HEADER HYDROLASE 03-MAY-06 2DOS TITLE STRUCTURAL BASIS FOR THE RECOGNITION OF LYS48-LINKED POLYUBIQUITIN TITLE 2 CHAIN BY THE JOSEPHIN DOMAIN OF ATAXIN-3, A PUTATIVE DEUBIQUITINATING TITLE 3 ENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATAXIN-3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JOSEPHIN DOMAIN; COMPND 5 SYNONYM: MACHADO-JOSEPH DISEASE PROTEIN 1, SPINOCEREBELLAR ATAXIA COMPND 6 TYPE 3 PROTEIN; COMPND 7 EC: 3.4.22.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1 KEYWDS DEUBIQUITINATING ENZYME, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.SUMIYOSHI REVDAT 5 01-MAY-24 2DOS 1 REMARK SEQADV REVDAT 4 31-DEC-14 2DOS 1 JRNL REVDAT 3 03-DEC-14 2DOS 1 JRNL VERSN REVDAT 2 24-FEB-09 2DOS 1 VERSN REVDAT 1 22-MAY-07 2DOS 0 JRNL AUTH T.SATOH,A.SUMIYOSHI,M.YAGI-UTSUMI,E.SAKATA,H.SASAKAWA, JRNL AUTH 2 E.KURIMOTO,Y.YAMAGUCHI,W.LI,C.A.JOAZEIRO,T.HIROKAWA,K.KATO JRNL TITL MODE OF SUBSTRATE RECOGNITION BY THE JOSEPHIN DOMAIN OF JRNL TITL 2 ATAXIN-3, WHICH HAS AN ENDO-TYPE DEUBIQUITINASE ACTIVITY. JRNL REF FEBS LETT. V. 588 4422 2014 JRNL REFN ISSN 0014-5793 JRNL PMID 25448680 JRNL DOI 10.1016/J.FEBSLET.2014.10.013 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CYANA 2.1 REMARK 3 AUTHORS : GUNTERT (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DOS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000025665. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 10MM SODIUM PHOSPHATE BUFFER REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.2MM JOSEPHIN DOMAIN U-15N,13C; REMARK 210 10MM SODIUM PHOSPHATE BUFFER; 90% REMARK 210 H2O, 10% D2O; 1.2MM JOSEPHIN REMARK 210 DOMAIN U-15N,13C; 10MM SODIUM REMARK 210 PHOSPHATE BUFFER; 99% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 920 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : ECA; AVANCE; DMX REMARK 210 SPECTROMETER MANUFACTURER : JEOL; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, CYANA 2.1, DELTA REMARK 210 4.3.3 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 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 7 147.29 -171.61 REMARK 500 1 LEU A 13 102.37 59.39 REMARK 500 1 THR A 54 159.20 179.43 REMARK 500 1 GLN A 64 73.81 63.57 REMARK 500 1 PRO A 65 -177.00 -69.77 REMARK 500 1 SER A 66 -169.72 51.98 REMARK 500 1 ASN A 68 -48.69 -156.96 REMARK 500 1 ASP A 70 -169.71 -111.41 REMARK 500 1 ASP A 71 -68.52 72.64 REMARK 500 1 PHE A 75 -169.09 -79.97 REMARK 500 1 LYS A 117 106.56 -40.63 REMARK 500 1 HIS A 119 145.19 179.39 REMARK 500 2 SER A 3 25.65 -150.83 REMARK 500 2 LYS A 8 101.07 60.28 REMARK 500 2 SER A 55 -75.67 -179.75 REMARK 500 2 GLN A 64 155.33 179.81 REMARK 500 2 PRO A 65 -170.52 -69.72 REMARK 500 2 ASN A 68 34.46 -179.96 REMARK 500 2 MET A 69 -75.54 69.13 REMARK 500 2 ASP A 70 -177.99 57.67 REMARK 500 2 ASP A 71 24.82 -140.91 REMARK 500 2 SER A 72 -75.19 -88.43 REMARK 500 2 PHE A 74 