 0.1932 0.2275 REMARK 3 19 1.4880 - 1.4615 1.00 4106 142 0.1948 0.2018 REMARK 3 20 1.4615 - 1.4367 1.00 4168 142 0.1986 0.2094 REMARK 3 21 1.4367 - 1.4135 1.00 4073 136 0.2119 0.2556 REMARK 3 22 1.4135 - 1.3918 1.00 4140 142 0.2140 0.2483 REMARK 3 23 1.3918 - 1.3713 0.98 4072 139 0.0000 0.2188 REMARK 3 24 1.3713 - 1.3520 0.95 3908 129 0.2465 0.2716 REMARK 3 25 1.3520 - 1.3338 0.89 3665 124 0.2604 0.2604 REMARK 3 26 1.3338 - 1.3165 0.82 3380 110 0.2705 0.2937 REMARK 3 27 1.3165 - 1.3000 0.73 3042 103 0.2756 0.2884 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) : 0.117 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.565 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.18 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 1874 REMARK 3 ANGLE : 0.839 2532 REMARK 3 CHIRALITY : 0.088 256 REMARK 3 PLANARITY : 0.007 334 REMARK 3 DIHEDRAL : 17.034 696 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7VBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1300023030. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 112547 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 18.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54900 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: PHENIX REMARK 200 STARTING MODEL: 6WJI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE MONOHYDRATE, 0.1 REMARK 280 M TRIS HYDROCHLORIDE PH 8.5, 30% W/V POLYETHYLENE GLYCOL 4000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 21.85500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.48500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.56500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.48500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.85500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.56500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 HIS B 249 REMARK 465 HIS B 250 REMARK 465 HIS B 251 REMARK 465 HIS B 252 REMARK 465 HIS B 253 REMARK 465 HIS B 254 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 482 O HOH B 465 2.09 REMARK 500 O HOH B 467 O HOH B 472 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 TYR B 268 89.21 -155.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 7VBF A 255 364 UNP P0DTC9 NCAP_SARS2 255 364 DBREF 7VBF B 255 364 UNP P0DTC9 NCAP_SARS2 255 364 SEQADV 7VBF HIS A 249 UNP P0DTC9 EXPRESSION TAG SEQADV 7VBF HIS A 250 UNP P0DTC9 EXPRESSION TAG SEQADV 7VBF HIS A 251 UNP P0DTC9 EXPRESSION TAG SEQADV 7VBF HIS A 252 UNP P0DTC9 EXPRESSION TAG SEQADV 7VBF HIS A 253 UNP P0DTC9 EXPRESSION TAG SEQADV 7VBF HIS A 254 UNP P0DTC9 EXPRESSION TAG SEQADV 7VBF HIS B 249 UNP P0DTC9 EXPRESSION TAG SEQADV 7VBF HIS B 250 UNP P0DTC9 EXPRESSION TAG SEQADV 7VBF HIS B 251 UNP P0DTC9 EXPRESSION TAG SEQADV 7VBF HIS B 252 UNP P0DTC9 EXPRESSION TAG SEQADV 7VBF HIS B 253 UNP P0DTC9 EXPRESSION TAG SEQADV 7VBF HIS B 254 UNP P0DTC9 EXPRESSION TAG SEQRES 1 A 116 HIS HIS HIS HIS HIS HIS SER LYS LYS PRO ARG GLN LYS SEQRES 2 A 116 ARG THR ALA THR LYS ALA TYR ASN VAL THR GLN ALA PHE SEQRES 3 A 116 GLY ARG ARG GLY PRO GLU GLN THR GLN GLY ASN PHE GLY SEQRES 4 A 116 ASP GLN GLU LEU ILE ARG GLN GLY THR ASP TYR LYS HIS SEQRES 5 A 116 TRP PRO GLN ILE ALA GLN PHE ALA PRO SER ALA SER ALA SEQRES 6 A 116 PHE PHE GLY MET SER ARG ILE GLY MET GLU VAL THR PRO SEQRES 7 A 116 SER GLY THR TRP LEU THR TYR THR GLY ALA ILE LYS LEU SEQRES 8 A 116 ASP ASP LYS ASP PRO ASN PHE LYS ASP GLN VAL ILE LEU SEQRES 9 A 116 LEU ASN LYS HIS ILE ASP ALA TYR LYS THR PHE PRO SEQRES 1 B 116 HIS HIS HIS HIS HIS HIS SER LYS LYS PRO ARG GLN LYS SEQRES 2 B 116 ARG THR ALA THR LYS ALA TYR ASN VAL THR GLN ALA PHE SEQRES 3 B 116 GLY ARG ARG GLY PRO GLU GLN THR GLN GLY ASN PHE GLY SEQRES 4 B 116 ASP GLN GLU LEU ILE ARG GLN GLY THR ASP TYR LYS HIS SEQRES 5 B 116 TRP PRO GLN ILE ALA GLN PHE ALA PRO SER ALA SER ALA SEQRES 6 B 116 PHE PHE GLY MET SER ARG ILE GLY MET GLU VAL THR PRO SEQRES 7 B 116 SER GLY THR TRP LEU THR TYR THR GLY ALA ILE LYS LEU SEQRES 8 B 116 ASP ASP LYS ASP PRO ASN PHE LYS ASP GLN VAL ILE LEU SEQRES 9 B 116 LEU ASN LYS HIS ILE ASP ALA TYR LYS THR PHE PRO FORMUL 3 HOH *189(H2 O) HELIX 1 AA1 PRO A 258 ARG A 262 5 5 HELIX 2 AA2 ASN A 269 GLY A 275 1 7 HELIX 3 AA3 ASP A 288 GLY A 295 1 8 HELIX 4 AA4 THR A 296 TYR A 298 5 3 HELIX 5 AA5 HIS A 300 GLN A 306 1 7 HELIX 6 AA6 SER A 310 SER A 318 1 9 HELIX 7 AA7 ASN A 345 ILE A 357 1 13 HELIX 8 AA8 ASP A 358 PHE A 363 5 6 HELIX 9 AA9 PRO B 258 ARG B 262 5 5 HELIX 10 AB1 ASN B 269 GLY B 275 1 7 HELIX 11 AB2 ASP B 288 GLY B 295 1 8 HELIX 12 AB3 THR B 296 TYR B 298 5 3 HELIX 13 AB4 HIS B 300 GLN B 306 1 7 HELIX 14 AB5 SER B 310 SER B 318 1 9 HELIX 15 AB6 ASN B 345 ILE B 357 1 13 HELIX 16 AB7 ASP B 358 PHE B 363 5 6 SHEET 1 AA1 4 ARG A 319 THR A 325 0 SHEET 2 AA1 4 GLY A 328 LYS A 338 -1 O THR A 334 N ARG A 319 SHEET 3 AA1 4 GLY B 328 LYS B 338 -1 O LEU B 331 N ILE A 337 SHEET 4 AA1 4 ARG B 319 THR B 325 -1 N ARG B 319 O THR B 334 CRYST1 43.710 65.130 84.970 90.00 90.00 90.00 P 21 21 21 8 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 0.022878 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015354 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011769 0.00000