HEADER VIRAL PROTEIN 24-JUN-19 6S3A TITLE COXSACKIE B3 2C PROTEIN IN COMPLEX WITH S-FLUOXETINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2C PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: COXSACKIEVIRUS B3; SOURCE 3 ORGANISM_TAXID: 12072; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: T7 EXPRESS IQ (BIOLABS) KEYWDS 2C, ENTEROVIRUS, HELICASE, ATPASE, COMPLEX, ANTIVIRAL, PORZAC, KEYWDS 2 FLUOXETINE, REPURPOSING, COXSACKIEVIRUS, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.EL KAZZI,N.PAPAGEORGIOU,F.P.FERRON,L.BAUER,F.VAN KUPPEVELD, AUTHOR 2 B.COUTARD REVDAT 2 01-JUN-22 6S3A 1 JRNL REVDAT 1 13-JAN-21 6S3A 0 JRNL AUTH D.L.HURDISS,P.EL KAZZI,L.BAUER,N.PAPAGEORGIOU,F.P.FERRON, JRNL AUTH 2 T.DONSELAAR,A.L.W.VAN VLIET,T.M.SHAMORKINA,J.SNIJDER, JRNL AUTH 3 B.CANARD,E.DECROLY,A.BRANCALE,T.ZEEV-BEN-MORDEHAI,F.FORSTER, JRNL AUTH 4 F.J.M.VAN KUPPEVELD,B.COUTARD JRNL TITL FLUOXETINE TARGETS AN ALLOSTERIC SITE IN THE ENTEROVIRUS 2C JRNL TITL 2 AAA+ ATPASE AND STABILIZES A RING-SHAPED HEXAMERIC COMPLEX. JRNL REF SCI ADV V. 8 J7615 2022 JRNL REFN ESSN 2375-2548 JRNL PMID 34985963 JRNL DOI 10.1126/SCIADV.ABJ7615 REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 31556 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 6S3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1292102782. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976251 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33298 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 44.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.07759 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.890 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 (%): 42.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES 0.1M PH 6,5, PEG 5000 27, 2M REMARK 280 AMMONIUM SULFATE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 24.19900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.57600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.59150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.57600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.19900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.59150 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 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 GLY A 115 REMARK 465 SER A 116 REMARK 465 ASP A 160 REMARK 465 PRO A 161 REMARK 465 ASP A 162 REMARK 465 HIS A 163 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 LYS A 117 CG CD CE NZ 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 SER A 152 -155.10 -137.49 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 710 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A 711 DISTANCE = 6.55 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 269 SG REMARK 620 2 CYS A 273 SG 108.6 REMARK 620 3 CYS A 281 SG 117.5 106.5 REMARK 620 4 CYS A 286 SG 112.3 105.5 105.