HEADER PROTEIN BINDING 03-MAY-12 2LSP TITLE SOLUTION STRUCTURES OF BRD4 SECOND BROMODOMAIN WITH NF-KB-K310AC TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NF-KB-K310AC PEPTIDE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: SECOND BROMODOMAIN; COMPND 9 SYNONYM: PROTEIN HUNK1; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: BRD4, HUNK1; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS NF-KB, BRD4, HIV, BROMODOMAIN, KIDNEY DISEASE, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.ZHANG,R.LIU,Y.ZHONG,A.N.PLOTNIKOV,W.ZHANG,E.RUSINOVA,G.GERONA- AUTHOR 2 NEVARRO,N.MOSHKINA,J.JOSHUA,P.Y.CHUANG,M.OHLMEYER,J.HE,M.-M.ZHOU REVDAT 2 28-AUG-13 2LSP 1 JRNL REVDAT 1 18-JUL-12 2LSP 0 JRNL AUTH G.ZHANG,R.LIU,Y.ZHONG,A.N.PLOTNIKOV,W.ZHANG,L.ZENG, JRNL AUTH 2 E.RUSINOVA,G.GERONA-NEVARRO,N.MOSHKINA,J.JOSHUA,P.Y.CHUANG, JRNL AUTH 3 M.OHLMEYER,J.C.HE,M.M.ZHOU JRNL TITL DOWN-REGULATION OF NF-KAPPA B TRANSCRIPTIONAL ACTIVITY IN JRNL TITL 2 HIV-ASSOCIATED KIDNEY DISEASE BY BRD4 INHIBITION. JRNL REF J.BIOL.CHEM. V. 287 28840 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22645123 JRNL DOI 10.1074/JBC.M112.359505 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3, 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 2LSP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-12. REMARK 100 THE RCSB ID CODE IS RCSB102785. 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 : AMBIENT REMARK 210 SAMPLE CONTENTS : 100 MM SODIUM PHOSPHATE, 5 MM [U REMARK 210 -100% 2H] DTT, 100% D2O; 100 MM REMARK 210 SODIUM PHOSPHATE, 5 MM [U-100% REMARK 210 2H] DTT, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D HN(CO)CACB; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 13C-EDITED-15N/13C REMARK 210 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ; 600 MHZ; 500 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 7.1, TALOS 3.70F1, REMARK 210 NMRVIEW 5.04, CNS 1.21 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, 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 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 O MET B 442 H LEU B 446 1.55 REMARK 500 O TYR B 377 HB2 SER B 401 1.56 REMARK 500 O MET B 425 HG CYS B 429 1.56 REMARK 500 O SER B 358 H LYS B 362 1.56 REMARK 500 O GLN B 353 H CYS B 357 1.58 REMARK 500 HZ2 LYS B 349 OE2 GLU B 460 1.58 REMARK 500 O LEU B 354 H SER B 358 1.58 REMARK 500 O CYS B 357 H LEU B 361 1.59 REMARK 500 O LEU B 446 H PHE B 450 1.59 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 1 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 TYR B 412 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 TYR B 412 CB - CG - CD2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 TYR B 412 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 TYR B 412 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 4 TYR B 412 CB - CG - CD2 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 TYR B 412 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 5 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 TYR B 412 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 6 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.0 DEGREES REMARK 500 6 TYR B 412 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 7 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.0 DEGREES REMARK 500 7 TYR B 412 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 8 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.3 DEGREES REMARK 500 8 TYR B 412 CB - CG - CD1 ANGL. DEV. = -4.1 DEGREES REMARK 500 9 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.0 DEGREES REMARK 500 9 TYR B 412 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 10 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.1 DEGREES REMARK 500 10 TYR B 412 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 11 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.5 DEGREES REMARK 500 11 TYR B 412 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 12 TYR B 412 CB - CG - CD2 ANGL. DEV. = 3.9 DEGREES REMARK 500 12 TYR B 412 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 13 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.5 DEGREES REMARK 500 13 TYR B 412 