HEADER PROTEIN BINDING 12-DEC-25 21HJ TITLE SOLUTION STRUCTURES OF BRD9 BROMODOMAIN IN COMPLEX WITH HISTONE H3 TITLE 2 LACTYL-LYSINE 18 (H3K18LA) PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 9; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RHABDOMYOSARCOMA ANTIGEN MU-RMS-40.8; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE H3.3C; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: HISTONE H3.5; COMPND 10 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: BRD9, UNQ3040/PRO9856; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS HISTONE LACTYLATION, BRD9, CHROMATIN REMODELING, CHROMATIN KEYWDS 2 ACCESSIBILITY, TRANSCRIPTION REGULATION, HEPATOCELLULAR CARCINOMA, KEYWDS 3 PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.WEI,L.ZENG REVDAT 1 11-MAR-26 21HJ 0 JRNL AUTH E.WEI,D.JI,Y.JIA,Z.SUN,C.GAO,C.ZENG,C.WANG,M.YU,G.SHANG, JRNL AUTH 2 L.XIE,W.ZHANG,Y.LI,Y.LIANG,B.JI,Y.YUE,Y.LIU,M.-M.ZHOU,L.ZENG JRNL TITL BRD9 RECOGNIZES LACTATE-INDUCED H3K18 LACTYLATION TO DRIVE JRNL TITL 2 ONCOGENIC CHROMATIN REMODELING IN HEPATOCELLULAR CARCINOMA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA, CNS REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), BRUNGER, REMARK 3 ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 21HJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 05-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1300067217. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 500 MM SODIUM CHLORIDE, 2.7 MM REMARK 210 POTASSIUM CHLORIDE, 10 MM SODIUM REMARK 210 PHOSPHATE, 1.8 MM POTASSIUM REMARK 210 PHOSPHATE, 2 MM DTT, 90% H2O/10% REMARK 210 D2O; 500 MM SODIUM CHLORIDE, 2.7 REMARK 210 MM POTASSIUM CHLORIDE, 10 MM REMARK 210 SODIUM PHOSPHATE, 1.8 MM REMARK 210 POTASSIUM PHOSPHATE, 2 MM DTT, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D HN(COCA)CB; 3D REMARK 210 HN(CO)CA; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 3D FILTERED-1H- REMARK 210 13C NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, TOPSPIN, NMRPIPE 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 HZ3 LYS A 54 HG11 VAL A 58 1.16 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 SER A 5 84.06 -156.57 REMARK 500 1 PRO A 38 -75.42 -67.95 REMARK 500 1 ASN A 60 45.67 70.00 REMARK 500 1 PRO A 85 4.82 -67.25 REMARK 500 1 LYS B 204 -41.09 -135.17 REMARK 500 1 GLN B 209 -125.01 54.82 REMARK 500 1 LEU B 210 173.28 66.59 REMARK 500 1 ALA B 211 43.65 -79.84 REMARK 500 1 LYS B 213 -46.23 71.29 REMARK 500 2 ASN A 3 -54.54 -132.35 REMARK 500 2 PRO A 38 -79.48 -73.17 REMARK 500 2 ILE A 43 -61.51 -90.59 REMARK 500 2 PRO A 85 11.67 -68.12 REMARK 500 2 ASN A 113 -4.18 76.14 REMARK 500 2 THR A 116 -69.23 -132.83 REMARK 500 2 GLN B 209 -57.11 -120.81 REMARK 500 2 LEU B 210 -167.53 58.58 REMARK 500 2 THR B 212 -60.65 -131.65 REMARK 500 3 ASN A 60 39.12 72.18 REMARK 500 3 PRO A 85 11.21 -69.75 REMARK 500 3 LEU A 110 -71.81 -78.78 REMARK 500 3 THR A 116 -73.91 -107.70 REMARK 500 3 XRW B 208 65.39 60.20 REMARK 500 3 ALA B 211 43.11 -93.53 REMARK 500 4 SER A 5 -167.26 -127.82 REMARK 500 4 PRO A 24 2.50 -68.62 REMARK 500 4 PRO