HEADER TRANSCRIPTION ACTIVATOR 24-MAR-04 1SSE TITLE SOLUTION STRUCTURE OF THE OXIDIZED FORM OF THE YAP1 REDOX DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AP-1 LIKE TRANSCRIPTION FACTOR YAP1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-CRD, RESIDUES 279-313; COMPND 5 SYNONYM: PHENANTHROLINE RESISTANCE PROTEIN PAR1, PLEIOTROPIC DRUG COMPND 6 RESISTANCE PROTEIN PDR4; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: AP-1 LIKE TRANSCRIPTION FACTOR YAP1; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: C-CRD, RESIDUES 565-650; COMPND 12 SYNONYM: PHENANTHROLINE RESISTANCE PROTEIN PAR1, PLEIOTROPIC DRUG COMPND 13 RESISTANCE PROTEIN PDR4; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: YAP1, SNQ3, PAR1, PDR4, YML007W, YM9571.12; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSET; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 13 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 14 ORGANISM_TAXID: 4932; SOURCE 15 GENE: YAP1, SNQ3, PAR1, PDR4, YML007W, YM9571.12; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PRSET KEYWDS DISULFIDE BOND, NUCLEAR EXPORT SIGNAL, NES, REDOX-REGULATION, KEYWDS 2 TRANSCRIPTION ACTIVATOR EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.J.WOOD,G.STORZ,N.TJANDRA REVDAT 3 02-MAR-22 1SSE 1 REMARK REVDAT 2 24-FEB-09 1SSE 1 VERSN REVDAT 1 31-AUG-04 1SSE 0 JRNL AUTH M.J.WOOD,G.STORZ,N.TJANDRA JRNL TITL STRUCTURAL BASIS FOR REDOX REGULATION OF YAP1 TRANSCRIPTION JRNL TITL 2 FACTOR LOCALIZATION. JRNL REF NATURE V. 430 917 2004 JRNL REFN ISSN 0028-0836 JRNL PMID 15318225 JRNL DOI 10.1038/NATURE02790 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.1, XPLOR-NIH 2.0.6 REMARK 3 AUTHORS : BRUNGER & SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE REMARK 3 (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: YAP1-RD STRUCTURES WERE CALCULATED WITH REMARK 3 1103 NOE DISTANCE RESTRAINTS, 54 HYDROGEN BOND RESTRAINTS, 92 REMARK 3 DIHEDRAL ANGLE RESTRAINTS AND 93 RESIDUAL DIPOLAR COUPLINGS. REMARK 3 RESIDUES 279-300 AND 565-592 ARE DISORDERED. REMARK 4 REMARK 4 1SSE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000021962. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 20 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM U-15N; U-15N & 13C.; 0.8 REMARK 210 MM U-15N & 13C. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; REMARK 210 4D_13C/15N-SEPARATED_NOESY; REMARK 210 HNCACB; EXPERIMENTS FOR RESIDUAL REMARK 210 DIPOLAR COUPLING MEASUREMENTS; REMARK 210 4D_13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PIPP 4.2.8, XWINNMR 2.5 REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STUCTURES WITH THE LOWEST ENERGY REMARK 210 AND NO NOE OR DIHEDRAL REMARK 210 VIOLATIONS > 0.5 A AND 5 DEGREES, REMARK 210 RESPECTIVELY. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: RESIDUAL DIPOLAR COUPLINGS (DN-H AND DCAH) WERE MEASURED REMARK 210 IN A SOLUTION COMPOSED OF PF1 PHAGE. 