HEADER HYDROLASE 13-MAR-26 29IK TITLE LASV CAP-SNATCHING ENDONUCLEASE, SFX APO STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-DIRECTED RNA POLYMERASE L; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN L,LARGE STRUCTURAL PROTEIN,REPLICASE,TRANSCRIPTASE; COMPND 5 EC: 2.7.7.48,3.1.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MAMMARENAVIRUS LASSAENSE; SOURCE 3 ORGANISM_TAXID: 3052310; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DRUG DEVELOPMENT, LASSA HEMORRHAGIC FEVER, L PROTEIN, ARENAVIRIDAE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.FALKE,P.Y.A.REINKE,J.M.SENST,P.LEWE,S.WITT,A.MEENTS,S.GUENTHER REVDAT 1 07-OCT-26 29IK 0 JRNL AUTH S.FALKE,P.Y.A.REINKE,D.ROSENBERG,P.FISCHER,J.MEYER, JRNL AUTH 2 M.GALCHENKOVA,A.TOLSTIKOVA,V.MARIANI,J.M.SENST,P.LEWE, JRNL AUTH 3 S.WITT,A.WAGNER,H.N.CHAPMAN,M.HUNTER,S.GUNTHER,A.MEENTS JRNL TITL PERSPECTIVES FOR PHARMACEUTICAL SCREENING AT XFEL SOURCES JRNL TITL 2 USING THE EXAMPLE OF LASSA VIRUS ENDONUCLEASE. JRNL REF ACTA CRYSTALLOGR D STRUCT 2026 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 42789322 JRNL DOI 10.1107/S2059798326009435 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 2.0-5936_9999 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14863 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1486 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 20.6000 - 4.5900 0.98 1312 146 0.2049 0.2277 REMARK 3 2 4.5900 - 3.6500 1.00 1254 139 0.1653 0.1630 REMARK 3 3 3.6500 - 3.1900 1.00 1229 137 0.1829 0.2062 REMARK 3 4 3.1900 - 2.9000 1.00 1222 136 0.2117 0.2864 REMARK 3 5 2.9000 - 2.6900 1.00 1211 135 0.2180 0.2752 REMARK 3 6 2.6900 - 2.5300 1.00 1196 132 0.2291 0.2761 REMARK 3 7 2.5300 - 2.4100 1.00 1194 134 0.2494 0.2908 REMARK 3 8 2.4100 - 2.3000 1.00 1201 133 0.2323 0.2646 REMARK 3 9 2.3000 - 2.2100 1.00 1194 132 0.2235 0.3080 REMARK 3 10 2.2100 - 2.1400 1.00 1177 130 0.2627 0.3287 REMARK 3 11 2.1400 - 2.0700 1.00 1187 132 0.3480 0.4000 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) : 0.297 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.196 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.77 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 : 0.007 1408 REMARK 3 ANGLE : 0.780 1905 REMARK 3 CHIRALITY : 0.048 221 REMARK 3 PLANARITY : 0.005 245 REMARK 3 DIHEDRAL : 16.439 541 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 29IK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAR-26. REMARK 100 THE DEPOSITION ID IS D_1292155009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-24 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : MFX REMARK 200 X-RAY GENERATOR MODEL : SLAC LCLS BEAMLINE MFX REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.265 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : SLAC EPIX10K 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14959 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 21.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 732.8 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AFTER LIMITED PROTEOLYSIS WITH REMARK 280 SUBTILISIN A, 7.5 MG/ML TARGET PROTEIN WERE MIXED WITH AN EQUAL REMARK 280 VOLUME OF CRYSTALLIZATION SOLUTION (10% W/V PEG 10000, 250 MM REMARK 280 MGSO4 AND 100 MM TRIS/HCL PH 9.0), BATCH MODE, TEMPERATURE 293K 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 67.69000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.13000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.13000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 101.53500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.13000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.13000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.84500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.13000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.13000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 101.53500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.13000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.13000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.84500 