HEADER GENE REGULATION 25-JUL-20 7JJG TITLE CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN (BD2) OF HUMAN TAF1 BOUND TITLE 2 TO ATR KINASE INHIBITOR AZ20 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_VARIANT: RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PNIC28.BSA4 KEYWDS BROMODOMAIN, TAF1, NON-BET, BET, KINASE INHIBITOR, ATR, DUAL BRD- KEYWDS 2 KINASE, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.R.KARIM,E.SCHONBRUNN REVDAT 4 18-OCT-23 7JJG 1 REMARK REVDAT 3 23-MAR-22 7JJG 1 JRNL REVDAT 2 09-MAR-22 7JJG 1 JRNL REVDAT 1 28-JUL-21 7JJG 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21688 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1085 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 36.7100 - 3.2000 1.00 2732 144 0.1684 0.1924 REMARK 3 2 3.2000 - 2.5400 1.00 2602 137 0.1685 0.1856 REMARK 3 3 2.5400 - 2.2200 1.00 2563 135 0.1561 0.1863 REMARK 3 4 2.2200 - 2.0200 1.00 2568 135 0.1590 0.1869 REMARK 3 5 2.0200 - 1.8700 1.00 2548 134 0.1710 0.2213 REMARK 3 6 1.8700 - 1.7600 1.00 2535 134 0.1811 0.2103 REMARK 3 7 1.7600 - 1.6700 1.00 2530 133 0.1901 0.2130 REMARK 3 8 1.6700 - 1.6000 1.00 2525 133 0.2062 0.2331 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.15 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 7JJG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250872. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-18 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 : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21689 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 36.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.176 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.24 REMARK 200 R MERGE FOR SHELL (I) : 0.78100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.490 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 (%): 50.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 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 23.37000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.65500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.73500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.65500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.37000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.73500 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 VCD 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 GOL A 1703 DBREF 7JJG A 1501 1635 UNP P21675 TAF1_HUMAN 1522 1656 SEQADV 7JJG SER A 1499 UNP P21675 EXPRESSION TAG SEQADV 7JJG 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 VCD A1701 53 HET EDO A1702 10 HET GOL A1703 14 HETNAM VCD 4-{4-[(3R)-3-METHYLMORPHOLIN-4-YL]-6-[1- HETNAM 2 VCD (METHYLSULFONYL)CYCLOPROPYL]PYRIMIDIN-2-YL}-1H-INDOLE HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 VCD C21 H24 N4 O3 S FORMUL 3 EDO C2 H6 O2 FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *155(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 14 TRP A1526 PRO A1527 HIS A1530 PRO A1531 SITE 2 AC1 14 VAL A1532 ASN A1533 PHE A1536 ASN A1583 SITE 3 AC1 14 TYR A1589 TYR A1601 THR A1605 EDO A1702 SITE 4 AC1 14 HOH A1819 HOH A1843 SITE 1 AC2 6 ARG A1565 ASP A1608 VCD A1701 HOH A1807 SITE 2 AC2 6 HOH A1822 HOH A1830 SITE 1 AC3 5 ASP A1503 ALA A1506 LYS A1534 HIS A1610 SITE 2 AC3 5 GLU A1627 CRYST1 46.740 57.470 59.310 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 0.021395 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017400 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016861 0.00000