PDB Short entry for 6BNH HEADER TRANSCRIPTION/OXIDOREDUCTASE 16-NOV-17 6BNH TITLE SOLUTION NMR STRUCTURES OF BRD4 ET DOMAIN WITH JMJD6 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ET DOMAIN RESIDUES 601-683; COMPND 5 SYNONYM: PROTEIN HUNK1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BIFUNCTIONAL ARGININE DEMETHYLASE AND LYSYL-HYDROXYLASE COMPND 9 JMJD6; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: RESIDUES 84-96; COMPND 12 SYNONYM: HISTONE ARGININE DEMETHYLASE JMJD6,JMJC DOMAIN-CONTAINING COMPND 13 PROTEIN 6,JUMONJI DOMAIN-CONTAINING PROTEIN 6,LYSYL-HYDROXYLASE COMPND 14 JMJD6,PEPTIDE-LYSINE 5-DIOXYGENASE JMJD6,PHOSPHATIDYLSERINE RECEPTOR, COMPND 15 PROTEIN PTDSR; COMPND 16 EC: 1.14.11.-; COMPND 17 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: BRD4, HUNK1; 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_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: JMJD6, KIAA0585, PTDSR; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA, BET, COMPLEX, TRANSCRIPTION-OXIDOREDUCTASE COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.KONUMA,D.YU,C.ZHAO,Y.JU,R.SHARMA,C.REN,Q.ZHANG,M.-M.ZHOU,L.ZENG REVDAT 2 14-JUN-23 6BNH 1 REMARK REVDAT 1 20-DEC-17 6BNH 0 JRNL AUTH T.KONUMA,D.YU,C.ZHAO,Y.JU,R.SHARMA,C.REN,Q.ZHANG,M.M.ZHOU, JRNL AUTH 2 L.ZENG JRNL TITL STRUCTURAL MECHANISM OF THE OXYGENASE JMJD6 RECOGNITION BY JRNL TITL 2 THE EXTRATERMINAL (ET) DOMAIN OF BRD4. JRNL REF SCI REP V. 7 16272 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 29176719 JRNL DOI 10.1038/S41598-017-16588-8 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BNH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1000231170. 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 : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 10 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 2 MM [U-100% 2H] REMARK 210 DTT, 95% H2O/5% D2O; 10 MM REMARK 210 SODIUM PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 2 MM [U-100% 2H] DTT, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D FILTERED REMARK 210 1H-13C NOESY ALIPHATIC; 3D REMARK 210 FILTERED 1H-13C NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS, NMRVIEW, NMRPIPE, REMARK 210 PROCHECKNMR, TOPSPIN REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS 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 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: 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 LYS A 77 -112.22 -76.26 REMARK 500 1 ARG A 79 70.62 -162.44 REMARK 500 1 LYS A 80 60.28 -159.16 REMARK 500 1 TRP B 202 36.05 -142.61 REMARK 500 1 THR B 203 -167.39 -78.42 REMARK 500 1 GLU B 205 -70.45 -55.73 REMARK 500 2 PRO A 42 5.32 -68.06 REMARK 500 2 LYS A 78 -83.31 -80.41 REMARK 500 2 ARG A 79 85.51 -166.52 REMARK 500 3 PRO A 42 -6.43 -57.96 REMARK 500 3 LYS A 78 -75.29 58.58 REMARK 500 3 ARG A 79 100.57 63.25 REMARK 500 3 THR B 203 -167.05 -76.47 REMARK 500 3 GLU B 205 -72.96 -54.48 REMARK 500 4 PRO A 42 -7.41 -57.35 REMARK 500 4 LYS A 77 94.96 49.36 REMARK 500 4 ARG A 79 79.02 58.97 REMARK 500 4 GLN A 82 58.13 -107.42 REMARK 500 4 TRP B 202 47.86 -153.33 REMARK 500 4 LEU B 207 -70.72 -65.65 REMARK 500 5 PRO A 42 2.27 -61.82 REMARK 500 5 ARG A 79 90.39 57.41 REMARK 500 5 GLU B 205 -73.02 -51.80 REMARK 500 6 TRP B 202 38.47 -140.55 REMARK 500 7 PRO A 42 2.40 -62.51 REMARK 500 7 ARG A 79 138.61 65.70 REMARK 500 7 LEU B 204 -66.19 -28.34 REMARK 500 7 ARG B 206 -70.56 -54.83 REMARK 500 8 PRO A 42 -6.86 -58.63 REMARK 500 8 ARG A 79 101.21 -163.54 REMARK 500 8 GLN A 82 102.27 -164.21 REMARK 500 8 TRP B 202 56.92 -91.75 REMARK 500 8 THR B 203 -166.38 -102.97 REMARK 500 8 LEU B 204 -62.45 -28.10 REMARK 500 9 GLU B 205 -72.39 -59.35 REMARK 500 10 PRO A 42 0.55 -61.37 REMARK 500 10 LYS A 77 -93.06 -53.53 REMARK 500 10 ARG A 79 77.70 59.09 REMARK 500 10 THR B 203 -168.34 -74.07 REMARK 500 10 GLU B 205 -73.83 -47.15 REMARK 500 11 PRO A 42 5.35 -67.74 REMARK 500 11 LYS A 77 77.88 -107.37 REMARK 500 11 PRO A 81 109.95 -56.00 REMARK 500 11 TRP B 202 50.84 -93.52 REMARK 500 12 LYS A 77 -98.55 -67.32 REMARK 500 12 THR B 203 -169.27 -75.89 REMARK 500 13 PRO A 42 2.88 -62.00 REMARK 500 13 LYS A 77 -127.16 -104.55 REMARK 500 13 LYS A 78 -50.30 -129.35 REMARK 500 13 GLU B 205 -70.22 -51.43 REMARK 500 REMARK 500 THIS ENTRY HAS 80 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30373 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURES OF BRD4 ET DOMAIN WITH JMJD6 PEPTIDE DBREF 6BNH A 1 83 UNP O60885 BRD4_HUMAN 601 683 DBREF 6BNH B 201 213 UNP Q6NYC1 JMJD6_HUMAN 84 96 SEQRES 1 A 83 SER GLU GLU GLU ASP LYS CYS LYS PRO MET SER TYR GLU SEQRES 2 A 83 GLU LYS ARG GLN LEU SER LEU ASP ILE ASN LYS LEU PRO SEQRES 3 A 83 GLY GLU LYS LEU GLY ARG VAL VAL HIS ILE ILE GLN SER SEQRES 4 A 83 ARG GLU PRO SER LEU LYS ASN SER ASN PRO ASP GLU ILE SEQRES 5 A 83 GLU ILE ASP PHE GLU THR LEU LYS PRO SER THR LEU ARG SEQRES 6 A 83 GLU LEU GLU ARG TYR VAL THR SER CYS LEU ARG LYS LYS SEQRES 7 A 83 ARG LYS PRO GLN ALA SEQRES 1 B 13 LYS TRP THR LEU GLU ARG LEU LYS ARG LYS TYR ARG ASN HELIX 1 AA1 GLU A 2 CYS A 7 1 6 HELIX 2 AA2 SER A 11 LEU A 25 1 15 HELIX 3 AA3 PRO A 26 GLU A 41 1 16 HELIX 4 AA4 ASN A 48 ILE A 52 5 5 HELIX 5 AA5 LYS A 60 ARG A 76 1 17 HELIX 6 AA6 GLU B 205 ARG B 212 1 8 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