HEADER VIRAL PROTEIN 01-NOV-20 7DE1 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 NUCLEOCAPSID PROTEIN C-TERMINAL RNA TITLE 2 BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL RNA BINDING DOMAIN; COMPND 5 SYNONYM: N,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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, NUCLEOCAPSID PROTEIN, RNA BINDING, C-TERMINAL DOMAIN, KEYWDS 2 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.CHEN,S.KANG REVDAT 3 29-NOV-23 7DE1 1 REMARK REVDAT 2 10-FEB-21 7DE1 1 JRNL REVDAT 1 27-JAN-21 7DE1 0 JRNL AUTH M.YANG,S.HE,X.CHEN,Z.HUANG,Z.ZHOU,Z.ZHOU,Q.CHEN,S.CHEN, JRNL AUTH 2 S.KANG JRNL TITL STRUCTURAL INSIGHT INTO THE SARS-COV-2 NUCLEOCAPSID PROTEIN JRNL TITL 2 C-TERMINAL DOMAIN REVEALS A NOVEL RECOGNITION MECHANISM FOR JRNL TITL 3 VIRAL TRANSCRIPTIONAL REGULATORY SEQUENCES. JRNL REF FRONT CHEM V. 8 24765 2020 JRNL REFN ESSN 2296-2646 JRNL PMID 33511102 JRNL DOI 10.3389/FCHEM.2020.624765 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 18.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 19027 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1903 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 18.7900 - 4.8000 0.99 1326 147 0.1718 0.1921 REMARK 3 2 4.7900 - 3.8200 1.00 1256 140 0.1380 0.1980 REMARK 3 3 3.8200 - 3.3400 1.00 1256 139 0.1687 0.2130 REMARK 3 4 3.3400 - 3.0300 1.00 1229 137 0.1814 0.2300 REMARK 3 5 3.0300 - 2.8200 1.00 1226 137 0.1852 0.2056 REMARK 3 6 2.8200 - 2.6500 1.00 1222 135 0.1845 0.2822 REMARK 3 7 2.6500 - 2.5200 1.00 1211 135 0.1831 0.2349 REMARK 3 8 2.5200 - 2.4100 1.00 1215 135 0.1778 0.2351 REMARK 3 9 2.4100 - 2.3200 1.00 1224 135 0.1598 0.2453 REMARK 3 10 2.3200 - 2.2400 1.00 1214 136 0.1779 0.2375 REMARK 3 11 2.2400 - 2.1700 1.00 1204 133 0.1759 0.2355 REMARK 3 12 2.1700 - 2.1100 0.99 1212 135 0.1656 0.1970 REMARK 3 13 2.1100 - 2.0500 0.99 1179 132 0.1856 0.2399 REMARK 3 14 2.0500 - 2.0000 0.96 1150 127 0.1887 0.2718 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.97 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 7DE1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300019225. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.3 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 : RIGAKU 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 : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD RUBY CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19057 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 18.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05880 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.5800 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) : 0.21260 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: NULL REMARK 200 STARTING MODEL: 2CJR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CHES (PH 9.3) , 40% PEG 6000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 22.60700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.71900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.60700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.71900 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: 5840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 SER A 250 REMARK 465 ALA A 251 REMARK 465 ALA A 252 REMARK 465 GLU A 253 REMARK 465 ALA A 254 REMARK 465 SER A 255 REMARK 465 LYS A 256 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 A 268 81.61 -150.79 REMARK 500 TYR B 268 82.69 -155.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 403 DBREF 7DE1 A 250 364 UNP P0DTC9 NCAP_SARS2 250 364 DBREF 7DE1 B 250 364 UNP P0DTC9 NCAP_SARS2 250 364 SEQRES 1 A 115 SER ALA ALA GLU ALA SER LYS LYS PRO ARG GLN LYS ARG SEQRES 2 A 115 THR ALA THR LYS ALA TYR ASN VAL THR GLN ALA PHE GLY SEQRES 3 A 115 ARG ARG GLY PRO GLU GLN THR GLN GLY ASN PHE GLY ASP SEQRES 4 A 115 GLN GLU LEU ILE ARG GLN GLY THR ASP TYR LYS HIS TRP SEQRES 5 A 115 PRO GLN ILE ALA GLN PHE ALA PRO SER ALA SER ALA PHE SEQRES 6 A 115 PHE GLY MET SER ARG ILE GLY MET GLU VAL THR PRO SER SEQRES 7 A 115 GLY THR TRP LEU THR TYR THR GLY ALA ILE LYS LEU ASP SEQRES 8 A 115 ASP LYS ASP PRO ASN PHE LYS ASP GLN VAL ILE LEU LEU SEQRES 9 A 115 ASN LYS HIS ILE ASP ALA TYR LYS THR PHE PRO SEQRES 1 B 115 SER ALA ALA GLU ALA SER LYS LYS PRO ARG GLN LYS ARG SEQRES 2 B 115 THR ALA THR LYS ALA TYR ASN VAL THR GLN ALA PHE GLY SEQRES 3 B 115 ARG ARG GLY PRO GLU GLN THR GLN GLY ASN PHE GLY ASP SEQRES 4 B 115 GLN GLU LEU ILE ARG GLN GLY THR ASP TYR LYS HIS TRP SEQRES 5 B 115 PRO GLN ILE ALA GLN PHE ALA PRO SER ALA SER ALA PHE SEQRES 6 B 115 PHE GLY MET SER ARG ILE GLY MET GLU VAL THR PRO SER SEQRES 7 B 115 GLY THR TRP LEU THR TYR THR GLY ALA ILE LYS LEU ASP SEQRES 8 B 115 ASP LYS ASP PRO ASN PHE LYS ASP GLN VAL ILE LEU LEU SEQRES 9 B 115 ASN LYS HIS ILE ASP ALA TYR LYS THR PHE PRO HET PEG B 401 17 HET PEG B 402 17 HET PEG B 403 17 HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 3 PEG 3(C4 H10 O3) FORMUL 6 HOH *240(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 ALA B 251 SER B 255 1 5 HELIX 10 AB1 LYS B 256 LYS B 257 5 2 HELIX 11 AB2 PRO B 258 ARG B 262 5 5 HELIX 12 AB3 ASN B 269 GLY B 275 1 7 HELIX 13 AB4 ASP B 288 GLY B 295 1 8 HELIX 14 AB5 THR B 296 TYR B 298 5 3 HELIX 15 AB6 HIS B 300 GLN B 306 1 7 HELIX 16 AB7 SER B 310 SER B 318 1 9 HELIX 17 AB8 ASN B 345 ILE B 357 1 13 HELIX 18 AB9 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 GLY A 328 N THR A 325 SHEET 3 AA1 4 GLY B 328 LYS B 338 -1 O ILE B 337 N LEU A 331 SHEET 4 AA1 4 ARG B 319 THR B 325 -1 N ARG B 319 O THR B 334 SITE 1 AC1 3 ASP B 358 ALA B 359 THR B 362 SITE 1 AC2 2 GLN B 303 PEG B 403 SITE 1 AC3 6 VAL A 350 GLN B 303 LEU B 352 PEG B 402 SITE 2 AC3 6 HOH B 557 HOH B 584 CRYST1 45.214 101.438 59.526 90.00 90.00 90.00 P 21 21 2 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 0.022117 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016799 0.00000