PDB Short entry for 2AGA HEADER TRANSCRIPTION 26-JUL-05 2AGA TITLE DE-UBIQUITINATING FUNCTION OF ATAXIN-3: INSIGHTS FROM THE SOLUTION TITLE 2 STRUCTURE OF THE JOSEPHIN DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACHADO-JOSEPH DISEASE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JOSEPHIN DOMAIN; COMPND 5 SYNONYM: ATAXIN-3, SPINOCEREBELLAR ATAXIA TYPE 3 PROTEIN; COMPND 6 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: ATXN3, ATX3, MJD, MJD1, SCA3; 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: PGEX6P-1 KEYWDS POLYGLUTAMINE, UBIQUITIN, UIM, ATAXIA, VCP/P97, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.MAO,F.SENIC-MATUGLIA,P.DI FIORE,S.POLO,M.E.HODSDON,P.DE CAMILLI REVDAT 4 14-JUN-23 2AGA 1 REMARK REVDAT 3 05-FEB-20 2AGA 1 REMARK SEQADV REVDAT 2 24-FEB-09 2AGA 1 VERSN REVDAT 1 30-AUG-05 2AGA 0 JRNL AUTH Y.MAO,F.SENIC-MATUGLIA,P.P.DI FIORE,S.POLO,M.E.HODSDON, JRNL AUTH 2 P.DE CAMILLI JRNL TITL DEUBIQUITINATING FUNCTION OF ATAXIN-3: INSIGHTS FROM THE JRNL TITL 2 SOLUTION STRUCTURE OF THE JOSEPHIN DOMAIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 12700 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 16118278 JRNL DOI 10.1073/PNAS.0506344102 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 1.0.5, CYANA 1.0.5 REMARK 3 AUTHORS : GUENTERT (CYANA), GUENTERT (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 2960 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 224 DIHEDRAL ANGLE RESTRAINTS,122 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS. REMARK 4 REMARK 4 2AGA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000033857. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 20 MM KPO4 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2MM JOSEPHIN DOMAIN U-15N,13C; REMARK 210 20MM PHOSPHATE BUFFER PH 6.4; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, SPARKY 3.106 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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 : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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: 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 LEU A 45 H GLU A 49 1.36 REMARK 500 O PHE A 66 H GLN A 69 1.41 REMARK 500 O GLU A 37 H ILE A 41 1.43 REMARK 500 O MET A 51 H GLU A 55 1.44 REMARK 500 O THR A 59 H GLU A 61 1.44 REMARK 500 O GLU A 48 H ARG A 52 1.47 REMARK 500 O TYR A 152 H PHE A 156 1.48 REMARK 500 O GLN A 44 H GLU A 48 1.50 REMARK 500 O TRP A 135 H ILE A 148 1.51 REMARK 500 HD1 HIS A 11 OE1 GLN A 14 1.53 REMARK 500 H GLU A 95 O LYS A 171 1.54 REMARK 500 O CYS A 119 H PHE A 126 1.58 REMARK 500 O TYR A 63 H LEU A 67 1.60 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 3 -47.90 86.12 REMARK 500 1 SER A 8 58.19 -155.07 REMARK 500 1 PHE A 10 -163.44 156.52 REMARK 500 1 GLU A 12 -103.99 -49.26 REMARK 500 1 LEU A 18 -50.69 -175.04 REMARK 500 1 GLN A 29 -5.35 78.94 REMARK 500 1 GLU A 31 -108.24 -56.19 REMARK 500 1 VAL A 58 7.47 49.65 REMARK 500 1 THR A 59 20.75 35.92 REMARK 500 1 SER A 60 -50.88 65.64 REMARK 500 1 SER A 71 -151.95 -84.85 REMARK 500 1 ASN A 73 -72.41 62.80 REMARK 500 1 MET A 74 165.53 177.55 REMARK 500 1 ASP A 76 21.12 -148.43 REMARK 500 1 SER A 101 106.32 -21.65 REMARK 500 1 ARG A 108 64.22 127.78 REMARK 500 1 LYS A 122 -84.44 