PDB Short entry for 1YZB HEADER TRANSCRIPTION 28-FEB-05 1YZB TITLE SOLUTION STRUCTURE OF THE JOSEPHIN DOMAIN OF ATAXIN-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACHADO-JOSEPH DISEASE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN OF ATAXIN-3; 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 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 KEYWDS PAPAIN-LIKE FOLD, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR G.NICASTRO,L.MASINO,R.P.MENON,P.P.KNOWLES,N.Q.MCDONALD,A.PASTORE REVDAT 4 02-MAR-22 1YZB 1 REMARK REVDAT 3 24-FEB-09 1YZB 1 VERSN REVDAT 2 09-AUG-05 1YZB 1 JRNL REVDAT 1 05-JUL-05 1YZB 0 JRNL AUTH G.NICASTRO,R.P.MENON,L.MASINO,P.P.KNOWLES,N.Q.MCDONALD, JRNL AUTH 2 A.PASTORE JRNL TITL THE SOLUTION STRUCTURE OF THE JOSEPHIN DOMAIN OF ATAXIN-3: JRNL TITL 2 STRUCTURAL DETERMINANTS FOR MOLECULAR RECOGNITION JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 10493 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 16020535 JRNL DOI 10.1073/PNAS.0501732102 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.NICASTRO,L.MASINO,T.A.FRENKIEL,G.KELLY,J.MCCORMICK, REMARK 1 AUTH 2 R.P.MENON,A.PASTORE REMARK 1 TITL ASSIGNMENT OF THE 1H, 13C, AND 15N RESONANCES OF THE REMARK 1 TITL 2 JOSEPHIN DOMAIN OF HUMAN ATAXIN-3 REMARK 1 REF J.BIOMOL.NMR V. 30 457 2004 REMARK 1 REFN ISSN 0925-2738 REMARK 1 PMID 15630566 REMARK 1 DOI 10.1007/S10858-004-4343-3 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.MASINO,G.NICASTRO,R.P.MENON,F.DAL PIAZ,L.CALDER,A.PASTORE REMARK 1 TITL CHARACTERIZATION OF THE STRUCTURE AND THE AMYLOIDOGENIC REMARK 1 TITL 2 PROPERTIES OF THE JOSEPHIN DOMAIN OF THE REMARK 1 TITL 3 POLYGLUTAMINE-CONTAINING PROTEIN ATAXIN-3 REMARK 1 REF J.MOL.BIOL. V. 344 1021 2004 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 15544810 REMARK 1 DOI 10.1016/J.JMB.2004.09.065 REMARK 1 REFERENCE 3 REMARK 1 AUTH L.MASINO,V.MUSI,R.P.MENON,P.FUSI,G.KELLY,T.A.FRENKIEL, REMARK 1 AUTH 2 Y.TROTTIER,A.PASTORE REMARK 1 TITL DOMAIN ARCHITECTURE OF THE POLYGLUTAMINE PROTEIN ATAXIN-3: A REMARK 1 TITL 2 GLOBULAR DOMAIN FOLLOWED BY A FLEXIBLE TAIL REMARK 1 REF FEBS LETT. V. 549 21 2003 REMARK 1 REFN ISSN 0014-5793 REMARK 1 PMID 12914917 REMARK 1 DOI 10.1016/S0014-5793(03)00748-8 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2000, ARIA 1.2 REMARK 3 AUTHORS : DELAGLIO F. (NMRPIPE), NILGES M. (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 5532 UNAMBIGUOUS AND 927 AMBIGUOUS RESTRAINTS, 114 DIHEDRAL REMARK 3 ANGLE RESTRAINTS, 44 DISTANCE RESTRAINTS FROM HYDROGEN BONDS. REMARK 4 REMARK 4 1YZB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032100. 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 : 20MM SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4MM OF JOSEPHIN 15N, 13C; 20MM REMARK 210 SODIUM PHOSPHATE BUFFER (PH 6.5); REMARK 210 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS 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: THE 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 HG LEU A 93 H ASN A 95 1.25 REMARK 500 O ARG A 110 HG SER A 111 1.59 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 13 75.61 -67.02 REMARK 500 1 THR A 54 -76.05 -70.60 REMARK 500 1 SER A 55 -65.19 -158.98 REMARK 500 1 GLN A 63 22.46 -76.47 