HEADER GENE REGULATION 15-AUG-20 7JSP TITLE CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN (BD2) OF HUMAN TAF1 BOUND TITLE 2 TO ATR KINASE INHIBITOR AZD6738 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL CYCLE GENE 1 PROTEIN,TBP-ASSOCIATED FACTOR 250 KDA, COMPND 5 P250,TRANSCRIPTION INITIATION FACTOR TFIID 250 KDA SUBUNIT,TAFII250; COMPND 6 EC: 2.3.1.48,2.7.11.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TAF1, BA2R, CCG1, CCGS, TAF2A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28.BSA4 KEYWDS BROMODOMAIN, TAF1, NON-BET, BET, KINASE INHIBITOR, ATR, DUAL BRD- KEYWDS 2 KINASE, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.R.KARIM,E.SCHONBRUNN REVDAT 4 18-OCT-23 7JSP 1 REMARK REVDAT 3 23-MAR-22 7JSP 1 JRNL REVDAT 2 09-MAR-22 7JSP 1 JRNL REVDAT 1 25-AUG-21 7JSP 0 JRNL AUTH R.M.KARIM,L.YANG,L.CHEN,M.J.BIKOWITZ,J.LU,D.GRASSIE, JRNL AUTH 2 Z.P.SHULTZ,J.M.LOPCHUK,J.CHEN,E.SCHONBRUNN JRNL TITL DISCOVERY OF DUAL TAF1-ATR INHIBITORS AND LIGAND-INDUCED JRNL TITL 2 STRUCTURAL CHANGES OF THE TAF1 TANDEM BROMODOMAIN. JRNL REF J.MED.CHEM. V. 65 4182 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35191694 JRNL DOI 10.1021/ACS.JMEDCHEM.1C01999 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 17416 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1097 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 21.7000 - 3.4000 0.99 2221 149 0.1531 0.1706 REMARK 3 2 3.4000 - 2.7000 0.99 2116 143 0.1738 0.2247 REMARK 3 3 2.7000 - 2.3600 0.99 2089 140 0.1742 0.2128 REMARK 3 4 2.3600 - 2.1400 0.99 2069 139 0.1788 0.2126 REMARK 3 5 2.1400 - 1.9900 0.98 2030 137 0.1890 0.2201 REMARK 3 6 1.9900 - 1.8700 0.97 2024 136 0.1966 0.2272 REMARK 3 7 1.8700 - 1.7800 0.93 1942 130 0.2188 0.2407 REMARK 3 8 1.7800 - 1.7000 0.89 1828 123 0.2264 0.2744 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.98 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 : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1499 THROUGH 1528 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.6268 1.6832 55.3750 REMARK 3 T TENSOR REMARK 3 T11: 0.2140 T22: 0.1980 REMARK 3 T33: 0.2218 T12: 0.0511 REMARK 3 T13: 0.0129 T23: -0.0364 REMARK 3 L TENSOR REMARK 3 L11: 2.3496 L22: 5.5334 REMARK 3 L33: 2.8971 L12: 2.5780 REMARK 3 L13: 0.7048 L23: 0.4934 REMARK 3 S TENSOR REMARK 3 S11: 0.0288 S12: 0.1426 S13: -0.2450 REMARK 3 S21: 0.0032 S22: 0.0016 S23: -0.0444 REMARK 3 S31: 0.5523 S32: 0.1494 S33: -0.0103 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1529 THROUGH 1549 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.1967 15.8014 71.1121 REMARK 3 T TENSOR REMARK 3 T11: 0.2125 T22: 0.1971 REMARK 3 T33: 0.1717 T12: -0.0037 REMARK 3 T13: -0.0075 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 7.5406 L22: 4.4215 REMARK 3 L33: 4.0913 L12: 0.5444 REMARK 3 L13: 0.4626 L23: -0.3978 REMARK 3 S TENSOR REMARK 3 S11: -0.0330 S12: -0.4181 S13: 0.4260 REMARK 3 S21: 0.4761 S22: -0.0113 S23: 0.0958 REMARK 3 S31: -0.1909 S32: 0.2055 S33: 0.0460 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1550 THROUGH 1587 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.6276 8.9728 62.1108 REMARK 3 T TENSOR REMARK 3 T11: 0.1433 T22: 0.1511 REMARK 3 T33: 0.0901 T12: 0.0242 REMARK 3 T13: 0.0235 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 3.4146 L22: 5.4062 REMARK 3 L33: 2.3573 L12: 1.6635 REMARK 3 L13: 0.9191 L23: 0.8906 REMARK 3 S TENSOR REMARK 3 S11: 0.0246 S12: -0.0155 S13: 0.0909 REMARK 3 S21: 0.2076 S22: -0.0104 S23: 0.1404 REMARK 3 S31: 0.1792 S32: -0.0444 S33: -0.0237 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1588 THROUGH 1607 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.0584 12.8789 51.4986 REMARK 3 T TENSOR REMARK 3 T11: 0.1879 T22: 0.3057 REMARK 3 T33: 0.1818 T12: 0.0158 REMARK 3 T13: -0.0006 T23: 0.0247 REMARK 3 L TENSOR REMARK 3 L11: 4.4383 L22: 10.0405 REMARK 3 L33: 5.0013 L12: 5.3714 REMARK 3 L13: 3.9723 L23: 5.3830 REMARK 3 S TENSOR REMARK 3 S11: -0.1843 S12: 