HEADER VIRAL PROTEIN 05-SEP-22 8AZ9 OBSLTE 04-OCT-23 8AZ9 8CRM TITLE SARS-COV-2 NON-STRUCTURAL PROTEIN-1 (NSP1) IN COMPLEX WITH 1-(2-(3- TITLE 2 CHLOROPHENYL)THIAZOL-4-YL)-N-METHYLMETHANAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOST TRANSLATION INHIBITOR NSP1; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: LEADER PROTEIN,NON-STRUCTURAL PROTEIN 1,NSP1; 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: REP, 1A-1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, NON-STRUCTURAL PROTEIN-1, FRAGMENT HIT, COMPLEX, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.MA,S.DAMFO,M.W.BOWLER,N.PINOTSIS,F.KOZIELSKI REVDAT 4 14-FEB-24 8AZ9 1 REMARK REVDAT 3 04-OCT-23 8AZ9 1 OBSLTE REVDAT 2 26-APR-23 8AZ9 1 SOURCE DBREF REVDAT 1 23-NOV-22 8AZ9 0 JRNL AUTH S.MA,S.DAMFO,J.LOU,N.PINOTSIS,M.W.BOWLER,S.HAIDER, JRNL AUTH 2 F.KOZIELSKI JRNL TITL TWO LIGAND-BINDING SITES ON SARS-COV-2 NON-STRUCTURAL JRNL TITL 2 PROTEIN 1 REVEALED BY FRAGMENT-BASED X-RAY SCREENING. JRNL REF INT J MOL SCI V. 23 2022 JRNL REFN ESSN 1422-0067 JRNL PMID 36293303 JRNL DOI 10.3390/IJMS232012448 REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 19313 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 985 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 35.6300 - 2.7100 0.99 2826 155 0.1503 0.1892 REMARK 3 2 2.7100 - 2.1500 0.99 2621 153 0.1553 0.2015 REMARK 3 3 2.1500 - 1.8800 1.00 2633 140 0.1301 0.2096 REMARK 3 4 1.8800 - 1.7100 0.99 2599 109 0.1374 0.2315 REMARK 3 5 1.7100 - 1.5900 1.00 2566 143 0.1505 0.2319 REMARK 3 6 1.5900 - 1.4900 1.00 2555 149 0.1486 0.2373 REMARK 3 7 1.4900 - 1.4200 1.00 2528 136 0.2054 0.2703 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) : 21.300 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 : 0.012 999 REMARK 3 ANGLE : 1.319 1369 REMARK 3 CHIRALITY : 0.090 162 REMARK 3 PLANARITY : 0.009 181 REMARK 3 DIHEDRAL : 8.529 146 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 8AZ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292125424. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.965459 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22326 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 35.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 7.280 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.36 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: 8A55 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: COMMERCIAL SCREEN INDEX 44 (0.1 M REMARK 280 HEPES PH 7.5, 25% W/V PEG3350) WAS CHOSEN FOR SARS-COV-2 NSP1 REMARK 280 (RESIDUES 10 TO 126) CRYSTALLISATION IN LARGE QUANTITIES USING REMARK 280 HANGING DROP METHOD. FROZEN STOCKS OF SARS-COV-2 NSP1 (RESIDUES REMARK 280 10 TO 126) WERE THAWED ON ICE AND CENTRIFUGED IN A THERMO REMARK 280 SCIENTIFIC PICO 17 MICROCENTRIFUGE, 24-PL ROTOR AT 4 DEGREES, REMARK 280 20000 RPM FOR 10 MIN TO REMOVE AGGREGATES BEFORE THE REMARK 280 DETERMINATION OF THE PROTEIN CONCENTRATION. SUBSEQUENTLY, THE REMARK 280 PROTEIN STOCK WAS DILUTED TO 20 MG/ML WITH PRECRYSTALLISATION REMARK 280 BUFFER (10 MM HEPES AND 300 MM NACL). 