PDB Short entry for 6BGH HEADER TRANSCRIPTION 28-OCT-17 6BGH TITLE SOLUTION NMR STRUCTURE OF BRD3 ET DOMAIN BOUND TO BRG1 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RING3-LIKE PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BRD3_ET; COMPND 8 CHAIN: B; COMPND 9 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION BROMODOMAIN BET PROTEIN, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.N.SZYSZKA,D.C.WAI,J.P.MACKAY REVDAT 2 20-JAN-21 6BGH 1 JRNL REMARK REVDAT 1 21-MAR-18 6BGH 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 REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BGH 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_1000230643. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298 REMARK 210 PH : 7; 7; 7 REMARK 210 IONIC STRENGTH : 50 NACL; 50 NACL; 50 NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 300 UM BRD3_ET, 600 UM BRG1, REMARK 210 0.02 % ROCHE COMPLETE PROTEASE REMARK 210 INHIBITOR, 166 UM DSS, 90% H2O/ REMARK 210 10% D2O; 300 UM [U-15N] BRD3_ET, REMARK 210 600 UM BRG1, 0.02 % ROCHE REMARK 210 COMPLETE PROTEASE INHIBITOR, 166 REMARK 210 UM DSS, 90% H2O/10% D2O; 300 UM REMARK 210 [U-13C; U-15N] BRD3_ET, 600 UM REMARK 210 BRG1, 0.02 % ROCHE COMPLETE REMARK 210 PROTEASE INHIBITOR, 166 UM DSS, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 3D 1H-13C NOESY; REMARK 210 3D 1H-15N NOESY; 3D 13C/15N (F2/ REMARK 210 F1) FILTERED, 1H-1H NOESY; 2D REMARK 210 13C/15N (F2/F1) FILTERED, 1H-1H REMARK 210 NOESY; 2D 13C/15N (F2/F1) REMARK 210 FILTERED, 1H-1H TOCSY; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-COSY; 2D 1H-1H REMARK 210 TOCSY; 2D 1H-1H NOESY; 3D HNCO; REMARK 210 2D 1H-15N HSQC; 3D HN(CA)CO; 3D REMARK 210 H(CC)(CO)HN; 3D HNCA; 3D CBCA(CO) REMARK 210 NH; 3D HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 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 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 11 PRO A 611 N - CD - CG ANGL. DEV. = -9.7 DEGREES REMARK 500 17 PRO A 611 C - N - CA ANGL. DEV. = 12.0 DEGREES REMARK 500 17 PRO A 611 CA - N - CD ANGL. DEV. = -8.8 DEGREES 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 ASP A 562 -167.18 -176.51 REMARK 500 1 SER A 563 -38.58 -145.23 REMARK 500 1 GLU A 564 91.59 47.07 REMARK 500 1 ARG A 602 -60.97 -97.82 REMARK 500 1 LEU A 606 -78.04 -37.19 REMARK 500 1 ASP A 608 -47.08 -150.67 REMARK 500 1 SER A 609 -44.71 164.98 REMARK 500 1 ASP A 617 -1.31 -59.80 REMARK 500 1 SER B1592 -83.64 -148.69 REMARK 500 1 LYS B1596 84.14 -64.69 REMARK 500 1 LYS B1598 72.50 48.31 REMARK 500 1 LEU B1599 107.20 -52.46 REMARK 500 2 TYR A 561 87.29 53.35 REMARK 500 2 GLU A 568 177.79 54.85 