HEADER RNA BINDING PROTEIN 21-JAN-25 9I2O TITLE PB2 CAP-BINDING DOMAIN OF HUMAN PATHOGENIC INFLUENZA A VIRUS H5N1 IN TITLE 2 COMPLEX WITH M7GTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYMERASE BASIC PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNA-DIRECTED RNA POLYMERASE SUBUNIT P3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS; SOURCE 3 ORGANISM_TAXID: 11320; SOURCE 4 GENE: PB2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS AVIAN INFLUENZA, RNA CAPPING, POLYMERASE COMPLEX, DRUG DEVELOPMENT, KEYWDS 2 RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.FALKE,P.LEWE,S.WITT,C.WRENGER,A.MEENTS REVDAT 1 29-JAN-25 9I2O 0 JRNL AUTH S.FALKE,P.LEWE,S.WITT,C.WRENGER,A.MEENTS JRNL TITL PB2 CAP-BINDING DOMAIN OF HUMAN PATHOGENIC INFLUENZA A VIRUS JRNL TITL 2 H5N1 IN COMPLEX WITH M7GTP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.72 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 43708 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3934 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 43.4400 - 5.2200 1.00 1423 146 0.1662 0.1836 REMARK 3 2 5.2100 - 4.1400 1.00 1414 149 0.1428 0.1562 REMARK 3 3 4.1400 - 3.6200 1.00 1410 150 0.1493 0.1602 REMARK 3 4 3.6200 - 3.2900 1.00 1440 127 0.1700 0.1858 REMARK 3 5 3.2800 - 3.0500 1.00 1419 132 0.1784 0.1829 REMARK 3 6 3.0500 - 2.8700 1.00 1438 144 0.1823 0.2239 REMARK 3 7 2.8700 - 2.7300 1.00 1393 136 0.1970 0.2339 REMARK 3 8 2.7300 - 2.6100 1.00 1433 150 0.1787 0.2058 REMARK 3 9 2.6100 - 2.5100 1.00 1444 146 0.1785 0.2162 REMARK 3 10 2.5100 - 2.4200 1.00 1408 133 0.1831 0.1635 REMARK 3 11 2.4200 - 2.3500 1.00 1415 141 0.1825 0.2372 REMARK 3 12 2.3500 - 2.2800 1.00 1439 130 0.1678 0.2017 REMARK 3 13 2.2800 - 2.2200 1.00 1417 142 0.1779 0.2171 REMARK 3 14 2.2200 - 2.1700 1.00 1441 142 0.1829 0.2764 REMARK 3 15 2.1700 - 2.1200 1.00 1421 137 0.1694 0.2810 REMARK 3 16 2.1200 - 2.0700 1.00 1421 143 0.1860 0.1963 REMARK 3 17 2.0700 - 2.0300 1.00 1401 142 0.1971 0.2190 REMARK 3 18 2.0300 - 1.9900 1.00 1420 141 0.1925 0.2613 REMARK 3 19 1.9900 - 1.9600 1.00 1443 140 0.2358 0.2736 REMARK 3 20 1.9600 - 1.9200 1.00 1433 146 0.2493 0.2562 REMARK 3 21 1.9200 - 1.8900 1.00 1387 138 0.2878 0.2726 REMARK 3 22 1.8900 - 1.8600 1.00 1413 140 0.2797 0.3019 REMARK 3 23 1.8600 - 1.8400 1.00 1447 140 0.2787 0.3116 REMARK 3 24 1.8400 - 1.8100 1.00 1424 140 0.3066 0.3240 REMARK 3 25 1.8100 - 1.7800 1.00 1412 142 0.3219 0.3336 REMARK 3 26 1.7800 - 1.7600 1.00 1423 142 0.3387 0.3644 REMARK 3 27 1.7600 - 1.7400 0.99 1446 136 0.3760 0.4312 REMARK 3 28 1.7400 - 1.7200 0.97 1349 139 0.4170 0.4029 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) : 0.289 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.489 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.79 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 : 0.008 1386 REMARK 3 ANGLE : 0.794 1872 REMARK 3 CHIRALITY : 0.060 207 REMARK 3 PLANARITY : 0.008 244 REMARK 3 DIHEDRAL : 16.444 547 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 9I2O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1292144375. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-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) : 1.033270 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 : 43754 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 43.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 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 <I/SIGMA(I)> 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 1.21.2-5419_9999 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PB2 CAP-BINDING DOMAIN (8 MG/ML) REMARK 280 IN COMPLEX WITH M7GTP WAS MIXED WITH CRYSTALLIZATION SOLUTION REMARK 280 (20% W/V PEG 6000, 1 M LITHIUM CHLORIDE, 0.1 M TRI-SODIUM REMARK 280 CITRATE AT PH 4.0) AT A RATIO OF 3:2 AND INCUBATED IN A SITTING REMARK 280 DROP VAPOR DIFFUSION PLATE., TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 36.67267 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 18.33633 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.50450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 9.16817 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 45.84083 