400 UL OF INDEX CONDITION REMARK 280 44 WAS ADDED INTO EACH RESERVOIR WELL. FIVE PROTEIN DROPS WERE REMARK 280 SET ON EACH COVER SLIP BY MIXING 1 UL OF PROTEIN SOLUTION WITH 1 REMARK 280 UL OF THE RESERVOIR. THE 24-WELL LINBRO PLATES WERE INCUBATED AT REMARK 280 18 DEGREES., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 70.60250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.40850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.40850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 105.90375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.40850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.40850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.30125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.40850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.40850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 105.90375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.40850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.40850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.30125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 70.60250 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: 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 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 B 403 LIES ON A SPECIAL POSITION. 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 B 47 CE NZ REMARK 470 LYS B 58 CD CE NZ REMARK 470 ARG B 77 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 81 CG ND1 CD2 CE1 NE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER B 17 N CA C O CB OG REMARK 480 CYS B 51 CA CB SG 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 HZ1 LYS B 120 O HOH B 302 1.49 REMARK 500 O HOH B 304 O HOH B 316 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8A55 RELATED DB: PDB DBREF 8AZ9 B 10 126 UNP P0DTD1 R1AB_SARS2 10 126 SEQRES 1 B 117 GLU LYS THR HIS VAL GLN LEU SER LEU PRO VAL LEU GLN SEQRES 2 B 117 VAL ARG ASP VAL LEU VAL ARG GLY PHE GLY ASP SER VAL SEQRES 3 B 117 GLU GLU VAL LEU SER GLU ALA ARG GLN HIS LEU LYS ASP SEQRES 4 B 117 GLY THR CYS GLY LEU VAL GLU VAL GLU LYS GLY VAL LEU SEQRES 5 B 117 PRO GLN LEU GLU GLN PRO TYR VAL PHE ILE LYS ARG SER SEQRES 6 B 117 ASP ALA ARG THR ALA PRO HIS GLY HIS VAL MET VAL GLU SEQRES 7 B 117 LEU VAL ALA GLU LEU GLU GLY ILE GLN TYR GLY ARG SER SEQRES 8 B 117 GLY GLU THR LEU GLY VAL LEU VAL PRO HIS VAL GLY GLU SEQRES 9 B 117 ILE PRO VAL ALA TYR ARG LYS VAL LEU LEU ARG LYS ASN HET OF6 B 201 26 HETNAM OF6 1-[2-(3-CHLOROPHENYL)-1,3-THIAZOL-4-YL]-~{N}-METHYL- HETNAM 2 OF6 METHANAMINE HETSYN OF6 1-(2-(3-CHLOROPHENYL)THIAZOL-4-YL)-N-METHYLMETHANAMINE FORMUL 2 OF6 C11 H11 CL N2 S FORMUL 3 HOH *120(H2 O) HELIX 1 AA1 GLN B 22 VAL B 26 5 5 HELIX 2 AA2 SER B 34 GLY B 49 1 16 HELIX 3 AA3 VAL B 60 LEU B 64 5 5 HELIX 4 AA4 ALA B 79 HIS B 83 5 5 SHEET 1 AA1 8 ILE B 95 TYR B 97 0 SHEET 2 AA1 8 VAL B 84 LEU B 92 -1 N ALA B 90 O TYR B 97 SHEET 3 AA1 8 ALA B 117 ARG B 124 1 O LEU B 122 N VAL B 84 SHEET 4 AA1 8 HIS B 13 VAL B 20 -1 N VAL B 20 O ALA B 117 SHEET 5 AA1 8 CYS B 51 VAL B 54 1 O LEU B 53 N PRO B 19 SHEET 6 AA1 8 THR B 103 PRO B 109 -1 O VAL B 108 N GLY B 52 SHEET 7 AA1 8 TYR B 68 ARG B 73 -1 N ILE B 71 O LEU B 104 SHEET 8 AA1 8 VAL B 84 LEU B 92 -1 O VAL B 89 N PHE B 70 CISPEP 1 GLN B 66 PRO B 67 0 -9.33 CRYST1 36.817 36.817 141.205 90.00 90.00 90.00 P 43 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 0.027161 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007082 0.00000