0.5016 S13: -0.0147 REMARK 3 S21: -0.2400 S22: 0.3583 S23: -0.1367 REMARK 3 S31: 0.0577 S32: 0.4286 S33: -0.1677 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1608 THROUGH 1635 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.6446 -12.3369 60.5659 REMARK 3 T TENSOR REMARK 3 T11: 0.4076 T22: 0.2975 REMARK 3 T33: 0.2703 T12: -0.1150 REMARK 3 T13: 0.0437 T23: -0.0325 REMARK 3 L TENSOR REMARK 3 L11: 6.9629 L22: 4.6275 REMARK 3 L33: 8.5984 L12: 5.4215 REMARK 3 L13: -7.5442 L23: -4.6416 REMARK 3 S TENSOR REMARK 3 S11: -0.0882 S12: 0.3151 S13: 0.1487 REMARK 3 S21: -0.0037 S22: 0.3507 S23: -0.0110 REMARK 3 S31: 0.1969 S32: -0.8001 S33: -0.0834 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 7JSP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000250869. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17425 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 21.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 4.951 REMARK 200 R MERGE (I) : 0.02200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 39.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.34 REMARK 200 R MERGE FOR SHELL (I) : 0.20300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.430 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: 3UV4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M CO(II) CHLORIDE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE (PH 4.6), 1 M 1,6-HEXANEDIOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 23.33500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.50000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.70500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.50000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.33500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.70500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue VJM A 1701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1703 DBREF 7JSP A 1501 1635 UNP P21675 TAF1_HUMAN 1522 1656 SEQADV 7JSP SER A 1499 UNP P21675 EXPRESSION TAG SEQADV 7JSP MET A 1500 UNP P21675 EXPRESSION TAG SEQRES 1 A 137 SER MET ASP ASP ASP GLN VAL ALA PHE SER PHE ILE LEU SEQRES 2 A 137 ASP ASN ILE VAL THR GLN LYS MET MET ALA VAL PRO ASP SEQRES 3 A 137 SER TRP PRO PHE HIS HIS PRO VAL ASN LYS LYS PHE VAL SEQRES 4 A 137 PRO ASP TYR TYR LYS VAL ILE VAL ASN PRO MET ASP LEU SEQRES 5 A 137 GLU THR ILE ARG LYS ASN ILE SER LYS HIS LYS TYR GLN SEQRES 6 A 137 SER ARG GLU SER PHE LEU ASP ASP VAL ASN LEU ILE LEU SEQRES 7 A 137 ALA ASN SER VAL LYS TYR ASN GLY PRO GLU SER GLN TYR SEQRES 8 A 137 THR LYS THR ALA GLN GLU ILE VAL ASN VAL CYS TYR GLN SEQRES 9 A 137 THR LEU THR GLU TYR ASP GLU HIS LEU THR GLN LEU GLU SEQRES 10 A 137 LYS ASP ILE CYS THR ALA LYS GLU ALA ALA LEU GLU GLU SEQRES 11 A 137 ALA GLU LEU GLU SER LEU ASP HET VJM A1701 53 HET EDO A1702 10 HET SO4 A1703 5 HETNAM VJM 4-(4-{1-[(R)-AMINO(HYDROXY)METHYL-LAMBDA~4~- HETNAM 2 VJM SULFANYL]CYCLOPROPYL}-6-[(3R)-3-METHYLMORPHOLIN-4- HETNAM 3 VJM YL]PYRIMIDIN-2-YL)-1H-PYRROLO[2,3-B]PYRIDINE HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 VJM C20 H26 N6 O2 S FORMUL 3 EDO C2 H6 O2 FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *117(H2 O) HELIX 1 AA1 SER A 1499 LYS A 1518 1 20 HELIX 2 AA2 SER A 1525 HIS A 1529 5 5 HELIX 3 AA3 ASP A 1539 ILE A 1544 1 6 HELIX 4 AA4 ASP A 1549 LYS A 1559 1 11 HELIX 5 AA5 SER A 1564 GLY A 1584 1 21 HELIX 6 AA6 SER A 1587 TYR A 1607 1 21 HELIX 7 AA7 TYR A 1607 LEU A 1634 1 28 SITE 1 AC1 13 TRP A1526 PRO A1527 HIS A1530 PRO A1531 SITE 2 AC1 13 VAL A1532 ASN A1533 PHE A1536 LEU A1569 SITE 3 AC1 13 ASN A1583 TYR A1589 TYR A1601 EDO A1702 SITE 4 AC1 13 HOH A1882 SITE 1 AC2 4 ARG A1565 VJM A1701 HOH A1818 HOH A1821 SITE 1 AC3 4 LYS A1581 TYR A1582 ASN A1583 GLY A1584 CRYST1 46.670 57.410 59.000 90.00 90.00 90.00 P 21 21 21 4 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 0.021427 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017419 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016949 0.00000