HEADER VIRAL PROTEIN 29-APR-21 7EQ4 TITLE CRYSTAL STRUCTURE OF THE N-TERMINUS OF NONSTRUCTURAL PROTEIN 1 FROM TITLE 2 SARS-COV-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOST TRANSLATION INHIBITOR NSP1; COMPND 3 CHAIN: A; 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_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS SARS-COV-2, NSP1, PROTEIN TRANSLATION, RIBOSOME, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,Z.KE,H.HU,K.ZHAO,J.XIAO,Y.XIA,Y.LI REVDAT 4 29-NOV-23 7EQ4 1 REMARK REVDAT 3 15-SEP-21 7EQ4 1 JRNL REVDAT 2 21-JUL-21 7EQ4 1 JRNL REVDAT 1 09-JUN-21 7EQ4 0 JRNL AUTH K.ZHAO,Z.KE,H.HU,Y.LIU,A.LI,R.HUA,F.GUO,J.XIAO,Y.ZHANG, JRNL AUTH 2 L.DUAN,X.F.YAN,Y.G.GAO,B.LIU,Y.XIA,Y.LI JRNL TITL STRUCTURAL BASIS AND FUNCTION OF THE N TERMINUS OF JRNL TITL 2 SARS-COV-2 NONSTRUCTURAL PROTEIN 1. JRNL REF MICROBIOL SPECTR V. 9 16921 2021 JRNL REFN ISSN 2165-0497 JRNL PMID 34132580 JRNL DOI 10.1128/SPECTRUM.00169-21 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 50465 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 2491 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 25.4600 - 3.2700 0.98 2598 149 0.1546 0.1761 REMARK 3 2 3.2700 - 2.6000 1.00 2667 130 0.1796 0.2058 REMARK 3 3 2.6000 - 2.2700 1.00 2663 138 0.1814 0.2133 REMARK 3 4 2.2700 - 2.0600 1.00 2694 140 0.1592 0.2222 REMARK 3 5 2.0600 - 1.9200 1.00 2653 121 0.1511 0.1734 REMARK 3 6 1.9200 - 1.8000 1.00 2662 164 0.1510 0.1878 REMARK 3 7 1.8000 - 1.7100 1.00 2668 131 0.1586 0.2118 REMARK 3 8 1.7100 - 1.6400 1.00 2690 133 0.1493 0.2091 REMARK 3 9 1.6400 - 1.5700 1.00 2651 135 0.1587 0.2242 REMARK 3 10 1.5700 - 1.5200 1.00 2628 161 0.1400 0.1899 REMARK 3 11 1.5200 - 1.4700 1.00 2681 147 0.1585 0.1744 REMARK 3 12 1.4700 - 1.4300 1.00 2681 128 0.1546 0.2104 REMARK 3 13 1.4300 - 1.3900 1.00 2664 145 0.1697 0.2133 REMARK 3 14 1.3900 - 1.3600 1.00 2602 154 0.1712 0.2672 REMARK 3 15 1.3600 - 1.3300 1.00 2723 142 0.1792 0.2193 REMARK 3 16 1.3300 - 1.3000 1.00 2644 102 0.1865 0.2436 REMARK 3 17 1.3000 - 1.2700 1.00 2728 109 0.1944 0.2139 REMARK 3 18 1.2700 - 1.2500 1.00 2677 162 0.2089 0.2409 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) : 0.093 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.562 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.13 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 : 0.005 885 REMARK 3 ANGLE : 0.900 1199 REMARK 3 CHIRALITY : 0.078 143 REMARK 3 PLANARITY : 0.005 155 REMARK 3 DIHEDRAL : 23.742 123 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 7EQ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1300022000. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-20 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9822 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 36.