REMARK 500 2 PRO A 611 -2.95 -53.68 REMARK 500 2 ASP A 617 -0.12 -50.19 REMARK 500 2 PHE A 618 -19.10 -47.80 REMARK 500 2 VAL B1593 -162.14 -117.79 REMARK 500 2 LYS B1594 135.43 82.59 REMARK 500 2 ILE B1597 -81.63 41.10 REMARK 500 2 LYS B1598 76.54 45.67 REMARK 500 2 ARG B1601 -67.05 70.67 REMARK 500 3 SER A 563 -36.51 -131.69 REMARK 500 3 GLU A 564 -170.81 65.33 REMARK 500 3 ILE A 616 79.04 -114.99 REMARK 500 3 ASP A 617 -1.45 -51.64 REMARK 500 3 PHE A 618 -18.16 -47.33 REMARK 500 3 LYS B1596 104.40 -47.94 REMARK 500 3 LYS B1598 78.35 52.73 REMARK 500 4 LYS A 639 83.09 44.85 REMARK 500 4 LYS B1596 81.83 -68.57 REMARK 500 4 LYS B1598 91.87 57.47 REMARK 500 5 TYR A 561 119.84 65.82 REMARK 500 5 GLU A 564 168.52 55.62 REMARK 500 5 LEU A 606 -77.57 -41.34 REMARK 500 5 ASP A 608 -48.70 -153.58 REMARK 500 5 SER A 609 -79.61 153.23 REMARK 500 5 ASP A 612 -51.59 -120.46 REMARK 500 5 GLU A 613 -45.97 152.01 REMARK 500 5 PHE A 618 10.03 -49.80 REMARK 500 5 LYS A 639 111.07 81.60 REMARK 500 5 LYS A 640 33.94 -96.56 REMARK 500 5 LYS B1594 117.09 68.97 REMARK 500 5 LYS B1596 101.74 -52.03 REMARK 500 5 ILE B1597 -74.75 -76.20 REMARK 500 5 LYS B1598 73.10 51.87 REMARK 500 6 TYR A 561 -82.70 59.31 REMARK 500 6 SER A 563 30.69 -142.50 REMARK 500 6 GLU A 564 92.64 49.86 REMARK 500 6 GLU A 567 -149.82 -99.40 REMARK 500 REMARK 500 THIS ENTRY HAS 185 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 A 607 0.08 SIDE CHAIN REMARK 500 1 ARG A 631 0.09 SIDE CHAIN REMARK 500 4 ARG A 627 0.08 SIDE CHAIN REMARK 500 6 ARG A 631 0.08 SIDE CHAIN REMARK 500 10 ARG A 578 0.08 SIDE CHAIN REMARK 500 10 ARG A 602 0.08 SIDE CHAIN REMARK 500 10 ARG A 631 0.07 SIDE CHAIN REMARK 500 11 ARG A 586 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30368 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF BRD3 ET DOMAIN BOUND TO BRG1 PEPTIDE DBREF 6BGH A 557 643 UNP Q15059 BRD3_HUMAN 557 643 DBREF 6BGH B 1591 1602 PDB 6BGH 6BGH 1591 1602 SEQRES 1 A 87 ALA SER ALA SER TYR ASP SER GLU GLU GLU GLU GLU GLY SEQRES 2 A 87 LEU PRO MET SER TYR ASP GLU LYS ARG GLN LEU SER LEU SEQRES 3 A 87 ASP ILE ASN ARG LEU PRO GLY GLU LYS LEU GLY ARG VAL SEQRES 4 A 87 VAL HIS ILE ILE GLN SER ARG GLU PRO SER LEU ARG ASP SEQRES 5 A 87 SER ASN PRO ASP GLU ILE GLU ILE ASP PHE GLU THR LEU SEQRES 6 A 87 LYS PRO THR THR LEU ARG GLU LEU GLU ARG TYR VAL LYS SEQRES 7 A 87 SER CYS LEU GLN LYS LYS GLN ARG LYS SEQRES 1 B 12 ARG SER VAL LYS VAL LYS ILE LYS LEU GLY ARG LYS HELIX 1 AA1 ALA A 557 ASP A 562 1 6 HELIX 2 AA2 SER A 573 LEU A 587 1 15 HELIX 3 AA3 PRO A 588 GLN A 600 1 13 HELIX 4 AA4 LYS A 622 LYS A 639 1 18 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