HEADER VIRAL PROTEIN 11-APR-15 4Z9P TITLE CRYSTAL STRUCTURE OF EBOLA VIRUS NUCLEOPROTEIN CORE DOMAIN AT 1.8A TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CORE DOMAIN (UNP RESIDUES 36-351); COMPND 5 SYNONYM: NUCLEOCAPSID PROTEIN,PROTEIN N; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZAIRE EBOLAVIRUS (STRAIN MAYINGA-76); SOURCE 3 ORGANISM_COMMON: ZEBOV; SOURCE 4 ORGANISM_TAXID: 128952; SOURCE 5 STRAIN: MAYINGA-76; SOURCE 6 GENE: NP; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EBOLA, FILOVIRIDAE, NUCLEOPROTEIN, RNA BINDING PROTEIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.GUO,S.S.DONG,P.YANG,G.B.LI,B.C.LIU,C.YANG,Z.H.RAO REVDAT 4 20-MAR-24 4Z9P 1 REMARK REVDAT 3 18-OCT-17 4Z9P 1 SOURCE REMARK REVDAT 2 03-JUN-15 4Z9P 1 REMARK REVDAT 1 20-MAY-15 4Z9P 0 JRNL AUTH S.DONG,P.YANG,G.LI,B.LIU,W.WANG,X.LIU,B.XIA,C.YANG,Z.LOU, JRNL AUTH 2 Y.GUO,Z.RAO JRNL TITL INSIGHT INTO THE EBOLA VIRUS NUCLEOCAPSID ASSEMBLY JRNL TITL 2 MECHANISM: CRYSTAL STRUCTURE OF EBOLA VIRUS NUCLEOPROTEIN JRNL TITL 3 CORE DOMAIN AT 1.8 A RESOLUTION. JRNL REF PROTEIN CELL V. 6 351 2015 JRNL REFN ESSN 1674-8018 JRNL PMID 25910597 JRNL DOI 10.1007/S13238-015-0163-3 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 29492 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1472 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 40.7297 - 3.9848 0.99 2721 159 0.1758 0.1901 REMARK 3 2 3.9848 - 3.1632 0.99 2610 124 0.1734 0.2239 REMARK 3 3 3.1632 - 2.7635 1.00 2610 129 0.2027 0.2302 REMARK 3 4 2.7635 - 2.5108 1.00 2572 126 0.1902 0.2292 REMARK 3 5 2.5108 - 2.3309 1.00 2540 144 0.1851 0.2355 REMARK 3 6 2.3309 - 2.1935 1.00 2558 116 0.2112 0.2514 REMARK 3 7 2.1935 - 2.0836 1.00 2492 153 0.1851 0.2359 REMARK 3 8 2.0836 - 1.9929 1.00 2551 113 0.1928 0.2405 REMARK 3 9 1.9929 - 1.9162 1.00 2524 136 0.2503 0.2837 REMARK 3 10 1.9162 - 1.8501 1.00 2496 141 0.2625 0.3099 REMARK 3 11 1.8501 - 1.7922 0.93 2346 131 0.2325 0.3119 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.57 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 : 0.007 2341 REMARK 3 ANGLE : 0.978 3154 REMARK 3 CHIRALITY : 0.044 359 REMARK 3 PLANARITY : 0.004 405 REMARK 3 DIHEDRAL : 15.232 858 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): 15.9015 21.3565 4.2416 REMARK 3 T TENSOR REMARK 3 T11: 0.1795 T22: 0.1913 REMARK 3 T33: 0.1251 T12: -0.0012 REMARK 3 T13: -0.0193 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 2.7176 L22: 1.9488 REMARK 3 L33: 0.6978 L12: 0.6181 REMARK 3 L13: -0.1114 L23: -0.1555 REMARK 3 S TENSOR REMARK 3 S11: -0.0369 S12: 0.1342 S13: -0.2547 REMARK 3 S21: -0.1271 S22: -0.0017 S23: 0.0217 REMARK 3 S31: 0.0431 S32: 0.0462 S33: 0.0180 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 4Z9P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208887. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97848 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29588 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.792 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.54600 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM AMMONIUM CITRATE TRIBASIC PH REMARK 280 7.0, 20% (W/V) PEG 3350, EVAPORATION, TEMPERATURE 289K 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 29.92250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 81.43850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.92250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 81.43850 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 436 LIES ON A SPECIAL POSITION. 