HEADER HYDROLASE 03-FEB-26 28JI TITLE LASV CAP-SNATCHING ENDONUCLEASE, CRYO 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 28JI 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. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2-5419_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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 30574 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1548 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 53.0800 - 3.5800 1.00 2856 168 0.1820 0.1876 REMARK 3 2 3.5800 - 2.8400 1.00 2713 145 0.2267 0.2565 REMARK 3 3 2.8400 - 2.4800 1.00 2654 147 0.2444 0.2771 REMARK 3 4 2.4800 - 2.2500 0.99 2594 159 0.2296 0.2638 REMARK 3 5 2.2500 - 2.0900 1.00 2643 122 0.2334 0.2354 REMARK 3 6 2.0900 - 1.9700 1.00 2607 137 0.2679 0.2717 REMARK 3 7 1.9700 - 1.8700 1.00 2586 142 0.2917 0.3415 REMARK 3 8 1.8700 - 1.7900 1.00 2610 136 0.2405 0.2693 REMARK 3 9 1.7900 - 1.7200 1.00 2599 123 0.2640 0.2511 REMARK 3 10 1.7200 - 1.6600 1.00 2580 139 0.2934 0.3243 REMARK 3 11 1.6600 - 1.6100 1.00 2584 130 0.3392 0.3484 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.533 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.61 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 1427 REMARK 3 ANGLE : 0.864 1928 REMARK 3 CHIRALITY : 0.054 222 REMARK 3 PLANARITY : 0.006 247 REMARK 3 DIHEDRAL : 14.194 551 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 28JI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1292151179. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-24 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 : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03322 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30633 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 53.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 26.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 : 1.300 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 (%): 57.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AFTER LIMITED PROTEOLYSIS WITH REMARK 280 SUBTILISIN A, 7.5 MG/ML PROTEIN WERE MIXED WITH AN EQUAL VOLUME REMARK 280 OF CRYSTALLIZATION SOLUTION (10% W/V PEG 10000, 250 MM MGSO4 AND REMARK 280 100 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 67.77550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.84350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.84350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 101.66325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.84350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.84350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.88775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.84350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.84350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 101.66325 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.84350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.84350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.88775 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 67.77550 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 TYR A 170 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 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 89 OD1 REMARK 620 2 HOH A 303 O 88.0 REMARK 620 3 HOH A 319 O 90.9 91.8 REMARK 620 4 HOH A 333 O 88.8 91.6 176.6 REMARK 620 5 HOH A 354 O 94.0 173.3 94.6 82.0 REMARK 620 6 HOH A 379 O 164.1 76.4 86.3 94.9 101.8 REMARK 620 N 1 2 3 4 5 DBREF 28JI 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 CYS 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 HET MG A 201 1 HET DTT A 202 8 HET DMS A 203 4 HET DMS A 204 10 HET SO4 A 205 5 HETNAM MG MAGNESIUM ION HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETNAM DMS DIMETHYL SULFOXIDE HETNAM SO4 SULFATE ION HETSYN DTT 1,4-DITHIOTHREITOL FORMUL 2 MG MG 2+ FORMUL 3 DTT C4 H10 O2 S2 FORMUL 4 DMS 2(C2 H6 O S) FORMUL 6 SO4 O4 S 2- FORMUL 7 HOH *93(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 ASN A 58 1 25 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 LEU A 167 1 15 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 ASP A 142 N GLU A 102 LINK SG CYS A 84 S4 DTT A 202 1555 1555 2.04 LINK OD1 ASP A 89 MG MG A 201 1555 1555 1.91 LINK MG MG A 201 O HOH A 303 1555 1555 2.29 LINK MG MG A 201 O HOH A 319 1555 1555 2.03 LINK MG MG A 201 O HOH A 333 1555 1555 2.04 LINK MG MG A 201 O HOH A 354 1555 1555 2.06 LINK MG MG A 201 O HOH A 379 1555 1555 2.17 CRYST1 57.687 57.687 135.551 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 0.017335 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017335 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007377 0.00000 CONECT 668 1395 CONECT 707 1387 CONECT 1387 707 1417 1433 1447 CONECT 1387 1468 1493 CONECT 1388 1389 CONECT 1389 1388 1390 CONECT 1390 1389 1391 1392 CONECT 1391 1390 CONECT 1392 1390 1393 1394 CONECT 1393 1392 CONECT 1394 1392 1395 CONECT 1395 668 1394 CONECT 1396 1397 1398 1399 CONECT 1397 1396 CONECT 1398 1396 CONECT 1399 1396 CONECT 1400 1401 1402 1403 CONECT 1401 1400 CONECT 1402 1400 1404 1405 1406 CONECT 1403 1400 1407 1408 1409 CONECT 1404 1402 CONECT 1405 1402 CONECT 1406 1402 CONECT 1407 1403 CONECT 1408 1403 CONECT 1409 1403 CONECT 1410 1411 1412 1413 1414 CONECT 1411 1410 CONECT 1412 1410 CONECT 1413 1410 CONECT 1414 1410 CONECT 1417 1387 CONECT 1433 1387 CONECT 1447 1387 CONECT 1468 1387 CONECT 1493 1387 MASTER 268 0 5 7 4 0 0 6 1475 1 36 16 END