HEADER RNA BINDING PROTEIN 15-MAY-26 26UI TITLE DIMERIC C-TERMINAL DOMAIN OF NUCLEOCAPSID PROTEIN OF SARS-COV-2. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: C-TERMINAL DOMAIN OF NUCLEOCAPSID PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: N; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS N-CTD, NUCLEOCAPSID PROTEIN, SARS-COV-2, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.KHAKERWALA,A.KUMAR,S.SINGH,G.D.GUPTA,R.D.MAKDE REVDAT 1 27-MAY-26 26UI 0 JRNL AUTH Z.KHAKERWALA,A.KUMAR,S.SINGH,G.D.GUPTA,R.D.MAKDE JRNL TITL DIMERIC C-TERMINAL DOMAIN OF NUCLEOCAPSID PROTEIN OF JRNL TITL 2 SARS-COV-2. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 30272 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 828 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 30.0100 - 4.1100 0.95 2687 168 0.1462 0.1724 REMARK 3 2 4.1100 - 3.2600 0.94 2616 160 0.1379 0.1932 REMARK 3 3 3.2600 - 2.8500 0.95 2713 114 0.1613 0.2205 REMARK 3 4 2.8500 - 2.5900 0.95 2715 122 0.1686 0.2416 REMARK 3 5 2.5900 - 2.4100 0.94 2675 124 0.1876 0.2194 REMARK 3 6 2.4100 - 2.2600 0.93 2623 144 0.1887 0.2637 REMARK 3 7 2.2600 - 2.1500 0.93 2635 137 0.1848 0.2287 REMARK 3 8 2.1500 - 2.0600 0.94 2676 139 0.1923 0.2947 REMARK 3 9 2.0600 - 1.9800 0.93 2600 124 0.2079 0.2542 REMARK 3 10 1.9800 - 1.9100 0.91 2591 127 0.2323 0.2738 REMARK 3 11 1.9100 - 1.8500 0.79 2240 142 0.2688 0.3217 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.213 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.188 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.17 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 : 0.006 1807 REMARK 3 ANGLE : 0.781 2443 REMARK 3 CHIRALITY : 0.053 250 REMARK 3 PLANARITY : 0.008 323 REMARK 3 DIHEDRAL : 15.940 677 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): 13.5023 -4.9319 12.1989 REMARK 3 T TENSOR REMARK 3 T11: 0.1482 T22: 0.1530 REMARK 3 T33: 0.1499 T12: -0.0036 REMARK 3 T13: 0.0018 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 0.0970 L22: 0.1657 REMARK 3 L33: 0.2088 L12: -0.0546 REMARK 3 L13: 0.0892 L23: 0.0342 REMARK 3 S TENSOR REMARK 3 S11: 0.0182 S12: -0.0063 S13: 0.0021 REMARK 3 S21: 0.0091 S22: -0.0424 S23: 0.0084 REMARK 3 S31: 0.0097 S32: 0.0175 S33: 0.0000 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 26UI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAY-26. REMARK 100 THE DEPOSITION ID IS D_1300074337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97777 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30272 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 43.