HEADER PROTEIN BINDING 28-OCT-17 6BGG TITLE SOLUTION NMR STRUCTURES OF THE BRD3 ET DOMAIN IN COMPLEX WITH A CHD4 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHD4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 290-301; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 3; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 557-644; COMPND 10 SYNONYM: RING3-LIKE PROTEIN; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: BRD3, KIAA0043, RING3L; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: ROSETTA2; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PGEX6P KEYWDS TRANSCRIPTION REGULATION, EPIGENETICS, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.C.C.WAI,T.N.SZYSZKA,A.E.CAMPBELL,C.KWONG,L.WILKINSON-WHITE, AUTHOR 2 A.P.G.SILVA,J.K.K.LOW,A.H.KWAN,R.GAMSJAEGER,B.LU,C.R.VAKOC, AUTHOR 3 G.A.BLOBEL,J.P.MACKAY REVDAT 5 14-JUN-23 6BGG 1 REMARK REVDAT 4 08-JAN-20 6BGG 1 REMARK REVDAT 3 23-MAY-18 6BGG 1 JRNL REVDAT 2 04-APR-18 6BGG 1 JRNL REVDAT 1 21-MAR-18 6BGG 0 JRNL AUTH D.C.C.WAI,T.N.SZYSZKA,A.E.CAMPBELL,C.KWONG, JRNL AUTH 2 L.E.WILKINSON-WHITE,A.P.G.SILVA,J.K.K.LOW,A.H.KWAN, JRNL AUTH 3 R.GAMSJAEGER,J.D.CHALMERS,W.M.PATRICK,B.LU,C.R.VAKOC, JRNL AUTH 4 G.A.BLOBEL,J.P.MACKAY JRNL TITL THE BRD3 ET DOMAIN RECOGNIZES A SHORT PEPTIDE MOTIF THROUGH JRNL TITL 2 A MECHANISM THAT IS CONSERVED ACROSS CHROMATIN REMODELERS JRNL TITL 3 AND TRANSCRIPTIONAL REGULATORS. JRNL REF J. BIOL. CHEM. V. 293 7160 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29567837 JRNL DOI 10.1074/JBC.RA117.000678 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WATER REFINEMENT USING RECOORD PROTOCOL REMARK 3 (NEDERVEEN 2015) REMARK 4 REMARK 4 6BGG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230801. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : .2 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 500 UM [U-13C; U-15N] BRD3, 500 REMARK 210 UM CHD4, 20 MM SODIUM PHOSPHATE, REMARK 210 50 MM SODIUM CHLORIDE, 1 MM DTT, REMARK 210 90% H2O/10% D2O; 500 UM [U-13C; REMARK 210 U-15N] BRD3, 500 UM CHD4, 20 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 1 MM DTT, 100% D2O; REMARK 210 500 UM BRD3, 500 UM CHD4, 20 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 1 MM DTT, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY ALIPHATIC; 3D 1H REMARK 210 -15N NOESY; 3D 1H-13C (F1)- REMARK 210 FILTERED NOESY ALIPHATIC; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D HNCO; HNCACO; 3D REMARK 210 HCCH-TOCSY; 3D H(CCO)NH; 2D REMARK 210 15N13C (F2,F1)-FILTERED) 1H-1H REMARK 210 NOESY; 2D 1H-15N HSQC; 2D 1H-1H REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.1.3, CYANA 3.97, REMARK 210 TOPSPIN 3.5.6 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY B 552 REMARK 465 PRO B 553 REMARK 465 LEU B 554 REMARK 465 GLY B 555 REMARK 465 SER B 556 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 OD1 ASP B 617 HG1 THR B 620 1.57 REMARK 500 REMARK 500 REMARK: NULL 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 1 TYR B 561 79.28 60.19 REMARK 500 1 LYS B 639 126.66 60.80 REMARK 500 1 GLN B 641 -42.00 170.27 REMARK 500 2 GLU B 565 81.26 65.79 REMARK 500 2 LYS B 639 -10.32 65.45 REMARK 500 3 VAL A 291 91.12 60.68 REMARK 500 3 ALA A 292 136.54 87.20 REMARK 500 3 TYR B 561 -165.64 -111.84 REMARK 500 3 GLN B 638 78.21 52.59 REMARK 500 4 ALA A 292 91.67 