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 123 REMARK 465 VAL A 124 REMARK 465 SER A 125 REMARK 465 SER A 126 REMARK 465 GLU A 139 REMARK 465 GLU A 140 REMARK 465 GLU A 141 REMARK 465 THR A 142 REMARK 465 THR A 143 REMARK 465 LYS A 257 REMARK 465 THR A 258 REMARK 465 GLU A 259 REMARK 465 ARG A 260 REMARK 465 GLY A 261 REMARK 465 ALA A 326 REMARK 465 HIS A 327 REMARK 465 GLY A 328 REMARK 465 SER A 329 REMARK 465 THR A 330 REMARK 465 LEU A 331 REMARK 465 ALA A 332 REMARK 465 GLY A 333 REMARK 465 VAL A 334 REMARK 465 GLU A 351 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 OE1 GLN A 341 NH1 ARG A 344 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 GLN A 67 -125.89 52.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 4Z9P A 36 351 UNP P18272 NCAP_EBOZM 36 351 SEQADV 4Z9P ALA A 35 UNP P18272 EXPRESSION TAG SEQRES 1 A 317 ALA VAL ARG GLN ARG VAL ILE PRO VAL TYR GLN VAL ASN SEQRES 2 A 317 ASN LEU GLU GLU ILE CYS GLN LEU ILE ILE GLN ALA PHE SEQRES 3 A 317 GLU ALA GLY VAL ASP PHE GLN GLU SER ALA ASP SER PHE SEQRES 4 A 317 LEU LEU MET LEU CYS LEU HIS HIS ALA TYR GLN GLY ASP SEQRES 5 A 317 TYR LYS LEU PHE LEU GLU SER GLY ALA VAL LYS TYR LEU SEQRES 6 A 317 GLU GLY HIS GLY PHE ARG PHE GLU VAL LYS LYS ARG ASP SEQRES 7 A 317 GLY VAL LYS ARG LEU GLU GLU LEU LEU PRO ALA VAL SER SEQRES 8 A 317 SER GLY LYS ASN ILE LYS ARG THR LEU ALA ALA MET PRO SEQRES 9 A 317 GLU GLU GLU THR THR GLU ALA ASN ALA GLY GLN PHE LEU SEQRES 10 A 317 SER PHE ALA SER LEU PHE LEU PRO LYS LEU VAL VAL GLY SEQRES 11 A 317 GLU LYS ALA CYS LEU GLU LYS VAL GLN ARG GLN ILE GLN SEQRES 12 A 317 VAL HIS ALA GLU GLN GLY LEU ILE GLN TYR PRO THR ALA SEQRES 13 A 317 TRP GLN SER VAL GLY HIS MET MET VAL ILE PHE ARG LEU SEQRES 14 A 317 MET ARG THR ASN PHE LEU ILE LYS PHE LEU LEU ILE HIS SEQRES 15 A 317 GLN GLY MET HIS MET VAL ALA GLY HIS ASP ALA ASN ASP SEQRES 16 A 317 ALA VAL ILE SER ASN SER VAL ALA GLN ALA ARG PHE SER SEQRES 17 A 317 GLY LEU LEU ILE VAL LYS THR VAL LEU ASP HIS ILE LEU SEQRES 18 A 317 GLN LYS THR GLU ARG GLY VAL ARG LEU HIS PRO LEU ALA SEQRES 19 A 317 ARG THR ALA LYS VAL LYS ASN GLU VAL ASN SER PHE LYS SEQRES 20 A 317 ALA ALA LEU SER SER LEU ALA LYS HIS GLY GLU TYR ALA SEQRES 21 A 317 PRO PHE ALA ARG LEU LEU ASN LEU SER GLY VAL ASN ASN SEQRES 22 A 317 LEU GLU HIS GLY LEU PHE PRO GLN LEU SER ALA ILE ALA SEQRES 23 A 317 LEU GLY VAL ALA THR ALA HIS GLY SER THR LEU ALA GLY SEQRES 24 A 317 VAL ASN VAL GLY GLU GLN TYR GLN GLN LEU ARG GLU ALA SEQRES 25 A 317 ALA THR GLU ALA GLU FORMUL 2 HOH *211(H2 O) HELIX 1 AA1 ASN A 48 ALA A 62 1 15 HELIX 2 AA2 PHE A 66 GLU A 68 5 3 HELIX 3 AA3 SER A 69 TYR A 83 1 15 HELIX 4 AA4 ASP A 86 GLU A 92 1 7 HELIX 5 AA5 SER A 93 GLY A 101 1 9 HELIX 6 AA6 ARG A 116 LEU A 121 5 6 HELIX 7 AA7 LYS A 128 ALA A 136 1 9 HELIX 8 AA8 ASN A 146 LEU A 156 1 11 HELIX 9 AA9 LYS A 160 VAL A 163 5 4 HELIX 10 AB1 GLY A 164 GLN A 182 1 19 HELIX 11 AB2 PRO A 188 GLN A 192 5 5 HELIX 12 AB3 SER A 193 ASN A 207 1 15 HELIX 13 AB4 ASN A 207 HIS A 220 1 14 HELIX 14 AB5 ASP A 226 ARG A 240 1 15 HELIX 15 AB6 LEU A 244 ILE A 254 1 11 HELIX 16 AB7 HIS A 265 ARG A 269 5 5 HELIX 17 AB8 THR A 270 LYS A 272 5 3 HELIX 18 AB9 VAL A 273 LYS A 289 1 17 HELIX 19 AC1 HIS A 290 ALA A 297 5 8 HELIX 20 AC2 GLY A 304 LEU A 312 5 9 HELIX 21 AC3 PHE A 313 THR A 325 1 13 HELIX 22 AC4 VAL A 336 ALA A 350 1 15 SHEET 1 AA1 2 ARG A 39 GLN A 45 0 SHEET 2 AA1 2 PHE A 104 LYS A 110 1 O ARG A 105 N ILE A 41 CRYST1 59.845 162.877 31.280 90.00 90.00 90.00 P 21 21 2 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 0.016710 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031969 0.00000