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 SER B 567 H LEU B 569 1.52 REMARK 500 O ARG B 604 HG1 THR B 607 1.56 REMARK 500 O ASN A 307 H CYS A 310 1.58 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 LEU A 280 -149.06 -68.49 REMARK 500 1 ASP A 281 -0.91 -157.56 REMARK 500 1 SER A 282 -161.53 -61.39 REMARK 500 1 ASN A 283 -71.88 62.12 REMARK 500 1 ASN A 287 84.82 -157.63 REMARK 500 1 ASP A 288 72.82 -158.06 REMARK 500 1 GLU A 292 -56.90 -168.70 REMARK 500 1 ASN A 293 -64.76 -171.27 REMARK 500 1 GLU A 297 -153.15 52.21 REMARK 500 1 GLN A 298 -7.92 -163.34 REMARK 500 1 SER A 300 -127.31 -124.75 REMARK 500 1 GLN A 308 -38.71 -35.64 REMARK 500 1 VAL A 309 -12.42 -46.80 REMARK 500 1 SER B 568 -51.62 67.19 REMARK 500 1 GLN B 570 80.05 -63.00 REMARK 500 1 ALA B 572 -169.24 -170.29 REMARK 500 1 ASN B 577 19.91 53.43 REMARK 500 1 ASP B 584 78.38 -69.03 REMARK 500 1 SER B 590 32.82 -160.01 REMARK 500 1 ARG B 597 -156.17 -109.99 REMARK 500 1 CYS B 598 -105.39 -59.02 REMARK 500 1 SER B 599 -18.12 -44.21 REMARK 500 1 THR B 607 -2.17 -46.54 REMARK 500 1 PRO B 609 6.71 -60.07 REMARK 500 1 LYS B 610 -93.58 -72.34 REMARK 500 1 TYR B 611 148.85 62.27 REMARK 500 1 SER B 612 -64.85 -176.77 REMARK 500 1 ASP B 613 69.26 -151.64 REMARK 500 1 ARG B 632 33.25 -80.39 REMARK 500 2 LEU A 280 21.44 -74.87 REMARK 500 2 SER A 282 175.57 53.05 REMARK 500 2 ASN A 283 -144.46 -77.62 REMARK 500 2 ASP A 288 -160.09 -76.86 REMARK 500 2 PHE A 289 27.03 -165.47 REMARK 500 2 ASN A 290 -142.39 -163.68 REMARK 500 2 PHE A 291 22.65 -170.34 REMARK 500 2 ASN A 293 -73.82 -168.59 REMARK 500 2 GLN A 294 74.75 51.06 REMARK 500 2 PHE A 295 44.54 -81.27 REMARK 500 2 ASP A 296 76.65 55.47 REMARK 500 2 VAL A 299 -83.88 -132.06 REMARK 500 2 SER A 300 -109.61 156.18 REMARK 500 2 VAL A 309 -16.74 -46.73 REMARK 500 2 SER B 568 -93.99 -169.46 REMARK 500 2 GLN B 570 -113.65 32.28 REMARK 500 2 ASN B 571 -32.39 -165.50 REMARK 500 2 ALA B 572 -164.85 -169.15 REMARK 500 2 LYS B 574 -170.52 -54.76 REMARK 500 2 ILE B 575 -77.16 -133.58 REMARK 500 2 ASN B 576 -84.89 -158.30 REMARK 500 REMARK 500 THIS ENTRY HAS 722 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1SSE A 279 313 UNP P19880 YAP1_YEAST 279 313 DBREF 1SSE B 565 650 UNP P19880 YAP1_YEAST 565 650 SEQRES 1 A 35 ASN LEU ASP SER ASN MET PHE SER ASN ASP PHE ASN PHE SEQRES 2 A 35 GLU ASN GLN PHE ASP GLU GLN VAL SER GLU PHE CYS SER SEQRES 3 A 35 LYS MET ASN GLN VAL CYS GLY THR ARG SEQRES 1 B 86 ASN GLY SER SER LEU GLN ASN ALA ASP LYS ILE ASN ASN SEQRES 2 B 86 GLY ASN ASP ASN ASP ASN ASP ASN ASP VAL VAL PRO SER SEQRES 3 B 86 LYS GLU GLY SER LEU LEU ARG CYS SER GLU ILE TRP ASP SEQRES 4 B 86 ARG ILE THR THR HIS PRO LYS TYR SER ASP ILE ASP VAL SEQRES 5 B 86 ASP GLY LEU CYS SER GLU LEU MET ALA LYS ALA LYS CYS SEQRES 6 B 86 SER GLU ARG GLY VAL VAL ILE ASN ALA GLU ASP VAL GLN SEQRES 7 B 86 LEU ALA LEU ASN LYS HIS MET ASN HELIX 1 1 ASP A 288 GLU A 292 5 5 HELIX 2 2 SER A 300 VAL A 309 1 10 HELIX 3 3 ARG B 597 THR B 607 1 11 HELIX 4 4 ASP B 615 MET B 624 1 10 HELIX 5 5 ALA B 638 LYS B 647 1 10 SHEET 1 A 2 LEU B 595 LEU B 596 0 SHEET 2 A 2 ILE B 636 ASN B 637 -1 O ILE B 636 N LEU B 596 SHEET 1 B 2 CYS B 629 SER B 630 0 SHEET 2 B 2 GLY B 633 VAL B 634 -1 O GLY B 633 N SER B 630 SSBOND 1 CYS A 303 CYS B 598 1555 1555 2.02 SSBOND 2 CYS A 310 CYS B 629 1555 1555 2.02 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