HEADER SIGNALING PROTEIN 21-JUL-21 7RJN TITLE CRYSTAL STRUCTURE OF HUMAN BROMODOMAIN CONTAINING PROTEIN 3 (BRD3) IN TITLE 2 COMPLEX WITH BCLTF1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RING3-LIKE PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BCL-2-ASSOCIATED TRANSCRIPTION FACTOR 1; COMPND 8 CHAIN: C, D; COMPND 9 FRAGMENT: UNP RESIDUES 330-339; COMPND 10 SYNONYM: BTF,BCLAF1 AND THRAP3 FAMILY MEMBER 1; COMPND 11 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: BRD3, KIAA0043, RING3L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PRIL; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS BRD3, BCL2TF, ACETYLLYSINE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.FEDOROV,K.ISLAM,A.GHOSH REVDAT 5 06-NOV-24 7RJN 1 REMARK REVDAT 4 15-NOV-23 7RJN 1 REMARK REVDAT 3 18-OCT-23 7RJN 1 JRNL REVDAT 2 24-AUG-22 7RJN 1 JRNL REVDAT 1 03-AUG-22 7RJN 0 JRNL AUTH S.WAGNER,E.FEDOROV,B.SUDHAMALLA,H.N.JNAWALI,R.DEBIEC, JRNL AUTH 2 A.GHOSH,K.ISLAM JRNL TITL UNCOVERING THE BROMODOMAIN INTERACTOME USING SITE-SPECIFIC JRNL TITL 2 AZIDE-ACETYLLYSINE PHOTOCHEMISTRY, PROTEOMIC PROFILING AND JRNL TITL 3 STRUCTURAL CHARACTERIZATION JRNL REF BIORXIV 2021 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2021.07.28.453719 REMARK 2 REMARK 2 RESOLUTION. 1.95 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21592 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) : 0.183 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 2.0200 - 1.9500 1.00 2010 98 0.2016 0.2496 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.40 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 7RJN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000258325. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) 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 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21679 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 29.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 13.90 REMARK 200 R MERGE FOR SHELL (I) : 0.67800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 6QJU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE, 30% W/V PEG4000, PH 4.6, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 292K 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 21.36450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.12100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.39650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.12100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.36450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.39650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 GLU A 144 REMARK 465 SER B 22 REMARK 465 GLU B 143 REMARK 465 GLU B 144 REMARK 465 THR C 330 REMARK 465 ALA C 331 REMARK 465 ALY C 332 REMARK 465 LEU C 337 REMARK 465 LYS C 338 REMARK 465 ARG C 339 REMARK 465 THR D 330 REMARK 465 ALA D 331 REMARK 465 ALY D 332 REMARK 465 LEU D 337 REMARK 465 LYS D 338 REMARK 465 ARG D 339 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 34 -177.04 -174.84 REMARK 500 ALY C 335 -110.85 -87.77 REMARK 500 ALY D 335 -108.47 -93.