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.3300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 8.00 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: 2HSX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE MONOHYDRATE, 0.1 REMARK 280 M GLYCINE PH 9.5, 30% W/V POLYETHYLENE GLYCOL 4000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 70.27300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.30250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.30250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 105.40950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.30250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.30250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.13650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.30250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.30250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 105.40950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.30250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.30250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.13650 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 70.27300 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 281 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 285 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 MET A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 ALA A 8 REMARK 465 THR A 77 REMARK 465 ALA A 78 REMARK 465 PRO A 79 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 ARG A 72 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 76 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 80 CG ND1 CD2 CE1 NE2 DBREF 7EQ4 A 10 124 UNP P0DTD1 R1AB_SARS2 11 125 SEQADV 7EQ4 MET A 1 UNP P0DTD1 INITIATING METHIONINE SEQADV 7EQ4 HIS A 2 UNP P0DTD1 EXPRESSION TAG SEQADV 7EQ4 HIS A 3 UNP P0DTD1 EXPRESSION TAG SEQADV 7EQ4 HIS A 4 UNP P0DTD1 EXPRESSION TAG SEQADV 7EQ4 HIS A 5 UNP P0DTD1 EXPRESSION TAG SEQADV 7EQ4 HIS A 6 UNP P0DTD1 EXPRESSION TAG SEQADV 7EQ4 HIS A 7 UNP P0DTD1 EXPRESSION TAG SEQADV 7EQ4 ALA A 8 UNP P0DTD1 EXPRESSION TAG SEQADV 7EQ4 SER A 9 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 124 MET HIS HIS HIS HIS HIS HIS ALA SER LYS THR HIS VAL SEQRES 2 A 124 GLN LEU SER LEU PRO VAL LEU GLN VAL ARG ASP VAL LEU SEQRES 3 A 124 VAL ARG GLY PHE GLY ASP SER VAL GLU GLU VAL LEU SER SEQRES 4 A 124 GLU ALA ARG GLN HIS LEU LYS ASP GLY THR CYS GLY LEU SEQRES 5 A 124 VAL GLU VAL GLU LYS GLY VAL LEU PRO GLN LEU GLU GLN SEQRES 6 A 124 PRO TYR VAL PHE ILE LYS ARG SER ASP ALA ARG THR ALA SEQRES 7 A 124 PRO HIS GLY HIS VAL MET VAL GLU LEU VAL ALA GLU LEU SEQRES 8 A 124 GLU GLY ILE GLN TYR GLY ARG SER GLY GLU THR LEU GLY SEQRES 9 A 124 VAL LEU VAL PRO HIS VAL GLY GLU ILE PRO VAL ALA TYR SEQRES 10 A 124 ARG LYS VAL LEU LEU ARG LYS FORMUL 2 HOH *85(H2 O) HELIX 1 AA1 GLN A 21 VAL A 25 5 5 HELIX 2 AA2 SER A 33 GLY A 48 1 16 HELIX 3 AA3 VAL A 59 LEU A 63 5 5 SHEET 1 AA1 8 ILE A 94 TYR A 96 0 SHEET 2 AA1 8 VAL A 83 LEU A 91 -1 N ALA A 89 O TYR A 96 SHEET 3 AA1 8 ALA A 116 ARG A 123 1 O LEU A 121 N VAL A 83 SHEET 4 AA1 8 HIS A 12 VAL A 19 -1 N VAL A 19 O ALA A 116 SHEET 5 AA1 8 CYS A 50 VAL A 53 1 O LEU A 52 N PRO A 18 SHEET 6 AA1 8 THR A 102 PRO A 108 -1 O VAL A 107 N GLY A 51 SHEET 7 AA1 8 TYR A 67 ARG A 72 -1 N VAL A 68 O LEU A 106 SHEET 8 AA1 8 VAL A 83 LEU A 91 -1 O VAL A 88 N PHE A 69 CISPEP 1 GLN A 65 PRO A 66 0 -5.66 CRYST1 36.605 36.605 140.546 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 0.027319 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027319 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007115 0.00000