REMARK 500 1 ASP A 70 -66.35 -124.22 REMARK 500 1 ARG A 103 64.48 73.36 REMARK 500 1 LYS A 117 -76.33 66.92 REMARK 500 1 PRO A 170 90.52 -69.43 REMARK 500 2 GLU A 7 -93.39 -82.53 REMARK 500 2 LYS A 8 122.36 -176.72 REMARK 500 2 GLN A 24 19.85 82.64 REMARK 500 2 TYR A 27 -32.84 -130.37 REMARK 500 2 SER A 55 -58.97 73.72 REMARK 500 2 SER A 66 -149.89 -127.30 REMARK 500 2 ASP A 71 45.36 -75.66 REMARK 500 2 ARG A 103 63.59 70.59 REMARK 500 2 GLU A 109 -156.01 -84.16 REMARK 500 2 ARG A 110 -41.08 -130.43 REMARK 500 2 LYS A 117 -80.68 64.84 REMARK 500 2 PRO A 170 94.55 -64.74 REMARK 500 2 LEU A 177 54.58 -108.83 REMARK 500 2 ILE A 181 151.82 -46.93 REMARK 500 3 GLU A 2 -67.82 -98.03 REMARK 500 3 PHE A 5 97.91 -64.12 REMARK 500 3 LYS A 8 122.91 69.58 REMARK 500 3 THR A 54 43.77 -90.29 REMARK 500 3 SER A 55 -60.07 71.84 REMARK 500 3 ARG A 103 74.18 43.22 REMARK 500 3 ARG A 110 -60.86 -91.20 REMARK 500 3 LYS A 117 -86.07 67.46 REMARK 500 4 THR A 54 -75.21 -73.29 REMARK 500 4 SER A 55 -63.55 -169.65 REMARK 500 4 PRO A 65 45.81 -73.97 REMARK 500 4 SER A 66 -159.58 -130.85 REMARK 500 4 ASP A 70 -51.93 -123.08 REMARK 500 4 SER A 72 20.65 -75.31 REMARK 500 4 ASN A 95 52.37 -95.94 REMARK 500 4 ARG A 103 60.96 64.16 REMARK 500 4 GLU A 109 -160.90 -76.02 REMARK 500 4 LYS A 117 -75.25 69.00 REMARK 500 4 LEU A 133 73.02 -114.43 REMARK 500 4 CYS A 172 -165.94 -114.19 REMARK 500 5 GLU A 7 -158.80 -76.68 REMARK 500 5 SER A 12 -102.41 -98.82 REMARK 500 5 GLN A 24 30.17 71.27 REMARK 500 5 THR A 54 39.64 -89.94 REMARK 500 5 SER A 55 -62.46 72.94 REMARK 500 5 GLN A 63 22.83 -76.02 REMARK 500 5 SER A 66 -70.79 -86.73 REMARK 500 5 ARG A 103 89.13 63.98 REMARK 500 REMARK 500 THIS ENTRY HAS 100 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1YZB A 1 182 UNP P54252 MJD1_HUMAN 1 182 SEQRES 1 A 182 MET GLU SER ILE PHE HIS GLU LYS GLN GLU GLY SER LEU SEQRES 2 A 182 CYS ALA GLN HIS CYS LEU ASN ASN LEU LEU GLN GLY GLU SEQRES 3 A 182 TYR PHE SER PRO VAL GLU LEU SER SER ILE ALA HIS GLN SEQRES 4 A 182 LEU ASP GLU GLU GLU ARG MET ARG MET ALA GLU GLY GLY SEQRES 5 A 182 VAL THR SER GLU ASP TYR ARG THR PHE LEU GLN GLN PRO SEQRES 6 A 182 SER GLY ASN MET ASP ASP SER GLY PHE PHE SER ILE GLN SEQRES 7 A 182 VAL ILE SER ASN ALA LEU LYS VAL TRP GLY LEU GLU LEU SEQRES 8 A 182 ILE LEU PHE ASN SER PRO GLU TYR GLN ARG LEU ARG ILE SEQRES 9 A 182 ASP PRO ILE ASN GLU ARG SER PHE ILE CYS ASN TYR LYS SEQRES 10 A 182 GLU HIS TRP PHE THR VAL ARG LYS LEU GLY LYS GLN TRP SEQRES 11 A 182 PHE ASN LEU ASN SER LEU LEU THR GLY PRO GLU LEU ILE SEQRES 12 A 182 SER ASP THR TYR LEU ALA LEU PHE LEU ALA GLN LEU GLN SEQRES 13 A 182 GLN GLU GLY TYR SER ILE PHE VAL VAL LYS GLY ASP LEU SEQRES 14 A 182 PRO ASP CYS GLU ALA ASP GLN LEU LEU GLN MET ILE ARG HELIX 1 1 LEU A 13 LEU A 23 1 11 HELIX 2 2 SER A 29 GLU A 50 1 22 HELIX 3 3 SER A 55 GLN A 63 1 9 HELIX 4 4 ILE A 77 VAL A 86 1 10 HELIX 5 5 ASP A 105 GLU A 109 5 5 HELIX 6 6 SER A 144 GLY A 159 1 16 HELIX 7 7 CYS A 172 LEU A 177 1 6 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 ASN A 115 O SER A 161 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 ASN A 134 -1 O LEU A 133 N THR A 122 SHEET 6 A 6 GLU A 141 ILE A 143 -1 O GLU A 141 N ASN A 132 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