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 14 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.2 DEGREES REMARK 500 14 TYR B 412 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 15 TYR B 412 CB - CG - CD2 ANGL. DEV. = 3.7 DEGREES REMARK 500 16 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.1 DEGREES REMARK 500 16 TYR B 412 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 17 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.3 DEGREES REMARK 500 17 TYR B 412 CB - CG - CD1 ANGL. DEV. = -4.1 DEGREES REMARK 500 18 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.3 DEGREES REMARK 500 18 TYR B 412 CB - CG - CD1 ANGL. DEV. = -4.1 DEGREES REMARK 500 19 TYR B 412 CB - CG - CD2 ANGL. DEV. = 4.2 DEGREES REMARK 500 19 TYR B 412 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 20 TYR B 412 CB - CG - CD2 ANGL. DEV. = 3.8 DEGREES REMARK 500 20 TYR B 412 CB - CG - CD1 ANGL. DEV. = -3.8 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 ALY A 7 94.31 -65.87 REMARK 500 1 MET A 10 104.45 62.44 REMARK 500 1 LYS A 11 88.37 -64.58 REMARK 500 1 ASP B 334 70.71 56.62 REMARK 500 1 GLN B 339 -67.95 -93.59 REMARK 500 1 PRO B 344 -85.84 -54.05 REMARK 500 1 LYS B 346 132.39 -178.40 REMARK 500 1 SER B 347 97.57 65.73 REMARK 500 1 VAL B 350 -75.10 -41.62 REMARK 500 1 LYS B 367 7.57 -63.35 REMARK 500 1 TYR B 372 41.06 -144.26 REMARK 500 1 ALA B 373 -5.57 -159.88 REMARK 500 1 ALA B 384 -65.00 -96.45 REMARK 500 1 LEU B 387 -87.39 -54.23 REMARK 500 1 HIS B 388 -28.31 73.80 REMARK 500 1 TYR B 390 -60.63 -23.08 REMARK 500 1 ILE B 393 -66.55 -93.48 REMARK 500 1 TYR B 412 107.91 -59.32 REMARK 500 1 ASP B 414 -171.53 173.35 REMARK 500 1 PRO B 458 -175.60 -62.44 REMARK 500 1 ASP B 459 -45.57 167.32 REMARK 500 2 GLU A 4 -79.83 64.93 REMARK 500 2 ALY A 7 96.53 -65.08 REMARK 500 2 ASP B 334 40.45 -85.00 REMARK 500 2 LYS B 346 -63.22 -147.85 REMARK 500 2 SER B 348 -30.46 145.56 REMARK 500 2 VAL B 350 -70.33 -54.39 REMARK 500 2 LYS B 367 7.65 -64.19 REMARK 500 2 TYR B 372 42.00 -146.61 REMARK 500 2 ALA B 373 -4.34 -161.01 REMARK 500 2 ALA B 384 -63.31 -95.87 REMARK 500 2 LEU B 387 -88.17 -60.25 REMARK 500 2 HIS B 388 -26.43 73.41 REMARK 500 2 TYR B 390 -57.30 -23.11 REMARK 500 2 ILE B 393 -66.64 -98.81 REMARK 500 2 ASP B 414 -174.50 170.83 REMARK 500 2 PHE B 418 -70.38 -56.30 REMARK 500 2 PRO B 435 8.56 -69.08 REMARK 500 2 PRO B 458 -175.56 -62.01 REMARK 500 2 ASP B 459 -39.57 -160.27 REMARK 500 3 GLU A 4 -71.12 -132.83 REMARK 500 3 THR A 5 -55.08 67.66 REMARK 500 3 PHE A 6 130.98 57.75 REMARK 500 3 SER A 8 -73.81 -46.39 REMARK 500 3 ILE A 9 119.86 78.17 REMARK 500 3 LYS A 12 -66.29 71.47 REMARK 500 3 GLN B 340 173.87 65.38 REMARK 500 3 GLU B 345 11.28 -141.22 REMARK 500 3 LYS B 346 -75.03 178.76 REMARK 500 3 SER B 347 -90.48 -148.10 REMARK 500 REMARK 500 THIS ENTRY HAS 418 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18439 RELATED DB: BMRB DBREF 2LSP A 1 13 UNP Q04206 TF65_HUMAN 304 316 DBREF 2LSP B 333 460 UNP O60885 BRD4_HUMAN 333 460 SEQRES 1 A 13 ARG THR TYR GLU THR PHE ALY SER ILE MET LYS LYS SER SEQRES 1 B 128 LYS ASP VAL PRO ASP SER GLN GLN HIS PRO ALA PRO GLU SEQRES 2 B 128 LYS SER SER LYS VAL SER GLU GLN LEU LYS CYS CYS SER SEQRES 3 B 128 GLY ILE LEU LYS GLU MET PHE ALA LYS LYS HIS ALA ALA SEQRES 4 B 128 TYR ALA TRP PRO PHE TYR LYS PRO VAL ASP VAL GLU ALA SEQRES 5 B 128 LEU GLY LEU HIS ASP TYR CYS ASP ILE ILE LYS HIS PRO SEQRES 6 B 128 MET ASP MET SER THR ILE LYS SER LYS LEU GLU ALA ARG SEQRES 7 B 128 GLU TYR ARG ASP ALA GLN GLU PHE GLY ALA ASP VAL ARG SEQRES 8 B 128 LEU MET PHE SER ASN CYS TYR LYS TYR ASN PRO PRO ASP SEQRES 9 B 128 HIS GLU VAL VAL ALA MET ALA ARG LYS LEU GLN ASP VAL SEQRES 10 B 128 PHE GLU MET ARG PHE ALA LYS MET PRO ASP GLU MODRES 2LSP ALY A 7 LYS N(6)-ACETYLLYSINE HET ALY A 7 26 HETNAM ALY N(6)-ACETYLLYSINE FORMUL 1 ALY C8 H16 N2 O3 HELIX 1 1 LYS B 349 PHE B 365 1 17 HELIX 2 2 LYS B 368 TYR B 372 5 5 HELIX 3 3 ASP B 389 ILE B 394 1 6 HELIX 4 4 ASP B 399 ALA B 409 1 11 HELIX 5 5 ASP B 414 ASN B 433 1 20 HELIX 6 6 HIS B 437 LYS B 456 1 20 LINK C PHE A 6 N ALY A 7 1555 1555 1.33 LINK C ALY A 7 N SER A 8 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20