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SFX A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 403 DBREF 6S3A A 116 329 UNP Q9E7C2 Q9E7C2_9ENTO 1216 1429 SEQADV 6S3A GLY A 115 UNP Q9E7C2 EXPRESSION TAG SEQRES 1 A 215 GLY SER LYS CYS ARG ILE GLU PRO VAL CYS LEU LEU LEU SEQRES 2 A 215 HIS GLY SER PRO GLY ALA GLY LYS SER VAL ALA THR ASN SEQRES 3 A 215 LEU ILE GLY ARG SER LEU ALA GLU LYS LEU ASN SER SER SEQRES 4 A 215 VAL TYR SER LEU PRO PRO ASP PRO ASP HIS PHE ASP GLY SEQRES 5 A 215 TYR LYS GLN GLN ALA VAL VAL ILE MET ASP ASP LEU CYS SEQRES 6 A 215 GLN ASN PRO ASP GLY LYS ASP VAL SER LEU PHE CYS GLN SEQRES 7 A 215 MET VAL SER SER VAL ASP PHE VAL PRO PRO MET ALA ALA SEQRES 8 A 215 LEU GLU GLU LYS GLY ILE LEU PHE THR SER PRO PHE VAL SEQRES 9 A 215 LEU ALA SER THR ASN ALA GLY SER ILE ASN ALA PRO THR SEQRES 10 A 215 VAL SER ASP SER ARG ALA LEU ALA ARG ARG PHE HIS PHE SEQRES 11 A 215 ASP MET ASN ILE GLU VAL ILE SER MET TYR SER GLN ASN SEQRES 12 A 215 GLY LYS ILE ASN MET PRO MET SER VAL LYS THR CYS ASP SEQRES 13 A 215 ASP GLU CYS CYS PRO VAL ASN PHE LYS LYS CYS CYS PRO SEQRES 14 A 215 LEU VAL CYS GLY LYS ALA ILE GLN PHE ILE ASP ARG ARG SEQRES 15 A 215 THR GLN VAL ARG TYR SER LEU ASP MET LEU VAL THR GLU SEQRES 16 A 215 MET PHE ARG GLU TYR ASN HIS ARG HIS SER VAL GLY THR SEQRES 17 A 215 THR LEU GLU ALA LEU PHE GLN HET SFX A 401 40 HET ZN A 402 1 HET CL A 403 1 HETNAM SFX (3S)-N-METHYL-3-PHENYL-3-[4-(TRIFLUOROMETHYL) HETNAM 2 SFX PHENOXY]PROPAN-1-AMINE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETSYN SFX FLUOXETINE FORMUL 2 SFX C17 H18 F3 N O FORMUL 3 ZN ZN 2+ FORMUL 4 CL CL 1- FORMUL 5 HOH *211(H2 O) HELIX 1 AA1 GLY A 134 LEU A 150 1 17 HELIX 2 AA2 ASP A 183 VAL A 194 1 12 HELIX 3 AA3 MET A 203 GLU A 207 5 5 HELIX 4 AA4 THR A 231 PHE A 242 1 12 HELIX 5 AA5 ASN A 261 LYS A 267 1 7 HELIX 6 AA6 SER A 302 SER A 319 1 18 HELIX 7 AA7 SER A 319 ALA A 326 1 8 HELIX 8 AA8 LEU A 327 GLN A 329 5 3 SHEET 1 AA1 7 VAL A 154 SER A 156 0 SHEET 2 AA1 7 VAL A 172 LEU A 178 1 O ILE A 174 N TYR A 155 SHEET 3 AA1 7 PHE A 217 THR A 222 1 O LEU A 219 N MET A 175 SHEET 4 AA1 7 VAL A 123 HIS A 128 1 N LEU A 125 O ALA A 220 SHEET 5 AA1 7 PHE A 244 VAL A 250 1 O ILE A 248 N HIS A 128 SHEET 6 AA1 7 ILE A 290 ASP A 294 -1 O ILE A 293 N ASN A 247 SHEET 7 AA1 7 ARG A 300 TYR A 301 -1 O TYR A 301 N PHE A 292 SHEET 1 AA2 2 SER A 255 GLN A 256 0 SHEET 2 AA2 2 LYS A 259 ILE A 260 -1 O LYS A 259 N GLN A 256 LINK SG CYS A 269 ZN ZN A 402 1555 1555 2.30 LINK SG CYS A 273 ZN ZN A 402 1555 1555 2.39 LINK SG CYS A 281 ZN ZN A 402 1555 1555 2.35 LINK SG CYS A 286 ZN ZN A 402 1555 1555 2.29 SITE 1 AC1 7 ASP A 176 LEU A 178 CYS A 179 PRO A 182 SITE 2 AC1 7 ASP A 186 PHE A 190 LEU A 238 SITE 1 AC2 4 CYS A 269 CYS A 273 CYS A 281 CYS A 286 SITE 1 AC3 5 SER A 233 GLN A 291 HOH A 549 HOH A 631 SITE 2 AC3 5 HOH A 697 CRYST1 48.398 53.183 79.152 90.00 90.00 90.00 P 21 21 21 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 0.020662 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018803 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012634 0.00000