HEADER VIRAL PROTEIN 10-JUN-21 7F2B TITLE CRYSTAL STRUCTURE OF SARS-COV-2 NUCLEOCAPSID PROTEIN C-TERMINAL RNA TITLE 2 BINDING DOMAIN AT 2.0A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: N,NUCLEOCAPSID PROTEIN,NC,PROTEIN N; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SARS-COV-2, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.LIU,Y.W.CHEN REVDAT 3 29-NOV-23 7F2B 1 REMARK REVDAT 2 16-NOV-22 7F2B 1 JRNL REVDAT 1 01-SEP-21 7F2B 0 JRNL AUTH Z.JIA,C.LIU,Y.CHEN,H.JIANG,Z.WANG,J.YAO,J.YANG,J.ZHU, JRNL AUTH 2 B.ZHANG,Z.YUCHI JRNL TITL CRYSTAL STRUCTURES OF THE SARS-COV-2 NUCLEOCAPSID PROTEIN JRNL TITL 2 C-TERMINAL DOMAIN AND DEVELOPMENT OF NUCLEOCAPSID-TARGETING JRNL TITL 3 NANOBODIES. JRNL REF FEBS J. V. 289 3813 2022 JRNL REFN ISSN 1742-464X JRNL PMID 34665939 JRNL DOI 10.1111/FEBS.16239 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3247 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 13448 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1350 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 29.9640 - 4.3051 1.00 1211 137 0.1682 0.1856 REMARK 3 2 4.3051 - 3.4187 1.00 1200 139 0.1370 0.1891 REMARK 3 3 3.4187 - 2.9870 1.00 1221 127 0.1658 0.2367 REMARK 3 4 2.9870 - 2.7141 1.00 1199 141 0.1653 0.2168 REMARK 3 5 2.7141 - 2.5196 1.00 1203 136 0.1697 0.2323 REMARK 3 6 2.5196 - 2.3711 1.00 1222 135 0.1610 0.2305 REMARK 3 7 2.3711 - 2.2524 1.00 1210 125 0.1511 0.2306 REMARK 3 8 2.2524 - 2.1544 1.00 1198 141 0.1478 0.2226 REMARK 3 9 2.1544 - 2.0715 1.00 1214 131 0.1472 0.2256 REMARK 3 10 2.0715 - 2.0000 1.00 1220 138 0.1517 0.2297 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.51 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7F2B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022593. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : 6.2 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 : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26164 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.964 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.14100 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 (%): 42.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1M POTASSIUM REMARK 280 PHOSPHATE PH 6.2, 52% V/VPEG 200, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 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 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: 6020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 B 276 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 299 CG CD CE NZ REMARK 470 LYS B 338 CG CD CE NZ REMARK 470 LYS A 266 CG CD CE NZ REMARK 470 ARG A 276 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 280 CG CD OE1 OE2 REMARK 470 GLN A 289 CG CD OE1 NE2 REMARK 470 ARG A 293 CG CD NE CZ NH1 NH2 REMARK 470 THR A 325 OG1 CG2 REMARK 470 PRO A 326 CG CD REMARK 470 LYS A 347 CG CD CE NZ 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 B 567 O HOH B 585 2.06 REMARK 500 O HOH B 534 O HOH A 555 2.07 REMARK 500 O HOH B 553 O HOH A 579 