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 7RJN A 24 144 UNP Q15059 BRD3_HUMAN 24 144 DBREF 7RJN B 24 144 UNP Q15059 BRD3_HUMAN 24 144 DBREF 7RJN C 330 339 UNP Q9NYF8 BCLF1_HUMAN 330 339 DBREF 7RJN D 330 339 UNP Q9NYF8 BCLF1_HUMAN 330 339 SEQADV 7RJN SER A 22 UNP Q15059 EXPRESSION TAG SEQADV 7RJN MET A 23 UNP Q15059 EXPRESSION TAG SEQADV 7RJN SER B 22 UNP Q15059 EXPRESSION TAG SEQADV 7RJN MET B 23 UNP Q15059 EXPRESSION TAG SEQRES 1 A 123 SER MET PRO GLU VAL SER ASN PRO SER LYS PRO GLY ARG SEQRES 2 A 123 LYS THR ASN GLN LEU GLN TYR MET GLN ASN VAL VAL VAL SEQRES 3 A 123 LYS THR LEU TRP LYS HIS GLN PHE ALA TRP PRO PHE TYR SEQRES 4 A 123 GLN PRO VAL ASP ALA ILE LYS LEU ASN LEU PRO ASP TYR SEQRES 5 A 123 HIS LYS ILE ILE LYS ASN PRO MET ASP MET GLY THR ILE SEQRES 6 A 123 LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP SER ALA SER SEQRES 7 A 123 GLU CYS MET GLN ASP PHE ASN THR MET PHE THR ASN CYS SEQRES 8 A 123 TYR ILE TYR ASN LYS PRO THR ASP ASP ILE VAL LEU MET SEQRES 9 A 123 ALA GLN ALA LEU GLU LYS ILE PHE LEU GLN LYS VAL ALA SEQRES 10 A 123 GLN MET PRO GLN GLU GLU SEQRES 1 B 123 SER MET PRO GLU VAL SER ASN PRO SER LYS PRO GLY ARG SEQRES 2 B 123 LYS THR ASN GLN LEU GLN TYR MET GLN ASN VAL VAL VAL SEQRES 3 B 123 LYS THR LEU TRP LYS HIS GLN PHE ALA TRP PRO PHE TYR SEQRES 4 B 123 GLN PRO VAL ASP ALA ILE LYS LEU ASN LEU PRO ASP TYR SEQRES 5 B 123 HIS LYS ILE ILE LYS ASN PRO MET ASP MET GLY THR ILE SEQRES 6 B 123 LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP SER ALA SER SEQRES 7 B 123 GLU CYS MET GLN ASP PHE ASN THR MET PHE THR ASN CYS SEQRES 8 B 123 TYR ILE TYR ASN LYS PRO THR ASP ASP ILE VAL LEU MET SEQRES 9 B 123 ALA GLN ALA LEU GLU LYS ILE PHE LEU GLN LYS VAL ALA SEQRES 10 B 123 GLN MET PRO GLN GLU GLU SEQRES 1 C 10 THR ALA ALY THR GLY ALY PHE LEU LYS ARG SEQRES 1 D 10 THR ALA ALY THR GLY ALY PHE LEU LYS ARG MODRES 7RJN ALY C 335 LYS MODIFIED RESIDUE MODRES 7RJN ALY D 335 LYS MODIFIED RESIDUE HET ALY C 335 12 HET ALY D 335 12 HET EDO A 201 4 HET EDO B 201 4 HET EDO B 202 4 HETNAM ALY N(6)-ACETYLLYSINE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ALY 2(C8 H16 N2 O3) FORMUL 5 EDO 3(C2 H6 O2) FORMUL 8 HOH *139(H2 O) HELIX 1 AA1 THR A 36 VAL A 45 1 10 HELIX 2 AA2 VAL A 45 LYS A 52 1 8 HELIX 3 AA3 ALA A 56 TYR A 60 5 5 HELIX 4 AA4 ASP A 72 ILE A 77 1 6 HELIX 5 AA5 ASP A 82 ASN A 92 1 11 HELIX 6 AA6 SER A 97 ASN A 116 1 20 HELIX 7 AA7 ASP A 120 ALA A 138 1 19 HELIX 8 AA8 THR B 36 VAL B 45 1 10 HELIX 9 AA9 VAL B 45 LYS B 52 1 8 HELIX 10 AB1 ALA B 56 TYR B 60 5 5 HELIX 11 AB2 ASP B 72 ILE B 77 1 6 HELIX 12 AB3 ASP B 82 ASN B 92 1 11 HELIX 13 AB4 SER B 97 ASN B 116 1 20 HELIX 14 AB5 ASP B 120 GLN B 139 1 20 LINK C GLY C 334 N ALY C 335 1555 1555 1.33 LINK C ALY C 335 N PHE C 336 1555 1555 1.33 LINK C GLY D 334 N ALY D 335 1555 1555 1.33 LINK C ALY D 335 N PHE D 336 1555 1555 1.33 CRYST1 42.729 54.793 122.242 90.00 90.00 90.00 P 21 21 21 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 0.023403 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018251 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008180 0.00000