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 67.69000 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 ALA A 171 REMARK 465 GLN A 172 REMARK 465 GLU A 173 REMARK 465 SER A 174 REMARK 465 ASN A 175 REMARK 465 SER A 176 REMARK 465 LEU A 177 REMARK 465 PHE A 178 REMARK 465 GLU A 179 REMARK 465 GLU A 180 REMARK 465 SER A 181 REMARK 465 GLU A 182 REMARK 465 TYR A 183 REMARK 465 SER A 184 REMARK 465 ARG A 185 REMARK 465 LEU A 186 REMARK 465 CYS A 187 REMARK 465 GLU A 188 REMARK 465 SER A 189 REMARK 465 LEU A 190 REMARK 465 SER A 191 REMARK 465 MET A 192 REMARK 465 THR A 193 REMARK 465 SER A 194 REMARK 465 GLY A 195 REMARK 465 ARG A 196 REMARK 465 LEU A 197 REMARK 465 SER A 198 REMARK 465 GLY A 199 REMARK 465 VAL A 200 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 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 89 OD1 REMARK 620 2 HOH A 401 O 86.4 REMARK 620 3 HOH A 411 O 85.9 154.5 REMARK 620 4 HOH A 414 O 83.2 76.4 78.6 REMARK 620 5 HOH A 420 O 88.5 112.9 91.1 167.2 REMARK 620 6 HOH A 430 O 178.0 92.3 95.9 98.0 90.6 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 28UA RELATED DB: PDB REMARK 900 RELATED ID: 28UB RELATED DB: PDB REMARK 900 RELATED ID: 28UC RELATED DB: PDB REMARK 900 RELATED ID: 28JG RELATED DB: PDB REMARK 900 RELATED ID: 28JH RELATED DB: PDB REMARK 900 RELATED ID: 28JI RELATED DB: PDB DBREF 29IK A 1 200 UNP Q6GWS2 Q6GWS2_LASSJ 1 200 SEQRES 1 A 200 MET GLU GLU ASP ILE ALA CYS VAL LYS ASP LEU VAL SER SEQRES 2 A 200 LYS TYR LEU VAL ASP ASN GLU ARG LEU SER ARG GLN LYS SEQRES 3 A 200 LEU ALA PHE LEU VAL GLN THR GLU PRO ARG MET LEU LEU SEQRES 4 A 200 MET GLU GLY LEU LYS LEU LEU SER LEU CYS ILE GLU VAL SEQRES 5 A 200 ASP SER CYS ASN ALA ASN GLY CYS GLU HIS ASN SER GLU SEQRES 6 A 200 ASP LYS SER VAL GLU ARG ILE LEU HIS ASP HIS GLY ILE SEQRES 7 A 200 LEU THR PRO SER LEU CSO PHE VAL VAL PRO ASP GLY TYR SEQRES 8 A 200 LYS LEU THR GLY ASN VAL LEU ILE LEU LEU GLU CYS PHE SEQRES 9 A 200 VAL ARG SER SER PRO ALA ASN PHE GLU GLN LYS TYR ILE SEQRES 10 A 200 GLU ASP PHE LYS LYS LEU GLU GLN LEU LYS GLU ASP LEU SEQRES 11 A 200 LYS SER VAL ASP ILE ASN LEU ILE PRO LEU ILE ASP GLY SEQRES 12 A 200 ARG THR SER PHE TYR ASN GLU GLN ILE PRO ASP TRP VAL SEQRES 13 A 200 ASN ASP LYS LEU ARG ASP THR LEU PHE SER LEU LEU LYS SEQRES 14 A 200 TYR ALA GLN GLU SER ASN SER LEU PHE GLU GLU SER GLU SEQRES 15 A 200 TYR SER ARG LEU CYS GLU SER LEU SER MET THR SER GLY SEQRES 16 A 200 ARG LEU SER GLY VAL MODRES 29IK CSO A 84 CYS MODIFIED RESIDUE HET CSO A 84 7 HET MG A 301 1 HETNAM CSO S-HYDROXYCYSTEINE HETNAM MG MAGNESIUM ION FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 MG MG 2+ FORMUL 3 HOH *30(H2 O) HELIX 1 AA1 MET A 1 LYS A 14 1 14 HELIX 2 AA2 ASN A 19 VAL A 31 1 13 HELIX 3 AA3 GLU A 34 GLY A 59 1 26 HELIX 4 AA4 SER A 68 HIS A 76 1 9 HELIX 5 AA5 SER A 108 GLN A 125 1 18 HELIX 6 AA6 LEU A 126 SER A 132 1 7 HELIX 7 AA7 PRO A 153 LYS A 169 1 17 SHEET 1 AA1 4 GLU A 61 HIS A 62 0 SHEET 2 AA1 4 GLY A 90 THR A 94 -1 O TYR A 91 N GLU A 61 SHEET 3 AA1 4 VAL A 97 VAL A 105 -1 O ILE A 99 N LYS A 92 SHEET 4 AA1 4 ASN A 136 ARG A 144 1 O LEU A 140 N LEU A 100 LINK C LEU A 83 N CSO A 84 1555 1555 1.33 LINK C CSO A 84 N PHE A 85 1555 1555 1.32 LINK OD1 ASP A 89 MG MG A 301 1555 1555 1.96 LINK MG MG A 301 O HOH A 401 1555 1555 2.23 LINK MG MG A 301 O HOH A 411 1555 1555 2.12 LINK MG MG A 301 O HOH A 414 1555 1555 2.26 LINK MG MG A 301 O HOH A 420 1555 1555 2.32 LINK MG MG A 301 O HOH A 430 1555 1555 2.04 CRYST1 58.260 58.260 135.380 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 0.017164 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017164 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007387 0.00000 CONECT 647 653 CONECT 653 647 654 CONECT 654 653 655 657 CONECT 655 654 656 CONECT 656 655 659 CONECT 657 654 658 660 CONECT 658 657 CONECT 659 656 CONECT 660 657 CONECT 698 1385 CONECT 1385 698 1386 1396 1399 CONECT 1385 1405 1415 CONECT 1386 1385 CONECT 1396 1385 CONECT 1399 1385 CONECT 1405 1385 CONECT 1415 1385 MASTER 275 0 2 7 4 0 0 6 1404 1 17 16 END