2.08 REMARK 500 O HOH B 576 O HOH B 586 2.10 REMARK 500 O HOH A 576 O HOH A 579 2.12 REMARK 500 O HOH A 561 O HOH A 584 2.15 REMARK 500 O HOH B 582 O HOH B 591 2.15 REMARK 500 O HOH A 503 O HOH A 539 2.17 REMARK 500 OG1 THR A 362 O HOH A 501 2.18 REMARK 500 O HOH A 585 O HOH A 592 2.19 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 81.98 -157.85 REMARK 500 TYR A 268 80.65 -154.57 REMARK 500 REMARK 500 REMARK: NULL 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 A 594 DISTANCE = 5.90 ANGSTROMS DBREF 7F2B B 257 362 UNP P0DTC9 NCAP_SARS2 257 362 DBREF 7F2B A 257 362 UNP P0DTC9 NCAP_SARS2 257 362 SEQRES 1 B 106 LYS PRO ARG GLN LYS ARG THR ALA THR LYS ALA TYR ASN SEQRES 2 B 106 VAL THR GLN ALA PHE GLY ARG ARG GLY PRO GLU GLN THR SEQRES 3 B 106 GLN GLY ASN PHE GLY ASP GLN GLU LEU ILE ARG GLN GLY SEQRES 4 B 106 THR ASP TYR LYS HIS TRP PRO GLN ILE ALA GLN PHE ALA SEQRES 5 B 106 PRO SER ALA SER ALA PHE PHE GLY MET SER ARG ILE GLY SEQRES 6 B 106 MET GLU VAL THR PRO SER GLY THR TRP LEU THR TYR THR SEQRES 7 B 106 GLY ALA ILE LYS LEU ASP ASP LYS ASP PRO ASN PHE LYS SEQRES 8 B 106 ASP GLN VAL ILE LEU LEU ASN LYS HIS ILE ASP ALA TYR SEQRES 9 B 106 LYS THR SEQRES 1 A 106 LYS PRO ARG GLN LYS ARG THR ALA THR LYS ALA TYR ASN SEQRES 2 A 106 VAL THR GLN ALA PHE GLY ARG ARG GLY PRO GLU GLN THR SEQRES 3 A 106 GLN GLY ASN PHE GLY ASP GLN GLU LEU ILE ARG GLN GLY SEQRES 4 A 106 THR ASP TYR LYS HIS TRP PRO GLN ILE ALA GLN PHE ALA SEQRES 5 A 106 PRO SER ALA SER ALA PHE PHE GLY MET SER ARG ILE GLY SEQRES 6 A 106 MET GLU VAL THR PRO SER GLY THR TRP LEU THR TYR THR SEQRES 7 A 106 GLY ALA ILE LYS LEU ASP ASP LYS ASP PRO ASN PHE LYS SEQRES 8 A 106 ASP GLN VAL ILE LEU LEU ASN LYS HIS ILE ASP ALA TYR SEQRES 9 A 106 LYS THR HET PO4 B 401 5 HET PO4 B 402 5 HET CL A 401 2 HET PO4 A 402 5 HET PO4 A 403 5 HET PO4 A 404 5 HET PO4 A 405 5 HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION FORMUL 3 PO4 6(O4 P 3-) FORMUL 5 CL CL 1- FORMUL 10 HOH *189(H2 O) HELIX 1 AA1 PRO B 258 ARG B 262 5 5 HELIX 2 AA2 ASN B 269 GLY B 275 1 7 HELIX 3 AA3 ASP B 288 GLY B 295 1 8 HELIX 4 AA4 THR B 296 TYR B 298 5 3 HELIX 5 AA5 HIS B 300 GLN B 306 1 7 HELIX 6 AA6 SER B 310 SER B 318 1 9 HELIX 7 AA7 ASN B 345 ILE B 357 1 13 HELIX 8 AA8 ASP B 358 THR B 362 5 5 HELIX 9 AA9 PRO A 258 ARG A 262 5 5 HELIX 10 AB1 ASN A 269 GLY A 275 1 7 HELIX 11 AB2 ASP A 288 GLY A 295 1 8 HELIX 12 AB3 THR A 296 TYR A 298 5 3 HELIX 13 AB4 HIS A 300 GLN A 306 1 7 HELIX 14 AB5 SER A 310 SER A 318 1 9 HELIX 15 AB6 ASN A 345 ILE A 357 1 13 HELIX 16 AB7 ASP A 358 THR A 362 5 5 SHEET 1 AA1 4 ARG B 319 THR B 325 0 SHEET 2 AA1 4 GLY B 328 LYS B 338 -1 O TRP B 330 N GLU B 323 SHEET 3 AA1 4 THR A 329 LYS A 338 -1 O ILE A 337 N LEU B 331 SHEET 4 AA1 4 ARG A 319 VAL A 324 -1 N ARG A 319 O THR A 334 CRYST1 36.889 37.207 42.845 78.69 74.65 65.46 P 1 2 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 0.027108 -0.012378 -0.006255 0.00000 SCALE2 0.000000 0.029546 -0.002919 0.00000 SCALE3 0.000000 0.000000 0.024321 0.00000