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.7 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM CHLORIDE, 0.1M SODIUM REMARK 280 ACETATE PH 5, 20% PEG 6000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.76350 REMARK 290 SMTRY3 2 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: 5160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 ALA A 253 REMARK 465 SER A 254 REMARK 465 LYS A 255 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 266 84.82 -154.15 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 610 DISTANCE = 7.00 ANGSTROMS REMARK 525 HOH B 523 DISTANCE = 6.02 ANGSTROMS DBREF 26UI A 253 419 UNP P0DTC9 NCAP_SARS2 254 364 DBREF 26UI B 252 362 UNP P0DTC9 NCAP_SARS2 254 364 SEQRES 1 A 111 ALA SER LYS LYS PRO ARG GLN LYS ARG THR ALA THR LYS SEQRES 2 A 111 ALA TYR ASN VAL THR GLN ALA PHE GLY ARG ARG GLY PRO SEQRES 3 A 111 GLU GLN THR GLN GLY ASN PHE GLY ASP GLN GLU LEU ILE SEQRES 4 A 111 ARG GLN GLY THR ASP TYR LYS HIS TRP PRO GLN ILE ALA SEQRES 5 A 111 GLN PHE ALA PRO SER ALA SER ALA PHE PHE GLY MET SER SEQRES 6 A 111 ARG ILE GLY MET GLU VAL THR PRO SER GLY THR TRP LEU SEQRES 7 A 111 THR TYR THR GLY ALA ILE LYS LEU ASP ASP LYS ASP PRO SEQRES 8 A 111 ASN PHE LYS ASP GLN VAL ILE LEU LEU ASN LYS HIS ILE SEQRES 9 A 111 ASP ALA TYR LYS THR PHE PRO SEQRES 1 B 111 ALA SER LYS LYS PRO ARG GLN LYS ARG THR ALA THR LYS SEQRES 2 B 111 ALA TYR ASN VAL THR GLN ALA PHE GLY ARG ARG GLY PRO SEQRES 3 B 111 GLU GLN THR GLN GLY ASN PHE GLY ASP GLN GLU LEU ILE SEQRES 4 B 111 ARG GLN GLY THR ASP TYR LYS HIS TRP PRO GLN ILE ALA SEQRES 5 B 111 GLN PHE ALA PRO SER ALA SER ALA PHE PHE GLY MET SER SEQRES 6 B 111 ARG ILE GLY MET GLU VAL THR PRO SER GLY THR TRP LEU SEQRES 7 B 111 THR TYR THR GLY ALA ILE LYS LEU ASP ASP LYS ASP PRO SEQRES 8 B 111 ASN PHE LYS ASP GLN VAL ILE LEU LEU ASN LYS HIS ILE SEQRES 9 B 111 ASP ALA TYR LYS THR PHE PRO FORMUL 3 HOH *233(H2 O) HELIX 1 AA1 PRO A 257 ARG A 261 5 5 HELIX 2 AA2 ASN A 268 GLY A 274 1 7 HELIX 3 AA3 ASP A 287 GLY A 294 1 8 HELIX 4 AA4 THR A 295 TYR A 297 5 3 HELIX 5 AA5 HIS A 299 GLN A 305 1 7 HELIX 6 AA6 SER A 309 SER A 373 1 9 HELIX 7 AA7 ASN A 400 ILE A 412 1 13 HELIX 8 AA8 ASP A 413 PHE A 418 5 6 HELIX 9 AA9 PRO B 256 ARG B 260 5 5 HELIX 10 AB1 ASN B 267 GLY B 273 1 7 HELIX 11 AB2 ASP B 286 GLY B 293 1 8 HELIX 12 AB3 THR B 294 TYR B 296 5 3 HELIX 13 AB4 HIS B 298 GLN B 304 1 7 HELIX 14 AB5 SER B 308 SER B 316 1 9 HELIX 15 AB6 ASN B 343 ILE B 355 1 13 HELIX 16 AB7 ASP B 356 PHE B 361 5 6 SHEET 1 AA1 4 ARG A 374 THR A 380 0 SHEET 2 AA1 4 GLY A 383 LYS A 393 -1 O THR A 389 N ARG A 374 SHEET 3 AA1 4 GLY B 326 LYS B 336 -1 O LEU B 329 N ILE A 392 SHEET 4 AA1 4 ARG B 317 THR B 323 -1 N ARG B 317 O THR B 332 CRYST1 43.463 43.527 54.969 90.00 107.58 90.00 P 1 21 1 4 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 0.023008 0.000000 0.007289 0.00000 SCALE2 0.000000 0.022974 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019083 0.00000 MASTER 252 0 0 16 4 0 0 6 1985 2 0 18 END