HEADER ANTITUMOR PROTEIN 19-JUN-02 1IXD TITLE SOLUTION STRUCTURE OF THE CAP-GLY DOMAIN FROM HUMAN CYLINDROMATOSIS TITLE 2 TOMOUR-SUPPRESSOR CYLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYLINDROMATOSIS TUMOUR-SUPPRESSOR CYLD; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CAP-GLY DOMAIN; COMPND 5 SYNONYM: PROBABLE UBIQUITIN CARBOXYL-TERMINAL HYDROLASE CYLD, COMPND 6 UBIQUITIN THIOLESTERASE CYLD, UBIQUITIN-SPECIFIC PROCESSING PROTEASE COMPND 7 CYLD, DEUBIQUITINATING ENZYME CYLD, HSPC057; COMPND 8 EC: 3.1.2.15; COMPND 9 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: FH04363; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P011213-03; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS STRUCTURAL GENOMICS, TUMOUR SUPPRESSOR, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, ANTITUMOR PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.SAITO,S.KOSHIBA,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 5 27-DEC-23 1IXD 1 REMARK REVDAT 4 23-FEB-22 1IXD 1 REMARK SEQADV REVDAT 3 24-FEB-09 1IXD 1 VERSN REVDAT 2 25-JAN-05 1IXD 1 SEQADV KEYWDS JRNL DBREF REVDAT 2 2 1 COMPND AUTHOR REVDAT 1 19-DEC-02 1IXD 0 JRNL AUTH K.SAITO,T.KIGAWA,S.KOSHIBA,K.SATO,Y.MATSUO,A.SAKAMOTO, JRNL AUTH 2 T.TAKAGI,M.SHIROUZU,T.YABUKI,E.NUNOKAWA,E.SEKI,T.MATSUDA, JRNL AUTH 3 M.AOKI,Y.MIYATA,N.HIRAKAWA,M.INOUE,T.TERADA,T.NAGASE, JRNL AUTH 4 R.KIKUNO,M.NAKAYAMA,O.OHARA,A.TANAKA,S.YOKOYAMA JRNL TITL THE CAP-GLY DOMAIN OF CYLD ASSOCIATES WITH THE PROLINE-RICH JRNL TITL 2 SEQUENCE IN NEMO/IKKGAMMA JRNL REF STRUCTURE V. 12 1719 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15341735 JRNL DOI 10.1016/J.STR.2004.07.012 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CNS 1.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER, A. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IXD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000005372. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8MM CAP-GLY DOMAIN U-15N,13C; REMARK 210 20MM PHOSPHATE BUFFER NA; 100MM REMARK 210 SODIUM CHLORIDE; 1MM REMARK 210 DITHIOTHREITOL; 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 : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRVIEW 5 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: 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 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 SER A 15 -43.18 -176.99 REMARK 500 1 HIS A 16 -58.09 -165.65 REMARK 500 1 ARG A 37 -64.14 -128.93 REMARK 500 1 ASP A 63 31.23 -98.88 REMARK 500 1 LYS A 78 37.66 -149.17 REMARK 500 1 SER A 91 30.67 -98.68 REMARK 500 1 GLN A 97 87.65 60.56 REMARK 500 2 SER A 5 89.55 -169.05 REMARK 500 2 ASN A 14 -79.81 62.97 REMARK 500 2 SER A 15 -47.21 -142.14 REMARK 500 2 LYS A 27 48.20 -94.98 REMARK 500 2 PRO A 31 83.28 -68.28 REMARK 500 2 ARG A 37 -63.36 -120.82 REMARK 500 2 VAL A 48 99.82 -65.68 REMARK 500 2 LYS A 78 40.03 -150.58 REMARK 500 2 SER A 86 34.42 -97.52 REMARK 500 2 SER A 91 30.92 -98.66 REMARK 500 2 LEU A 96 99.10 -171.52 REMARK 