HEADER TRANSCRIPTION/INHIBITOR 25-JAN-23 8FXO TITLE BROMODOMAIN OF CBP LIGANDED WITH ICBP8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CREB-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN; COMPND 5 SYNONYM: HISTONE LYSINE ACETYLTRANSFERASE CREBBP,PROTEIN-LYSINE COMPND 6 ACETYLTRANSFERASE CREBBP; COMPND 7 EC: 2.3.1.48,2.3.1.-; COMPND 8 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: CREBBP, CBP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS BROMODOMAIN, SMALL MOLECULE LIGAND, COMPLEX, TRANSCRIPTION, KEYWDS 2 TRANSCRIPTION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.SCHONBRUNN,M.BIKOWITZ REVDAT 2 05-JUN-24 8FXO 1 JRNL REVDAT 1 07-FEB-24 8FXO 0 JRNL AUTH N.A.M.SHENDY,M.BIKOWITZ,L.H.SIGUA,Y.ZHANG,A.MERCIER, JRNL AUTH 2 Y.KHASHANA,S.NANCE,Q.LIU,I.M.DELAHUNTY,S.ROBINSON,V.GOEL, JRNL AUTH 3 M.G.REES,M.A.RONAN,T.WANG,M.KOCAK,J.A.ROTH,Y.WANG, JRNL AUTH 4 B.B.FREEMAN,B.A.ORR,B.J.ABRAHAM,M.F.ROUSSEL,E.SCHONBRUNN, JRNL AUTH 5 J.QI,A.D.DURBIN JRNL TITL GROUP 3 MEDULLOBLASTOMA TRANSCRIPTIONAL NETWORKS COLLAPSE JRNL TITL 2 UNDER DOMAIN SPECIFIC EP300/CBP INHIBITION. JRNL REF NAT COMMUN V. 15 3483 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38664416 JRNL DOI 10.1038/S41467-024-47102-0 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 12728 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1018 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 32.3400 - 3.3300 0.99 1753 153 0.1568 0.1743 REMARK 3 2 3.3300 - 2.6400 0.98 1686 147 0.1862 0.1985 REMARK 3 3 2.6400 - 2.3100 0.99 1689 146 0.1802 0.2149 REMARK 3 4 2.3100 - 2.1000 0.97 1667 145 0.1913 0.2325 REMARK 3 5 2.1000 - 1.9500 0.99 1686 147 0.1817 0.2668 REMARK 3 6 1.9500 - 1.8300 0.99 1669 144 0.1808 0.2415 REMARK 3 7 1.8300 - 1.7400 0.91 1560 136 0.2452 0.3014 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 NULL REMARK 3 ANGLE : 1.042 NULL REMARK 3 CHIRALITY : 0.057 144 REMARK 3 PLANARITY : 0.009 180 REMARK 3 DIHEDRAL : 15.930 137 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -13.2068 12.9891 6.5007 REMARK 3 T TENSOR REMARK 3 T11: 0.1465 T22: 0.1928 REMARK 3 T33: 0.1674 T12: 0.0237 REMARK 3 T13: 0.0611 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 2.8034 L22: 2.2709 REMARK 3 L33: 2.7046 L12: 0.7359 REMARK 3 L13: 0.4055 L23: -0.4100 REMARK 3 S TENSOR REMARK 3 S11: -0.0239 S12: 0.0011 S13: -0.0448 REMARK 3 S21: 0.1546 S22: 0.1042 S23: 0.0334 REMARK 3 S31: -0.0705 S32: -0.2558 S33: -0.0536 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 8FXO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000271787. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS FEB 5, 2021 REMARK 200 DATA SCALING SOFTWARE : XSCALE FEB 5, 2021 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12730 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 32.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M REMARK 280 TRIS HYDROCHLORIDE PH 8.5, 30% W/V POLYETHYLENE GLYCOL 4000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.27000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.31500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.27000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.31500 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1311 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1386 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1396 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1415 LIES ON A SPECIAL POSITION. 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 LYS A 1082 REMARK 465 LYS A 1083 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A1089 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1303 O HOH A 1322 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG A 1169 OD1 ASP A 1190 4445 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1413 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A1414 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A1415 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A1416 DISTANCE = 7.68 ANGSTROMS DBREF 8FXO A 1082 1197 UNP Q92793 CBP_HUMAN 1082 1197 SEQRES 1 A 116 LYS LYS ILE PHE LYS PRO GLU GLU LEU ARG GLN ALA LEU SEQRES 2 A 116 MET PRO THR LEU GLU ALA LEU TYR ARG GLN ASP PRO GLU SEQRES 3 A 116 SER LEU PRO PHE ARG GLN PRO VAL ASP PRO GLN LEU LEU SEQRES 4 A 116 GLY ILE PRO ASP TYR PHE ASP ILE VAL LYS ASN PRO MET SEQRES 5 A 116 ASP LEU SER THR ILE LYS ARG LYS LEU ASP THR GLY GLN SEQRES 6 A 116 TYR GLN GLU PRO TRP GLN TYR VAL ASP ASP VAL TRP LEU SEQRES 7 A 116 MET PHE ASN ASN ALA TRP LEU TYR ASN ARG LYS THR SER SEQRES 8 A 116 ARG VAL TYR LYS PHE CYS SER LYS LEU ALA GLU VAL PHE SEQRES 9 A 116 GLU GLN GLU ILE ASP PRO VAL MET GLN SER LEU GLY HET YN5 A1201 41 HETNAM YN5 (6S)-1-(2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL)-6-{(5M)-5-(3, HETNAM 2 YN5 5-DIMETHYL-1,2-OXAZOL-4-YL)-1-[(1S,4R)-4- HETNAM 3 YN5 METHOXYCYCLOHEXYL]-1H-BENZIMIDAZOL-2-YL}PIPERIDIN-2- HETNAM 4 YN5 ONE FORMUL 2 YN5 C32 H36 N4 O5 FORMUL 3 HOH *116(H2 O) HELIX 1 AA1 LYS A 1086 ARG A 1103 1 18 HELIX 2 AA2 SER A 1108 ARG A 1112 5 5 HELIX 3 AA3 ASP A 1116 GLY A 1121 1 6 HELIX 4 AA4 ASP A 1124 VAL A 1129 1 6 HELIX 5 AA5 ASP A 1134 THR A 1144 1 11 HELIX 6 AA6 GLU A 1149 ASN A 1168 1 20 HELIX 7 AA7 SER A 1172 GLY A 1197 1 26 CISPEP 1 ASP A 1105 PRO A 1106 0 6.89 CRYST1 90.540 34.630 40.440 90.00 93.25 90.00 C 1 2 1 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 0.011045 0.000000 0.000627 0.00000 SCALE2 0.000000 0.028877 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024768 0.00000