HEADER VIRAL PROTEIN 05-SEP-22 8AZ8 TITLE SARS-COV-2 NON-STRUCTURAL PROTEIN-1 (NSP1) IN COMPLEX WITH 2- TITLE 2 (BENZYLAMINO)ETHAN-1-OL 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,N.PINOTSIS,M.W.BOWLER,F.KOZIELSKI REVDAT 2 31-JAN-24 8AZ8 1 REMARK REVDAT 1 23-NOV-22 8AZ8 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. 1.18 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) : 1.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 30521 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1531 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 35.4700 - 2.6200 1.00 3098 171 0.1701 0.2171 REMARK 3 2 2.6200 - 2.0800 1.00 2923 153 0.1682 0.1925 REMARK 3 3 2.0800 - 1.8200 1.00 2868 144 0.1492 0.1926 REMARK 3 4 1.8200 - 1.6500 1.00 2817 159 0.1514 0.1931 REMARK 3 5 1.6500 - 1.5300 1.00 2820 143 0.1408 0.1790 REMARK 3 6 1.5300 - 1.5000 1.00 1111 58 0.1324 0.2013 REMARK 3 7 1.4300 - 1.3700 0.99 2272 109 0.1541 0.2223 REMARK 3 8 1.3700 - 1.3100 1.00 2780 152 0.1619 0.2574 REMARK 3 9 1.3100 - 1.2600 1.00 2753 151 0.1738 0.1982 REMARK 3 10 1.2600 - 1.2200 1.00 2778 147 0.1864 0.2314 REMARK 3 11 1.2200 - 1.1800 1.00 2770 144 0.1946 0.2633 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.34 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 8AZ8 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_1292125416. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-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) : 0.96546 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30526 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.180 REMARK 200 RESOLUTION RANGE LOW (A) : 35.471 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 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 (%): 32.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 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 70.68300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.32150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.32150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 106.02450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.32150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.32150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.34150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.32150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.32150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 106.02450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.32150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.32150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.34150 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 70.68300 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 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 ASN B 126 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 MET B 9 CG SD CE REMARK 470 GLU B 10 CG CD OE1 OE2 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 THR B 78 OG1 CG2 REMARK 470 HIS B 81 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 124 CD NE CZ NH1 NH2 REMARK 470 LYS B 125 CG CD CE NZ 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 OE2 GLU B 41 O HOH B 301 2.13 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 HIS B 81 -128.56 58.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8A55 RELATED DB: PDB DBREF 8AZ8 B 10 126 UNP P0DTD1 R1AB_SARS2 10 126 SEQADV 8AZ8 MET B 9 UNP P0DTD1 INITIATING METHIONINE SEQRES 1 B 118 MET GLU LYS THR HIS VAL GLN LEU SER LEU PRO VAL LEU SEQRES 2 B 118 GLN VAL ARG ASP VAL LEU VAL ARG GLY PHE GLY ASP SER SEQRES 3 B 118 VAL GLU GLU VAL LEU SER GLU ALA ARG GLN HIS LEU LYS SEQRES 4 B 118 ASP GLY THR CYS GLY LEU VAL GLU VAL GLU LYS GLY VAL SEQRES 5 B 118 LEU PRO GLN LEU GLU GLN PRO TYR VAL PHE ILE LYS ARG SEQRES 6 B 118 SER ASP ALA ARG THR ALA PRO HIS GLY HIS VAL MET VAL SEQRES 7 B 118 GLU LEU VAL ALA GLU LEU GLU GLY ILE GLN TYR GLY ARG SEQRES 8 B 118 SER GLY GLU THR LEU GLY VAL LEU VAL PRO HIS VAL GLY SEQRES 9 B 118 GLU ILE PRO VAL ALA TYR ARG LYS VAL LEU LEU ARG LYS SEQRES 10 B 118 ASN HET OEI B 201 24 HETNAM OEI 2-[(PHENYLMETHYL)AMINO]ETHANOL HETSYN OEI 2-(BENZYLAMINO)ETHAN-1-OL FORMUL 2 OEI C9 H13 N O FORMUL 3 HOH *85(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 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 VAL B 69 O LEU B 107 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 -8.40 CRYST1 36.643 36.643 141.366 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 0.027290 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027290 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007074 0.00000