500 2 GLN A 97 162.70 60.58 REMARK 500 2 SER A 99 -54.00 -134.54 REMARK 500 2 SER A 103 -71.14 67.66 REMARK 500 3 ALA A 9 33.21 -168.25 REMARK 500 3 MET A 10 72.13 -177.87 REMARK 500 3 HIS A 16 -51.48 -158.36 REMARK 500 3 PRO A 31 90.55 -68.86 REMARK 500 3 ARG A 37 -66.18 -130.61 REMARK 500 3 GLU A 57 99.65 -65.57 REMARK 500 3 LYS A 78 40.52 -149.10 REMARK 500 3 SER A 86 31.63 -99.87 REMARK 500 3 SER A 91 30.66 -98.70 REMARK 500 3 SER A 99 -168.86 59.43 REMARK 500 3 SER A 102 -66.64 -164.41 REMARK 500 4 LEU A 8 82.90 59.96 REMARK 500 4 MET A 10 64.72 -169.83 REMARK 500 4 ASN A 14 -177.19 60.17 REMARK 500 4 HIS A 16 -72.19 -130.49 REMARK 500 4 PRO A 31 91.31 -69.28 REMARK 500 4 VAL A 48 97.65 -64.46 REMARK 500 4 ALA A 75 177.80 -59.77 REMARK 500 4 LYS A 78 36.02 -147.14 REMARK 500 4 SER A 86 31.19 -97.23 REMARK 500 4 LEU A 96 97.60 60.64 REMARK 500 4 GLN A 97 54.27 -149.97 REMARK 500 4 PRO A 98 -168.54 -71.78 REMARK 500 4 SER A 102 156.35 61.02 REMARK 500 5 SER A 2 77.72 60.79 REMARK 500 5 SER A 3 -177.05 60.41 REMARK 500 5 SER A 5 -177.90 60.74 REMARK 500 5 ALA A 9 29.30 -149.81 REMARK 500 5 MET A 10 81.33 -164.59 REMARK 500 REMARK 500 THIS ENTRY HAS 227 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 THE STRAND OF TYR33-GLY40 CONTAINS BULGE STRUCTURE AT ARG37 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSK001000012.1 RELATED DB: TARGETDB DBREF 1IXD A 8 98 UNP Q9NQC7 CYLD_HUMAN 460 550 SEQADV 1IXD GLY A 1 UNP Q9NQC7 CLONING ARTIFACT SEQADV 1IXD SER A 2 UNP Q9NQC7 CLONING ARTIFACT SEQADV 1IXD SER A 3 UNP Q9NQC7 CLONING ARTIFACT SEQADV 1IXD GLY A 4 UNP Q9NQC7 CLONING ARTIFACT SEQADV 1IXD SER A 5 UNP Q9NQC7 CLONING ARTIFACT SEQADV 1IXD SER A 6 UNP Q9NQC7 CLONING ARTIFACT SEQADV 1IXD GLY A 7 UNP Q9NQC7 CLONING ARTIFACT SEQADV 1IXD SER A 99 UNP Q9NQC7 CLONING ARTIFACT SEQADV 1IXD GLY A 100 UNP Q9NQC7 CLONING ARTIFACT SEQADV 1IXD PRO A 101 UNP Q9NQC7 CLONING ARTIFACT SEQADV 1IXD SER A 102 UNP Q9NQC7 CLONING ARTIFACT SEQADV 1IXD SER A 103 UNP Q9NQC7 CLONING ARTIFACT SEQADV 1IXD GLY A 104 UNP Q9NQC7 CLONING ARTIFACT SEQRES 1 A 104 GLY SER SER GLY SER SER GLY LEU ALA MET PRO PRO GLY SEQRES 2 A 104 ASN SER HIS GLY LEU GLU VAL GLY SER LEU ALA GLU VAL SEQRES 3 A 104 LYS GLU ASN PRO PRO PHE TYR GLY VAL ILE ARG TRP ILE SEQRES 4 A 104 GLY GLN PRO PRO GLY LEU ASN GLU VAL LEU ALA GLY LEU SEQRES 5 A 104 GLU LEU GLU ASP GLU CYS ALA GLY CYS THR ASP GLY THR SEQRES 6 A 104 PHE ARG GLY THR ARG TYR PHE THR CYS ALA LEU LYS LYS SEQRES 7 A 104 ALA LEU PHE VAL LYS LEU LYS SER CYS ARG PRO ASP SER SEQRES 8 A 104 ARG PHE ALA SER LEU GLN PRO SER GLY PRO SER SER GLY SHEET 1 A 5 LEU A 80 LYS A 83 0 SHEET 2 A 5 LEU A 49 GLU A 53 -1 N LEU A 52 O LEU A 80 SHEET 3 A 5 TYR A 33 GLY A 40 -1 N GLY A 40 O LEU A 49 SHEET 4 A 5 LEU A 23 GLU A 25 -1 N ALA A 24 O GLY A 34 SHEET 5 A 5 CYS A 87 PRO A 89 -1 O ARG A 88 N GLU A 25 SHEET 1 B 2 THR A 65 PHE A 66 0 SHEET 2 B 2 THR A 69 ARG A 70 -1 O THR A 69 N PHE A 66 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