HEADER SIGNALING PROTEIN 08-OCT-04 1WR1 TITLE THE COMPLEX STRUCTURE OF DSK2P UBA WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: UBIQUITIN-LIKE PROTEIN DSK2; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: C-TERMINAL UBA DOMAIN; COMPND 9 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: UBI4 (1224-1451); 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: PET-24A; 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: DSK2 (982-1120); 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: PGEX-KG KEYWDS UBA DOMAIN, UBA-UBIQUITIN COMPLEX, DSK2, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.OHNO,J.G.JEE,K.FUJIWARA,T.TENNO,N.GODA,H.TOCHIO,H.HIROAKI, AUTHOR 2 H.KOBAYASHI,M.SHIRAKAWA REVDAT 4 27-SEP-23 1WR1 1 REMARK REVDAT 3 09-SEP-20 1WR1 1 TITLE REMARK SEQADV REVDAT 2 24-FEB-09 1WR1 1 VERSN REVDAT 1 19-APR-05 1WR1 0 JRNL AUTH A.OHNO,J.JEE,K.FUJIWARA,T.TENNO,N.GODA,H.TOCHIO,H.KOBAYASHI, JRNL AUTH 2 H.HIROAKI,M.SHIRAKAWA JRNL TITL STRUCTURE OF THE UBA DOMAIN OF DSK2P IN COMPLEX WITH JRNL TITL 2 UBIQUITIN MOLECULAR DETERMINANTS FOR UBIQUITIN RECOGNITION. JRNL REF STRUCTURE V. 13 521 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 15837191 JRNL DOI 10.1016/J.STR.2005.01.011 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, AMBER 7 REMARK 3 AUTHORS : PEARLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WR1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000023898. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 20MM POTASSIUM PHOSPHATE, 5MM REMARK 210 POTASSIUM CHLORIDE REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : U-15N, 13C UBIQUITIN + DSK2-UBA REMARK 210 COMPLEX (0.9MM); U-15N, 13C DSK2- REMARK 210 UBA + UBIQUITIN COMPLEX (1.0MM) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 4D_13C/15N-SEPARATED_NOESY; REMARK 210 3D_15N-SEPARATED_NOESY; 3D_13C-SEPARATED_NOESY; 3D_13C-EDITED/ REMARK 210 13C-FILTERED-NOESY; 3D_13C-SEPARATED_ROESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : DRX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1C, NMRPIPE 2.1, SPARKY REMARK 210 3.1.0.0, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS, ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 : 16 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 MET A 1 N 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 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG B 331 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 PRO B 316 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 3 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 PRO B 316 CA - N - CD ANGL. DEV. = -8.8 DEGREES REMARK 500 4 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 PRO B 316 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 5 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG B 356 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 PRO B 316 CA - N - CD ANGL. DEV. = -9.2 DEGREES REMARK 500 7 ARG B 331 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG B 356 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 PRO B 316 CA - N - CD ANGL. DEV. = -9.0 DEGREES REMARK 500 9 ARG B 356 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 10 ARG B 331 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 11 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 11 PRO B 316 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 12 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 12 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 12 PRO B 316 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 12 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 13 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 13 ARG B 356 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 PRO B 316 