HEADER VIRAL PROTEIN 30-AUG-22 8GQC TITLE CRYSTAL STRUCTURE OF THE SARS-UNIQUE DOMAIN (SUD) OF SARS-COV-2 (1.35 TITLE 2 ANGSTROM RESOLUTION) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPAIN-LIKE PROTEASE NSP3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SUD DOMAIN; COMPND 5 SYNONYM: NON-STRUCTURAL PROTEIN 3,NSP3,PL2-PRO,PAPAIN-LIKE COMPND 6 PROTEINASE,PL-PRO; COMPND 7 EC: 3.4.19.12,3.4.22.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, NSP3, SUD DOMAIN, G4-BINDING, VIRUS REPLICATION, DRUG KEYWDS 2 TARGET, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.QIN,Z.LI,S.AUMONIER,M.WANG,S.CUI REVDAT 3 14-FEB-24 8GQC 1 JRNL REVDAT 2 29-NOV-23 8GQC 1 REMARK REVDAT 1 12-JUL-23 8GQC 0 JRNL AUTH B.QIN,Z.LI,K.TANG,T.WANG,Y.XIE,S.AUMONIER,M.WANG,S.YUAN, JRNL AUTH 2 S.CUI JRNL TITL IDENTIFICATION OF THE SARS-UNIQUE DOMAIN OF SARS-COV-2 AS AN JRNL TITL 2 ANTIVIRAL TARGET. JRNL REF NAT COMMUN V. 14 3999 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37414753 JRNL DOI 10.1038/S41467-023-39709-6 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.4 REMARK 3 NUMBER OF REFLECTIONS : 55555 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 2713 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 37.8500 - 3.6000 1.00 3897 194 0.1496 0.1592 REMARK 3 2 3.6000 - 2.8600 1.00 3731 228 0.1427 0.1525 REMARK 3 3 2.8600 - 2.5000 1.00 3735 185 0.1349 0.1818 REMARK 3 4 2.5000 - 2.2700 1.00 3712 190 0.1345 0.1407 REMARK 3 5 2.2700 - 2.1100 1.00 3702 175 0.1115 0.1558 REMARK 3 6 2.1100 - 1.9800 1.00 3713 174 0.1262 0.1597 REMARK 3 7 1.9800 - 1.8800 1.00 3683 194 0.1167 0.1393 REMARK 3 8 1.8800 - 1.8000 1.00 3694 180 0.1217 0.1479 REMARK 3 9 1.8000 - 1.7300 1.00 3638 188 0.1296 0.1545 REMARK 3 10 1.7300 - 1.6700 1.00 3698 175 0.1427 0.2176 REMARK 3 11 1.6700 - 1.6200 1.00 3686 179 0.1544 0.1904 REMARK 3 12 1.6200 - 1.5700 1.00 3634 227 0.1680 0.2055 REMARK 3 13 1.5700 - 1.5300 0.85 3103 159 0.1730 0.2509 REMARK 3 14 1.5300 - 1.5000 0.57 2074 106 0.1737 0.2060 REMARK 3 15 1.5000 - 1.4600 0.40 1483 66 0.1987 0.2894 REMARK 3 16 1.4600 - 1.4300 0.24 860 43 0.2174 0.2932 REMARK 3 17 1.4300 - 1.4000 0.20 460 36 0.2339 0.2948 REMARK 3 18 1.4000 - 1.3800 0.20 250 13 0.2275 0.2499 REMARK 3 19 1.3800 - 1.3500 0.02 89 1 0.3159 0.2766 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 22.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.85 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 8GQC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300031866. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 274 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99995 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55560 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 37.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.1 REMARK 200 DATA REDUNDANCY IN SHELL : 19.40 REMARK 200 R MERGE FOR SHELL (I) : 1.73300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 2W2G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.20 M LITHIUM SULFATE MONOHYDRATE, REMARK 280 0.10 M TRIS PH= 8.50, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.59133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.18267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.18267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.59133 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 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 LYS A 413 REMARK 465 ILE A 414 REMARK 465 LYS A 415 REMARK 465 ALA A 416 REMARK 465 ALA A 488 REMARK 465 GLY A 489 REMARK 465 GLY A 