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 MET A 296 REMARK 465 GLY A 297 REMARK 465 SER A 298 REMARK 465 SER A 299 REMARK 465 HIS A 300 REMARK 465 HIS A 301 REMARK 465 HIS A 302 REMARK 465 HIS A 303 REMARK 465 HIS A 304 REMARK 465 HIS A 305 REMARK 465 SER A 306 REMARK 465 SER A 307 REMARK 465 GLY A 308 REMARK 465 GLU A 309 REMARK 465 ASN A 310 REMARK 465 LEU A 311 REMARK 465 TYR A 312 REMARK 465 PHE A 313 REMARK 465 GLN A 314 REMARK 465 GLY A 315 REMARK 465 HIS A 316 REMARK 465 MET A 317 REMARK 465 ARG A 318 REMARK 465 ILE A 319 REMARK 465 SER A 320 DBREF 9I2O A 318 483 UNP Q6DNL8 PB2_I02A6 318 483 SEQADV 9I2O MET A 296 UNP Q6DNL8 INITIATING METHIONINE SEQADV 9I2O GLY A 297 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O SER A 298 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O SER A 299 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O HIS A 300 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O HIS A 301 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O HIS A 302 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O HIS A 303 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O HIS A 304 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O HIS A 305 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O SER A 306 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O SER A 307 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O GLY A 308 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O GLU A 309 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O ASN A 310 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O LEU A 311 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O TYR A 312 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O PHE A 313 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O GLN A 314 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O GLY A 315 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O HIS A 316 UNP Q6DNL8 EXPRESSION TAG SEQADV 9I2O MET A 317 UNP Q6DNL8 EXPRESSION TAG SEQRES 1 A 188 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 188 GLU ASN LEU TYR PHE GLN GLY HIS MET ARG ILE SER SER SEQRES 3 A 188 SER PHE SER PHE GLY GLY PHE THR PHE LYS ARG THR SER SEQRES 4 A 188 GLY SER SER VAL LYS LYS GLU GLU GLU VAL LEU THR GLY SEQRES 5 A 188 ASN LEU GLN THR LEU LYS ILE ARG VAL HIS GLU GLY TYR SEQRES 6 A 188 GLU GLU PHE THR MET VAL GLY ARG ARG ALA THR ALA ILE SEQRES 7 A 188 LEU ARG LYS ALA THR ARG ARG LEU ILE GLN LEU ILE VAL SEQRES 8 A 188 SER GLY ARG ASP GLU GLN SER ILE ALA GLU ALA ILE ILE SEQRES 9 A 188 VAL ALA MET VAL PHE SER GLN GLU ASP CYS MET ILE LYS SEQRES 10 A 188 ALA VAL ARG GLY ASP LEU ASN PHE VAL ASN ARG ALA ASN SEQRES 11 A 188 GLN ARG LEU ASN PRO MET HIS GLN LEU LEU ARG HIS PHE SEQRES 12 A 188 GLN LYS ASP ALA LYS VAL LEU PHE GLN ASN TRP GLY ILE SEQRES 13 A 188 GLU PRO ILE ASP ASN VAL MET GLY MET ILE GLY ILE LEU SEQRES 14 A 188 PRO ASP MET THR PRO SER THR GLU MET SER LEU ARG GLY SEQRES 15 A 188 VAL ARG VAL SER LYS MET HET MGT A 501 49 HETNAM MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE FORMUL 2 MGT C11 H20 N5 O14 P3 FORMUL 3 HOH *71(H2 O) HELIX 1 AA1 ASP A 390 GLN A 406 1 17 HELIX 2 AA2 GLU A 407 LYS A 412 1 6 HELIX 3 AA3 ASN A 422 GLN A 426 5 5 HELIX 4 AA4 ASN A 429 ASP A 441 1 13 HELIX 5 AA5 ALA A 442 GLY A 450 1 9 SHEET 1 AA1 8 SER A 322 PHE A 325 0 SHEET 2 AA1 8 PHE A 328 GLY A 335 -1 O PHE A 330 N PHE A 323 SHEET 3 AA1 8 GLU A 361 VAL A 366 -1 O VAL A 366 N THR A 329 SHEET 4 AA1 8 ALA A 370 ALA A 377 -1 O LEU A 374 N PHE A 363 SHEET 5 AA1 8 ARG A 380 GLY A 388 -1 O GLN A 383 N ARG A 375 SHEET 6 AA1 8 VAL A 478 SER A 481 1 O SER A 481 N VAL A 386 SHEET 7 AA1 8 MET A 460 ILE A 463 -1 N ILE A 461 O VAL A 480 SHEET 8 AA1 8 PRO A 469 SER A 470 -1 O SER A 470 N GLY A 462 SHEET 1 AA2 2 VAL A 338 LEU A 345 0 SHEET 2 AA2 2 THR A 351 GLU A 358 -1 O GLU A 358 N VAL A 338 SHEET 1 AA3 2 ILE A 451 PRO A 453 0 SHEET 2 AA3 2 MET A 473 LEU A 475 -1 O SER A 474 N GLU A 452 CRYST1 81.750 81.750 55.009 90.00 90.00 120.00 P 65 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 0.012232 0.007062 0.000000 0.00000 SCALE2 0.000000 0.014125 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018179 0.00000