A 38 -74.01 -69.88 REMARK 500 4 ASN A 60 38.90 72.76 REMARK 500 4 PRO A 85 8.51 -66.59 REMARK 500 4 ASP A 115 -64.99 -153.34 REMARK 500 4 THR A 116 -66.32 -96.25 REMARK 500 4 LYS B 213 -157.52 62.90 REMARK 500 5 THR A 6 120.95 69.56 REMARK 500 5 ILE A 43 -60.71 -91.60 REMARK 500 5 GLU A 114 90.46 69.88 REMARK 500 5 PRO B 206 49.05 -81.90 REMARK 500 5 ALA B 214 -76.28 -94.92 REMARK 500 6 SER A 5 -65.99 -128.28 REMARK 500 6 THR A 6 114.48 64.86 REMARK 500 6 PRO A 38 -82.24 -67.69 REMARK 500 6 ASN A 60 63.02 67.70 REMARK 500 6 PRO A 85 3.73 -68.42 REMARK 500 6 LEU A 110 -73.06 -82.17 REMARK 500 6 LEU A 111 -53.18 -123.17 REMARK 500 6 ALA B 205 90.73 63.15 REMARK 500 6 XRW B 208 -56.61 -141.88 REMARK 500 6 GLN B 209 81.71 60.37 REMARK 500 6 THR B 212 36.58 -90.59 REMARK 500 6 ALA B 214 46.93 -171.39 REMARK 500 7 PRO A 7 -1.13 -41.89 REMARK 500 REMARK 500 THIS ENTRY HAS 155 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36817 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURES OF BRD9 BROMODOMAIN IN COMPLEX WITH HISTONE H3 REMARK 900 LACTYL-LYSINE 18 (H3K18LA) PEPTIDE DBREF 21HJ A 1 117 UNP Q9H8M2 BRD9_HUMAN 134 250 DBREF 21HJ B 201 215 UNP Q6NXT2 H3C_HUMAN 12 26 SEQRES 1 A 117 ALA GLU ASN GLU SER THR PRO ILE GLN GLN LEU LEU GLU SEQRES 2 A 117 HIS PHE LEU ARG GLN LEU GLN ARG LYS ASP PRO HIS GLY SEQRES 3 A 117 PHE PHE ALA PHE PRO VAL THR ASP ALA ILE ALA PRO GLY SEQRES 4 A 117 TYR SER MET ILE ILE LYS HIS PRO MET ASP PHE GLY THR SEQRES 5 A 117 MET LYS ASP LYS ILE VAL ALA ASN GLU TYR LYS SER VAL SEQRES 6 A 117 THR GLU PHE LYS ALA ASP PHE LYS LEU MET CYS ASP ASN SEQRES 7 A 117 ALA MET THR TYR ASN ARG PRO ASP THR VAL TYR TYR LYS SEQRES 8 A 117 LEU ALA LYS LYS ILE LEU HIS ALA GLY PHE LYS MET MET SEQRES 9 A 117 SER LYS GLN ALA ALA LEU LEU GLY ASN GLU ASP THR ALA SEQRES 1 B 15 THR GLY GLY LYS ALA PRO ARG XRW GLN LEU ALA THR LYS SEQRES 2 B 15 ALA ALA MODRES 21HJ XRW B 208 LYS MODIFIED RESIDUE HET XRW B 208 30 HETNAM XRW N~6~-[(2S)-2-HYDROXYPROPANOYL]-L-LYSINE FORMUL 2 XRW C9 H18 N2 O4 HELIX 1 AA1 THR A 6 LYS A 22 1 17 HELIX 2 AA2 GLY A 39 ILE A 44 1 6 HELIX 3 AA3 ASP A 49 ALA A 59 1 11 HELIX 4 AA4 VAL A 65 ASN A 83 1 19 HELIX 5 AA5 THR A 87 ASN A 113 1 27 HELIX 6 AA6 GLN B 209 LYS B 213 5 5 LINK C ARG B 207 N XRW B 208 1555 1555 1.32 LINK C XRW B 208 N GLN B 209 1555 1555 1.33 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 1957 1982 CONECT 1979 1981 1983 2009 CONECT 1980 1981 1987 1993 1994 CONECT 1981 1979 1980 1982 1995 CONECT 1982 1957 1981 1996 CONECT 1983 1979 CONECT 1984 1988 1990 1997 1998 CONECT 1985 1986 1990 1991 CONECT 1986 1985 1989 1992 1999 CONECT 1987 1980 1988 2000 2001 CONECT 1988 1984 1987 2002 2003 CONECT 1989 1986 2004 2005 2006 CONECT 1990 1984 1985 2007 CONECT 1991 1985 CONECT 1992 1986 2008 CONECT 1993 1980 CONECT 1994 1980 CONECT 1995 1981 CONECT 1996 1982 CONECT 1997 1984 CONECT 1998 1984 CONECT 1999 1986 CONECT 2000 1987 CONECT 2001 1987 CONECT 2002 1988 CONECT 2003 1988 CONECT 2004 1989 CONECT 2005 1989 CONECT 2006 1989 CONECT 2007 1990 CONECT 2008 1992 CONECT 2009 1979 MASTER 163 0 1 6 0 0 0 6 1048 2 32 11 END