HEADER TRANSCRIPTION REGULATOR 14-MAY-10 2KY6 TITLE STRUCTURE OF ARC92VBD/MED25ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 25; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VP16-BINDING-DOMAIN (VBD) ACTIVATOR-INTERACTING DOMAIN COMPND 5 (ACID) (UNP RESIDUES 391-553); COMPND 6 SYNONYM: MEDIATOR COMPLEX SUBUNIT 25, ACTIVATOR-RECRUITED COFACTOR 92 COMPND 7 KDA COMPONENT, ARC92, ACTIVATOR INTERACTION DOMAIN-CONTAINING PROTEIN COMPND 8 1, P78; 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: MED25, ACID1, ARC92, PTOV2, TCBAP0758; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: P-HIS-PARALLEL; SOURCE 10 OTHER_DETAILS: HIS-GB1-TEV-TAG KEYWDS MEDIATOR, ARC, VP16 BINDING DOMAIN, ACID, TRANSCRIPTION REGULATOR EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR A.G.MILBRADT,Z.J.SUN,P.SELENKO,K.TAKEUCHI,A.M.NAAR,G.WAGNER REVDAT 2 20-APR-11 2KY6 1 JRNL REVDAT 1 09-MAR-11 2KY6 0 JRNL AUTH A.G.MILBRADT,M.KULKARNI,T.YI,K.TAKEUCHI,Z.Y.SUN,R.E.LUNA, JRNL AUTH 2 P.SELENKO,A.M.NAAR,G.WAGNER JRNL TITL STRUCTURE OF THE VP16 TRANSACTIVATOR TARGET IN THE MEDIATOR. JRNL REF NAT.STRUCT.MOL.BIOL. V. 18 410 2011 JRNL REFN ISSN 1545-9993 JRNL PMID 21378963 JRNL DOI 10.1038/NSMB.1999 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CYANA CALCULATION, CNS IN WATER BOX REMARK 4 REMARK 4 2KY6 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-10. REMARK 100 THE RCSB ID CODE IS RCSB101720. 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 : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 50-1000 UM [U-99% 15N] ARC92VBD, REMARK 210 95% H2O/5% D2O; 1.0 MM ARC92VBD, REMARK 210 100% D2O; 200-1000 UM [U-99% 13C; REMARK 210 U-99% 15N] ARC92VBD, 95% H2O/5% REMARK 210 D2O; 700 UM [U-100% 13C; U-100% REMARK 210 15N; U-80% 2H] ARC92VBD, 95% H2O/ REMARK 210 5% D2O; 700 UM [ILV-100% 13C1H; U REMARK 210 -100% 15N; U-100% 2H] ARC92VBD, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-1H NOESY; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D HNCO; 3D HNCA; 3D HN(CO)CA; 3D REMARK 210 HNCACB; 3D HCCH-TOCSY; 2D 1H-13C REMARK 210 HSQC; 4D HMQCNOESYHMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 900 MHZ; 750 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, CARA 1.8.4, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: 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 394 40.30 -76.67 REMARK 500 1 PRO A 412 74.93 -68.99 REMARK 500 1 PRO A 414 103.56 -47.62 REMARK 500 1 ALA A 415 -29.39 -154.12 REMARK 500 1 SER A 416 -143.25 -147.06 REMARK 500 1 ASP A 418 -60.28 68.52 REMARK 500 1 ALA A 419 -70.68 -53.47 REMARK 500 1 ASN A 420 78.74 -106.74 REMARK 500 1 PRO A 463 -36.14 -35.01 REMARK 500 1 LYS A 478 -83.55 -124.39 REMARK 500 1 HIS A 502 75.86 -69.78 REMARK 500 1 THR A 503 -41.04 -154.37 REMARK 500 1 PRO A 505 42.58 -98.36 REMARK 500 1 GLU A 507 -72.98 67.91 REMARK 500 1 LYS A 520 28.05 49.26 REMARK 500 1 VAL A 547 70.90 73.71 REMARK 500 1 LYS A 551 96.63 57.25 REMARK 500 1 LEU A 552 119.81 -164.35 REMARK 500 2 ALA A 415 23.60 -146.37 REMARK 500 2 ASP A 418 76.96 50.14 REMARK 500 2 ASN A 420 84.03 -151.88 REMARK 500 2 LYS A 478 -95.61 -117.07 REMARK 500 2 PRO A 501 105.31 -57.78 REMARK 500 2 THR A 503 -63.31 -94.67 REMARK 500 2 GLU A 507 -66.84 68.24 REMARK 500 2 LYS A 520 18.18 51.30 REMARK 500 2 LYS A 551 134.56 75.21 REMARK 500 3 VAL A 395 22.68 -77.14 REMARK 500 3 PRO A 414 59.03 -68.94 REMARK 500 3 ALA A 415 14.08 -151.03 REMARK 500 3 SER A 416 -159.34 -157.23 REMARK 500 3 ASP A 418 78.35 -60.50 REMARK 500 3 ALA A 419 -60.92 -175.59 REMARK 500 3 THR A 441 32.53 -88.36 REMARK 500 3 GLU A 507 -55.18 71.15 REMARK 500 3 ARG A 509 -39.25 -138.44 REMARK 500 3 VAL A 547 86.03 75.79 REMARK 500 4 GLN A 393 43.10 -91.25 REMARK 500 4 SER A 394 96.83 -68.02 REMARK 500 4 ALA A 415 20.83 -174.34 REMARK 500 4 SER A 416 -153.35 -136.07 REMARK 500 4 ASP A 418 82.84 57.20 REMARK 500 4 ALA A 419 -70.16 -123.39 REMARK 500 4 PRO A 463 28.88 -72.92 REMARK 500 4 LYS A 478 -71.97 -118.20 REMARK 500 4 HIS A 502 91.78 -61.78 REMARK 500 4 CYS A 506 22.09 -76.18 REMARK 500 4 ARG A 509 -41.23 -147.73 REMARK 500 4 LYS A 520 25.83 49.97 REMARK 500 4 GLN A 548 32.34 -99.28 REMARK 500 REMARK 500 THIS ENTRY HAS 268 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 6 ARG A 469 0.08 SIDE CHAIN REMARK 500 16 ARG A 425 0.11 SIDE CHAIN REMARK 500 16 ARG A 469 0.08 SIDE CHAIN REMARK 500 25 ARG A 469 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 19 LYS A 520 24.8 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL DBREF 2KY6 A 391 553 UNP Q71SY5 MED25_HUMAN 391 553 SEQADV 2KY6 GLY A 388 UNP Q71SY5 EXPRESSION TAG SEQADV 2KY6 GLU A 389 UNP Q71SY5 EXPRESSION TAG SEQADV 2KY6 PHE A 390 UNP Q71SY5 EXPRESSION TAG SEQRES 1 A 166 GLY GLU PHE GLY GLN GLN SER VAL SER ASN LYS LEU LEU SEQRES 2 A 166 ALA TRP SER GLY VAL LEU GLU TRP GLN GLU LYS PRO LYS SEQRES 3 A 166 PRO ALA SER VAL ASP ALA ASN THR LYS LEU THR ARG SER SEQRES 4 A 166 LEU PRO CYS GLN VAL TYR VAL ASN HIS GLY GLU ASN LEU SEQRES 5 A 166 LYS THR GLU GLN TRP PRO GLN LYS LEU ILE MET GLN LEU SEQRES 6 A 166 ILE PRO GLN GLN LEU LEU THR THR LEU GLY PRO LEU PHE SEQRES 7 A 166 ARG ASN SER ARG MET VAL GLN PHE HIS PHE THR ASN LYS SEQRES 8 A 166 ASP LEU GLU SER LEU LYS GLY LEU TYR ARG ILE MET GLY SEQRES 9 A 166 ASN GLY PHE ALA GLY CYS VAL HIS PHE PRO HIS THR ALA SEQRES 10 A 166 PRO CYS GLU VAL ARG VAL LEU MET LEU LEU TYR SER SER SEQRES 11 A 166 LYS LYS LYS ILE PHE MET GLY LEU ILE PRO TYR ASP GLN SEQRES 12 A 166 SER GLY PHE VAL ASN GLY ILE ARG GLN VAL ILE THR ASN SEQRES 13 A 166 HIS LYS GLN VAL GLN GLN GLN LYS LEU GLU HELIX 1 1 LYS A 440 TRP A 444 5 5 HELIX 2 2 GLN A 455 GLY A 462 1 8 HELIX 3 3 PRO A 463 ARG A 466 5 4 HELIX 4 4 ASP A 479 GLY A 493 1 15 HELIX 5 5 ASP A 529 GLN A 546 1 18 SHEET 1 A 8 LYS A 398 GLN A 409 0 SHEET 2 A 8 THR A 424 ASN A 434 -1 O CYS A 429 N GLY A 404 SHEET 3 A 8 SER A 468 PHE A 475 -1 O HIS A 474 N GLN A 430 SHEET 4 A 8 PHE A 522 PRO A 527 -1 O GLY A 524 N VAL A 471 SHEET 5 A 8 VAL A 510 TYR A 515 -1 N LEU A 514 O MET A 523 SHEET 6 A 8 PHE A 494 HIS A 499 -1 N VAL A 498 O LEU A 511 SHEET 7 A 8 LYS A 447 PRO A 454 -1 N GLN A 451 O CYS A 497 SHEET 8 A 8 LYS A 398 GLN A 409 1 N GLU A 407 O LEU A 448 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