490 REMARK 465 ILE A 541 REMARK 465 ILE A 542 REMARK 465 SER A 543 REMARK 465 ASN A 544 REMARK 465 GLU A 545 REMARK 465 LYS A 546 REMARK 465 GLN A 547 REMARK 465 GLU A 548 REMARK 465 ILE A 549 REMARK 465 SER A 675 REMARK 465 SER A 676 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 H ASP A 455 O HOH A 708 1.54 REMARK 500 OD1 ASP A 455 O HOH A 703 2.02 REMARK 500 O HOH A 813 O HOH A 1001 2.10 REMARK 500 O HOH A 832 O HOH A 927 2.11 REMARK 500 O HOH A 808 O HOH A 1009 2.16 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 ASP A 505 -176.46 -170.12 REMARK 500 CYS A 531 36.45 71.38 REMARK 500 VAL A 635 -58.71 69.94 REMARK 500 REMARK 500 REMARK: NULL DBREF 8GQC A 413 676 UNP P0DTC1 R1A_SARS2 1231 1494 SEQADV 8GQC CYS A 516 UNP P0DTC1 LEU 1334 ENGINEERED MUTATION SEQADV 8GQC CYS A 647 UNP P0DTC1 TYR 1465 ENGINEERED MUTATION SEQRES 1 A 264 LYS ILE LYS ALA CYS VAL GLU GLU VAL THR THR THR LEU SEQRES 2 A 264 GLU GLU THR LYS PHE LEU THR GLU ASN LEU LEU LEU TYR SEQRES 3 A 264 ILE ASP ILE ASN GLY ASN LEU HIS PRO ASP SER ALA THR SEQRES 4 A 264 LEU VAL SER ASP ILE ASP ILE THR PHE LEU LYS LYS ASP SEQRES 5 A 264 ALA PRO TYR ILE VAL GLY ASP VAL VAL GLN GLU GLY VAL SEQRES 6 A 264 LEU THR ALA VAL VAL ILE PRO THR LYS LYS ALA GLY GLY SEQRES 7 A 264 THR THR GLU MET LEU ALA LYS ALA LEU ARG LYS VAL PRO SEQRES 8 A 264 THR ASP ASN TYR ILE THR THR TYR PRO GLY GLN GLY CYS SEQRES 9 A 264 ASN GLY TYR THR VAL GLU GLU ALA LYS THR VAL LEU LYS SEQRES 10 A 264 LYS CYS LYS SER ALA PHE TYR ILE LEU PRO SER ILE ILE SEQRES 11 A 264 SER ASN GLU LYS GLN GLU ILE LEU GLY THR VAL SER TRP SEQRES 12 A 264 ASN LEU ARG GLU MET LEU ALA HIS ALA GLU GLU THR ARG SEQRES 13 A 264 LYS LEU MET PRO VAL CYS VAL GLU THR LYS ALA ILE VAL SEQRES 14 A 264 SER THR ILE GLN ARG LYS TYR LYS GLY ILE LYS ILE GLN SEQRES 15 A 264 GLU GLY VAL VAL ASP TYR GLY ALA ARG PHE TYR PHE TYR SEQRES 16 A 264 THR SER LYS THR THR VAL ALA SER LEU ILE ASN THR LEU SEQRES 17 A 264 ASN ASP LEU ASN GLU THR LEU VAL THR MET PRO LEU GLY SEQRES 18 A 264 TYR VAL THR HIS GLY LEU ASN LEU GLU GLU ALA ALA ARG SEQRES 19 A 264 CYS MET ARG SER LEU LYS VAL PRO ALA THR VAL SER VAL SEQRES 20 A 264 SER SER PRO ASP ALA VAL THR ALA TYR ASN GLY TYR LEU SEQRES 21 A 264 THR SER SER SER FORMUL 2 HOH *314(H2 O) HELIX 1 AA1 LEU A 425 LYS A 429 5 5 HELIX 2 AA2 HIS A 446 THR A 451 1 6 HELIX 3 AA3 ILE A 458 ASP A 464 1 7 HELIX 4 AA4 THR A 492 ARG A 500 1 9 HELIX 5 AA5 GLN A 514 GLY A 518 5 5 HELIX 6 AA6 THR A 520 LYS A 529 1 10 HELIX 7 AA7 ASN A 556 ARG A 568 1 13 HELIX 8 AA8 THR A 577 TYR A 588 1 12 HELIX 9 AA9 THR A 612 ASN A 624 1 13 HELIX 10 AB1 ASN A 640 ARG A 649 1 10 HELIX 11 AB2 SER A 661 SER A 674 1 14 SHEET 1 AA1 3 VAL A 418 GLU A 420 0 SHEET 2 AA1 3 ALA A 534 ILE A 537 1 O PHE A 535 N GLU A 419 SHEET 3 AA1 3 ASN A 506 THR A 509 1 N THR A 509 O TYR A 536 SHEET 1 AA2 3 LEU A 435 ILE A 439 0 SHEET 2 AA2 3 LEU A 478 VAL A 482 1 O THR A 479 N LEU A 437 SHEET 3 AA2 3 VAL A 472 GLU A 475 -1 N VAL A 473 O ALA A 480 SHEET 1 AA3 3 MET A 571 CYS A 574 0 SHEET 2 AA3 3 ARG A 603 TYR A 607 1 O TYR A 605 N VAL A 573 SHEET 3 AA3 3 GLY A 596 ASP A 599 -1 N GLY A 596 O PHE A 606 SHEET 1 AA4 2 LEU A 627 THR A 629 0 SHEET 2 AA4 2 ALA A 655 VAL A 657 1 O THR A 656 N LEU A 627 SSBOND 1 CYS A 516 CYS A 647 1555 1555 2.07 CISPEP 1 ALA A 465 PRO A 466 0 3.24 CRYST1 87.012 87.012 76.774 90.00 90.00 120.00 P 31 2 1 6 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 0.011493 0.006635 0.000000 0.00000 SCALE2 0.000000 0.013271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013025 0.00000