88.02 51.03 REMARK 500 2 SER A 76 171.61 178.18 REMARK 500 2 ARG A 110 -63.43 -108.90 REMARK 500 2 LYS A 117 -87.49 58.77 REMARK 500 3 GLN A 64 153.80 64.32 REMARK 500 3 SER A 66 -68.94 72.27 REMARK 500 3 ASP A 70 -42.45 -179.09 REMARK 500 3 PHE A 75 -174.09 52.97 REMARK 500 3 LYS A 117 106.24 -40.03 REMARK 500 3 HIS A 119 144.10 -179.90 REMARK 500 3 GLU A 158 -71.88 -87.32 REMARK 500 4 SER A 3 28.51 -161.12 REMARK 500 4 GLU A 7 141.25 -179.26 REMARK 500 4 SER A 12 145.05 66.06 REMARK 500 4 GLN A 64 156.95 179.25 REMARK 500 4 PRO A 65 -170.98 -69.74 REMARK 500 4 MET A 69 -169.85 -70.30 REMARK 500 4 ASP A 70 -75.53 -78.06 REMARK 500 4 PHE A 75 -168.94 -61.03 REMARK 500 4 SER A 76 177.07 178.35 REMARK 500 4 LYS A 117 106.69 -43.17 REMARK 500 4 GLU A 118 44.72 70.39 REMARK 500 4 HIS A 119 148.89 179.63 REMARK 500 5 GLU A 2 -61.20 73.70 REMARK 500 5 LYS A 8 109.91 64.08 REMARK 500 5 SER A 12 -74.88 -108.76 REMARK 500 5 THR A 54 163.11 64.38 REMARK 500 5 GLN A 64 69.94 60.53 REMARK 500 REMARK 500 THIS ENTRY HAS 120 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2DOS A 1 171 UNP P54252 ATX3_HUMAN 1 171 SEQADV 2DOS GLY A -4 UNP P54252 CLONING ARTIFACT SEQADV 2DOS PRO A -3 UNP P54252 CLONING ARTIFACT SEQADV 2DOS LEU A -2 UNP P54252 CLONING ARTIFACT SEQADV 2DOS GLY A -1 UNP P54252 CLONING ARTIFACT SEQADV 2DOS SER A 0 UNP P54252 CLONING ARTIFACT SEQRES 1 A 176 GLY PRO LEU GLY SER MET GLU SER ILE PHE HIS GLU LYS SEQRES 2 A 176 GLN GLU GLY SER LEU CYS ALA GLN HIS CYS LEU ASN ASN SEQRES 3 A 176 LEU LEU GLN GLY GLU TYR PHE SER PRO VAL GLU LEU SER SEQRES 4 A 176 SER ILE ALA HIS GLN LEU ASP GLU GLU GLU ARG MET ARG SEQRES 5 A 176 MET ALA GLU GLY GLY VAL THR SER GLU ASP TYR ARG THR SEQRES 6 A 176 PHE LEU GLN GLN PRO SER GLY ASN MET ASP ASP SER GLY SEQRES 7 A 176 PHE PHE SER ILE GLN VAL ILE SER ASN ALA LEU LYS VAL SEQRES 8 A 176 TRP GLY LEU GLU LEU ILE LEU PHE ASN SER PRO GLU TYR SEQRES 9 A 176 GLN ARG LEU ARG ILE ASP PRO ILE ASN GLU ARG SER PHE SEQRES 10 A 176 ILE CYS ASN TYR LYS GLU HIS TRP PHE THR VAL ARG LYS SEQRES 11 A 176 LEU GLY LYS GLN TRP PHE ASN LEU ASN SER LEU LEU THR SEQRES 12 A 176 GLY PRO GLU LEU ILE SER ASP THR TYR LEU ALA LEU PHE SEQRES 13 A 176 LEU ALA GLN LEU GLN GLN GLU GLY TYR SER ILE PHE VAL SEQRES 14 A 176 VAL LYS GLY ASP LEU PRO ASP HELIX 1 1 CYS A 14 LEU A 23 1 10 HELIX 2 2 SER A 29 GLU A 50 1 22 HELIX 3 3 THR A 54 GLN A 63 1 10 HELIX 4 4 SER A 76 VAL A 86 1 11 HELIX 5 5 SER A 96 ARG A 103 1 8 HELIX 6 6 SER A 144 GLY A 159 1 16 SHEET 1 A 6 GLU A 90 LEU A 93 0 SHEET 2 A 6 SER A 161 LYS A 166 -1 O LYS A 166 N GLU A 90 SHEET 3 A 6 SER A 111 TYR A 116 -1 N ILE A 113 O PHE A 163 SHEET 4 A 6 HIS A 119 LEU A 126 -1 O VAL A 123 N PHE A 112 SHEET 5 A 6 GLN A 129 LEU A 133 -1 O PHE A 131 N ARG A 124 SHEET 6 A 6 GLU A 141 ILE A 143 -1 O ILE A 143 N TRP A 130 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