58.33 REMARK 500 4 TYR B 561 101.05 68.28 REMARK 500 4 GLU B 565 -60.87 -130.04 REMARK 500 4 SER B 609 -159.78 -71.39 REMARK 500 4 ARG B 642 -56.91 72.98 REMARK 500 4 LYS B 643 -53.44 -166.44 REMARK 500 5 LEU A 294 -64.38 73.37 REMARK 500 5 LYS A 295 91.82 52.22 REMARK 500 5 SER B 560 -174.23 178.13 REMARK 500 5 GLU B 564 167.55 71.79 REMARK 500 6 LEU A 294 -77.21 -82.79 REMARK 500 6 LYS A 295 97.12 57.24 REMARK 500 6 LEU A 298 -92.25 -85.23 REMARK 500 7 ALA A 292 137.36 74.33 REMARK 500 7 PRO A 293 39.95 -78.68 REMARK 500 7 TYR B 561 88.53 69.63 REMARK 500 7 GLU B 568 33.38 -82.10 REMARK 500 7 GLN B 638 41.76 -74.87 REMARK 500 7 LYS B 639 102.35 54.85 REMARK 500 7 GLN B 641 -37.79 65.69 REMARK 500 8 GLU B 564 161.29 70.77 REMARK 500 8 LYS B 643 -52.26 -124.43 REMARK 500 9 LEU A 294 -159.75 -166.85 REMARK 500 9 LYS A 295 121.48 85.65 REMARK 500 9 GLN B 638 85.24 57.88 REMARK 500 10 VAL A 291 -67.68 68.63 REMARK 500 10 ALA A 292 85.53 58.09 REMARK 500 10 PRO A 293 79.60 -69.04 REMARK 500 10 LEU A 294 83.89 58.39 REMARK 500 10 LYS A 297 106.91 67.96 REMARK 500 10 GLU B 564 -166.94 -113.69 REMARK 500 10 LYS B 640 -71.59 -93.14 REMARK 500 11 VAL A 291 81.11 57.29 REMARK 500 11 ILE A 296 -168.60 -102.20 REMARK 500 11 LYS A 297 84.02 70.10 REMARK 500 11 SER B 609 -157.98 -84.83 REMARK 500 11 GLN B 641 158.23 178.54 REMARK 500 12 LEU A 298 -84.59 -75.94 REMARK 500 12 LYS B 643 -48.68 -173.11 REMARK 500 13 ALA A 292 99.37 52.58 REMARK 500 13 SER B 558 -43.89 -150.88 REMARK 500 REMARK 500 THIS ENTRY HAS 78 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG B 627 0.09 SIDE CHAIN REMARK 500 2 ARG B 602 0.07 SIDE CHAIN REMARK 500 3 ARG B 602 0.11 SIDE CHAIN REMARK 500 7 ARG B 602 0.11 SIDE CHAIN REMARK 500 10 ARG B 602 0.07 SIDE CHAIN REMARK 500 11 ARG B 602 0.10 SIDE CHAIN REMARK 500 12 ARG B 602 0.09 SIDE CHAIN REMARK 500 13 ARG B 607 0.07 SIDE CHAIN REMARK 500 19 ARG B 631 0.13 SIDE CHAIN REMARK 500 20 ARG B 594 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30367 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURES OF THE BRD3 ET DOMAIN IN COMPLEX WITH A REMARK 900 CHD4 PEPTIDE DBREF 6BGG A 290 301 PDB 6BGG 6BGG 290 301 DBREF 6BGG B 557 644 UNP Q15059 BRD3_HUMAN 557 644 SEQADV 6BGG GLY B 552 UNP Q15059 EXPRESSION TAG SEQADV 6BGG PRO B 553 UNP Q15059 EXPRESSION TAG SEQADV 6BGG LEU B 554 UNP Q15059 EXPRESSION TAG SEQADV 6BGG GLY B 555 UNP Q15059 EXPRESSION TAG SEQADV 6BGG SER B 556 UNP Q15059 EXPRESSION TAG SEQRES 1 A 12 LYS VAL ALA PRO LEU LYS ILE LYS LEU GLY GLY PHE SEQRES 1 B 93 GLY PRO LEU GLY SER ALA SER ALA SER TYR ASP SER GLU SEQRES 2 B 93 GLU GLU GLU GLU GLY LEU PRO MET SER TYR ASP GLU LYS SEQRES 3 B 93 ARG GLN LEU SER LEU ASP ILE ASN ARG LEU PRO GLY GLU SEQRES 4 B 93 LYS LEU GLY ARG VAL VAL HIS ILE ILE GLN SER ARG GLU SEQRES 5 B 93 PRO SER LEU ARG ASP SER ASN PRO ASP GLU ILE GLU ILE SEQRES 6 B 93 ASP PHE GLU THR LEU LYS PRO THR THR LEU ARG GLU LEU SEQRES 7 B 93 GLU ARG TYR VAL LYS SER CYS LEU GLN LYS LYS GLN ARG SEQRES 8 B 93 LYS PRO HELIX 1 AA1 GLU B 566 LEU B 570 5 5 HELIX 2 AA2 SER B 573 ARG B 586 1 14 HELIX 3 AA3 PRO B 588 GLU B 603 1 16 HELIX 4 AA4 GLU B 603 SER B 609 1 7 HELIX 5 AA5 LYS B 622 LEU B 637 1 16 SHEET 1 AA1 2 LYS A 295 LYS A 297 0 SHEET 2 AA1 2 GLU B 615 ASP B 617 -1 O ILE B 616 N ILE A 296 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1