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 14 ARG B 331 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 16 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG B 337 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 17 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 18 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 18 ARG B 337 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 19 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 PRO B 316 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 19 ARG B 349 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 51 ANGLE DEVIATIONS. 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 GLU A 64 19.03 55.93 REMARK 500 1 ARG A 74 -59.60 62.44 REMARK 500 1 SER B 319 -173.65 61.17 REMARK 500 2 ALA A 46 29.94 47.90 REMARK 500 2 ARG A 74 5.32 56.93 REMARK 500 2 ASP B 346 76.31 -66.64 REMARK 500 4 GLU A 64 18.69 56.61 REMARK 500 4 ARG A 74 18.98 53.34 REMARK 500 4 ILE B 325 6.09 -65.85 REMARK 500 5 ALA A 46 27.86 48.41 REMARK 500 5 GLU A 64 22.43 49.41 REMARK 500 6 ALA A 46 47.58 38.66 REMARK 500 6 GLU A 64 19.05 53.35 REMARK 500 6 SER B 319 88.30 -69.53 REMARK 500 7 ILE B 318 -56.82 66.29 REMARK 500 8 GLU A 64 20.58 49.31 REMARK 500 8 ILE B 318 -86.26 44.19 REMARK 500 8 ASP B 346 78.55 -69.81 REMARK 500 9 ALA A 46 28.54 48.79 REMARK 500 9 GLU A 64 20.37 48.51 REMARK 500 10 GLU A 64 21.97 49.46 REMARK 500 10 ILE B 325 71.72 54.52 REMARK 500 11 GLU A 64 22.48 48.77 REMARK 500 11 ARG A 74 -60.95 -132.89 REMARK 500 11 ILE B 325 -2.94 -59.71 REMARK 500 13 GLU A 64 20.74 49.72 REMARK 500 14 GLU A 64 19.00 57.93 REMARK 500 14 ARG A 74 -69.78 54.62 REMARK 500 14 SER B 319 18.87 48.95 REMARK 500 14 ILE B 325 25.15 -75.80 REMARK 500 15 GLU A 64 18.81 54.54 REMARK 500 16 PHE B 344 77.10 -102.29 REMARK 500 18 ARG A 74 -0.29 45.80 REMARK 500 18 ILE B 318 -82.71 52.06 REMARK 500 19 ALA A 46 28.95 47.86 REMARK 500 19 GLU A 64 26.00 47.08 REMARK 500 20 ALA A 46 29.31 48.10 REMARK 500 20 GLU A 64 19.89 50.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF UBIQUITIN DBREF 1WR1 A 1 76 UNP P61864 UBIQ_YEAST 1 76 DBREF 1WR1 B 328 373 UNP P48510 DSK2_YEAST 328 373 SEQADV 1WR1 PRO B 316 UNP P48510 CLONING ARTIFACT SEQADV 1WR1 GLY B 317 UNP P48510 CLONING ARTIFACT SEQADV 1WR1 ILE B 318 UNP P48510 CLONING ARTIFACT SEQADV 1WR1 SER B 319 UNP P48510 CLONING ARTIFACT SEQADV 1WR1 GLY B 320 UNP P48510 CLONING ARTIFACT SEQADV 1WR1 GLY B 321 UNP P48510 CLONING ARTIFACT SEQADV 1WR1 GLY B 322 UNP P48510 CLONING ARTIFACT SEQADV 1WR1 GLY B 323 UNP P48510 CLONING ARTIFACT SEQADV 1WR1 GLY B 324 UNP P48510 CLONING ARTIFACT SEQADV 1WR1 ILE B 325 UNP P48510 CLONING ARTIFACT SEQADV 1WR1 LEU B 326 UNP P48510 CLONING ARTIFACT SEQADV 1WR1 ASP B 327 UNP P48510 CLONING ARTIFACT SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU SER SER ASP THR ILE ASP ASN VAL SEQRES 3 A 76 LYS SER LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 58 PRO GLY ILE SER GLY GLY GLY GLY GLY ILE LEU ASP PRO SEQRES 2 B 58 GLU GLU ARG TYR GLU HIS GLN LEU ARG GLN LEU ASN ASP SEQRES 3 B 58 MET GLY PHE PHE ASP PHE ASP ARG ASN VAL ALA ALA LEU SEQRES 4 B 58 ARG ARG SER GLY GLY SER VAL GLN GLY ALA LEU ASP SER SEQRES 5 B 58 LEU LEU ASN GLY ASP VAL HELIX 1 1 THR A 22 GLN A 31 1 10 HELIX 2 2 LEU A 56 ASN A 60 5 5 HELIX 3 3 GLY B 323 LEU B 326 5 4 HELIX 4 4 ASP B 327 TYR B 332 1 6 HELIX 5 5 TYR B 332 GLY B 343 1 12 HELIX 6 6 ASP B 346 GLY B 358 1 13 HELIX 7 7 SER B 360 GLY B 371 1 12 SHEET 1 A 5 THR A 12 LEU A 15 0 SHEET 2 A 5 ILE A 3 LYS A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 SER A 65 LEU A 71 1 O SER A 65 N PHE A 4 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 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