53.95 REMARK 500 1 GLU A 123 -68.68 -109.11 REMARK 500 1 ASN A 139 -74.39 176.68 REMARK 500 1 SER A 140 -29.21 172.03 REMARK 500 1 THR A 143 25.35 46.82 REMARK 500 1 TYR A 165 106.96 158.26 REMARK 500 1 SER A 166 70.62 -167.72 REMARK 500 1 GLN A 184 -68.11 -161.80 REMARK 500 1 MET A 185 107.66 -42.85 REMARK 500 1 GLN A 189 -56.69 -177.53 REMARK 500 2 SER A 8 59.30 -151.67 REMARK 500 2 PHE A 10 -161.90 160.63 REMARK 500 2 GLU A 12 -101.44 -47.65 REMARK 500 2 SER A 17 37.54 33.64 REMARK 500 2 LEU A 18 -52.02 -121.14 REMARK 500 2 GLN A 29 112.57 68.00 REMARK 500 2 GLU A 31 101.26 -58.22 REMARK 500 2 THR A 59 14.74 52.72 REMARK 500 2 SER A 60 -49.17 77.13 REMARK 500 2 LEU A 67 -32.54 -35.26 REMARK 500 2 SER A 71 -157.93 -102.59 REMARK 500 2 ASN A 73 -73.76 64.76 REMARK 500 2 MET A 74 176.89 174.02 REMARK 500 2 ASN A 100 -64.25 -23.74 REMARK 500 2 SER A 101 110.91 -8.36 REMARK 500 2 ARG A 108 57.93 133.28 REMARK 500 2 ASN A 113 98.62 -20.35 REMARK 500 2 GLU A 114 97.58 -30.34 REMARK 500 2 ARG A 115 -149.34 -175.84 REMARK 500 2 LYS A 122 -90.55 35.24 REMARK 500 2 HIS A 124 139.38 97.24 REMARK 500 2 ASN A 139 -73.80 -174.83 REMARK 500 2 SER A 140 -27.95 169.55 REMARK 500 2 THR A 143 25.29 49.76 REMARK 500 REMARK 500 THIS ENTRY HAS 612 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6742 RELATED DB: BMRB REMARK 900 NMR CHIMICAL SHIFTS DBREF 2AGA A 6 190 UNP P54252 MJD1_HUMAN 1 185 SEQADV 2AGA GLY A 1 UNP P54252 CLONING ARTIFACT SEQADV 2AGA PRO A 2 UNP P54252 CLONING ARTIFACT SEQADV 2AGA LEU A 3 UNP P54252 CLONING ARTIFACT SEQADV 2AGA GLY A 4 UNP P54252 CLONING ARTIFACT SEQADV 2AGA SER A 5 UNP P54252 CLONING ARTIFACT SEQRES 1 A 190 GLY PRO LEU GLY SER MET GLU SER ILE PHE HIS GLU LYS SEQRES 2 A 190 GLN GLU GLY SER LEU CYS ALA GLN HIS CYS LEU ASN ASN SEQRES 3 A 190 LEU LEU GLN GLY GLU TYR PHE SER PRO VAL GLU LEU SER SEQRES 4 A 190 SER ILE ALA HIS GLN LEU ASP GLU GLU GLU ARG MET ARG SEQRES 5 A 190 MET ALA GLU GLY GLY VAL THR SER GLU ASP TYR ARG THR SEQRES 6 A 190 PHE LEU GLN GLN PRO SER GLY ASN MET ASP ASP SER GLY SEQRES 7 A 190 PHE PHE SER ILE GLN VAL ILE SER ASN ALA LEU LYS VAL SEQRES 8 A 190 TRP GLY LEU GLU LEU ILE LEU PHE ASN SER PRO GLU TYR SEQRES 9 A 190 GLN ARG LEU ARG ILE ASP PRO ILE ASN GLU ARG SER PHE SEQRES 10 A 190 ILE CYS ASN TYR LYS GLU HIS TRP PHE THR VAL ARG LYS SEQRES 11 A 190 LEU GLY LYS GLN TRP PHE ASN LEU ASN SER LEU LEU THR SEQRES 12 A 190 GLY PRO GLU LEU ILE SER ASP THR TYR LEU ALA LEU PHE SEQRES 13 A 190 LEU ALA GLN LEU GLN GLN GLU GLY TYR SER ILE PHE VAL SEQRES 14 A 190 VAL LYS GLY ASP LEU PRO ASP CYS GLU ALA ASP GLN LEU SEQRES 15 A 190 LEU GLN MET ILE ARG VAL GLN GLN HELIX 1 1 GLY A 4 ILE A 9 5 6 HELIX 2 2 ALA A 20 LEU A 28 1 9 HELIX 3 3 SER A 34 GLY A 57 1 24 HELIX 4 4 SER A 60 GLN A 68 1 9 HELIX 5 5 ILE A 82 GLY A 93 1 12 HELIX 6 6 SER A 101 ILE A 109 1 9 HELIX 7 7 SER A 149 GLY A 164 1 16 HELIX 8 8 CYS A 177 GLN A 184 1 8 SHEET 1 A 6 GLU A 95 LEU A 98 0 SHEET 2 A 6 ILE A 167 LYS A 171 -1 O LYS A 171 N GLU A 95 SHEET 3 A 6 SER A 116 ASN A 120 -1 N SER A 116 O VAL A 170 SHEET 4 A 6 TRP A 125 LEU A 131 -1 O PHE A 126 N CYS A 119 SHEET 5 A 6 GLN A 134 LEU A 138 -1 O PHE A 136 N ARG A 129 SHEET 6 A 6 GLU A 146 ILE A 148 -1 O ILE A 148 N TRP A 135 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