HEADER HYDROLASE INHIBITOR 10-JUN-19 6K7W TITLE SOLUTION STRUCTURE OF THE CS1 DOMAIN OF USP19 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 19; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN SPECIFIC PEPTIDASE 19,DEUBIQUITINATING ENZYME 19, COMPND 5 UBIQUITIN THIOESTERASE 19,UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 19, COMPND 6 ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 9; COMPND 7 EC: 3.4.19.12; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: USP19, KIAA0891, ZMYND9; SOURCE 6 EXPRESSION_SYSTEM: ESCHENBACHIA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1408200 KEYWDS CS DOMAIN, AUTOINHIBITORY REGULATION, HYDROLASE INHIBITOR EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR W.XUE,H.Y.HU REVDAT 4 15-MAY-24 6K7W 1 REMARK REVDAT 3 14-JUN-23 6K7W 1 REMARK REVDAT 2 23-DEC-20 6K7W 1 JRNL REVDAT 1 10-JUN-20 6K7W 0 JRNL AUTH W.XUE,S.X.ZHANG,W.T.HE,J.Y.HONG,L.L.JIANG,H.Y.HU JRNL TITL DOMAIN INTERACTIONS REVEAL AUTO-INHIBITION OF THE JRNL TITL 2 DEUBIQUITINATING ENZYME USP19 AND ITS ACTIVATION BY HSP90 IN JRNL TITL 3 THE MODULATION OF HUNTINGTIN AGGREGATION. JRNL REF BIOCHEM.J. V. 477 4295 2020 JRNL REFN ESSN 1470-8728 JRNL PMID 33094816 JRNL DOI 10.1042/BCJ20200536 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, ARIA REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), LINGE, O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6K7W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1300012283. 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 : 0.08 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 GB1-CS1(113-204)-L117A, 20 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 0.05 % V/V SODIUM REMARK 210 AZIDE, 90 % V/V H2O, 10 % V/V REMARK 210 D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCO; 3D HNCACB; 3D HNHA; 2D REMARK 210 1H-1H NOESY; 3D HCCH-TOCSY; 3D REMARK 210 1H-13C NOESY; 3D H(CCO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW, SPARKY, CNS, ARIA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 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 HG21 VAL A 133 HG12 VAL A 135 1.32 REMARK 500 H VAL A 154 O TRP A 162 1.58 REMARK 500 H THR A 148 O ASP A 151 1.58 REMARK 500 O ILE A 170 HG CYS A 174 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 4 TYR A 167 CE1 TYR A 167 CZ 0.106 REMARK 500 4 TYR A 167 CZ TYR A 167 CE2 -0.089 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 ALA A 117 -114.52 -152.11 REMARK 500 1 VAL A 135 30.30 -88.96 REMARK 500 1 GLU A 169 -69.33 64.74 REMARK 500 1 ILE A 170 91.73 -37.61 REMARK 500 1 LYS A 181 -24.04 179.81 REMARK 500 1 LYS A 192 -74.71 -79.22 REMARK 500 2 LEU A 116 -39.24 174.98 REMARK 500 2 ALA A 117 -70.79 -95.19 REMARK 500 2 GLU A 169 -67.72 69.93 REMARK 500 2 ILE A 170 86.82 -12.27 REMARK 500 2 LYS A 181 -29.74 -159.23 REMARK 500 2 LYS A 192 -74.31 -74.48 REMARK 500 2 VAL A 203 -73.44 -121.28 REMARK 500 3 LEU A 116 -60.06 -153.90 REMARK 500 3 ALA A 117 -86.26 -171.01 REMARK 500 3 GLU A 169 -34.59 72.62 REMARK 500 3 ILE A 170 75.98 -58.94 REMARK 500 3 LYS A 181 -32.67 174.14 REMARK 500 3 LYS A 192 -138.39 -95.59 REMARK 500 3 VAL A 203 -72.34 -127.82 REMARK 500 4 LEU A 116 -69.30 -146.84 REMARK 500 4 ALA A 117 -110.33 -150.59 REMARK 500 4 GLN A 160 97.30 -67.78 REMARK 500 4 GLU A 169 -67.34 70.25 REMARK 500 4 ILE A 170 86.56 -39.73 REMARK 500 4 LYS A 181 -42.54 173.91 REMARK 500 4 LYS A 192 -60.01 -101.04 REMARK 500 4 VAL A 203 -87.81 -111.32 REMARK 500 5 GLU A 115 -73.27 64.10 REMARK 500 5 LEU A 116 -41.50 -140.21 REMARK 500 5 ALA A 117 -55.49 -156.82 REMARK 500 5 GLU A 169 -60.66 73.76 REMARK 500 5 ILE A 170 90.06 -41.74 REMARK 500 5 LYS A 181 -21.12 -176.90 REMARK 500 5 LYS A 192 -158.82 -90.08 REMARK 500 5 VAL A 203 -59.94 -136.01 REMARK 500 6 GLU A 115 47.86 -80.45 REMARK 500 6 LEU A 116 -82.01 -132.62 REMARK 500 6 ALA A 117 17.49 -152.77 REMARK 500 6 GLU A 169 -72.05 66.00 REMARK 500 6 ILE A 170 75.79 -12.30 REMARK 500 6 LYS A 181 2.19 -157.33 REMARK 500 6 VAL A 203 -67.77 -165.47 REMARK 500 7 LEU A 116 -78.37 -147.41 REMARK 500 7 ALA A 117 13.20 174.04 REMARK 500 7 GLU A 169 -60.53 69.49 REMARK 500 7 ILE A 170 92.43 -43.06 REMARK 500 7 LYS A 181 -29.96 -175.06 REMARK 500 7 LYS A 192 -137.84 -100.40 REMARK 500 8 LEU A 116 -59.63 -158.31 REMARK 500 REMARK 500 THIS ENTRY HAS 69 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 4 TYR A 167 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36262 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE CS1 DOMAIN OF USP19 DBREF 6K7W A 113 204 UNP O94966 UBP19_HUMAN 113 204 SEQADV 6K7W ALA A 117 UNP O94966 LEU 117 ENGINEERED MUTATION SEQRES 1 A 92 THR PRO GLU LEU ALA LEU ASP TRP ARG GLN SER ALA GLU SEQRES 2 A 92 GLU VAL ILE VAL LYS LEU ARG VAL GLY VAL GLY PRO LEU SEQRES 3 A 92 GLN LEU GLU ASP VAL ASP ALA ALA PHE THR ASP THR ASP SEQRES 4 A 92 CYS VAL VAL ARG PHE ALA GLY GLY GLN GLN TRP GLY GLY SEQRES 5 A 92 VAL PHE TYR ALA GLU ILE LYS SER SER CYS ALA LYS VAL SEQRES 6 A 92 GLN THR ARG LYS GLY SER LEU LEU HIS LEU THR LEU PRO SEQRES 7 A 92 LYS LYS VAL PRO MET LEU THR TRP PRO SER LEU LEU VAL SEQRES 8 A 92 GLU HELIX 1 AA1 GLN A 139 VAL A 143 5 5 SHEET 1 AA1 4 ASP A 119 GLN A 122 0 SHEET 2 AA1 4 GLU A 126 LEU A 131 -1 O ILE A 128 N ARG A 121 SHEET 3 AA1 4 LEU A 185 PRO A 190 -1 O LEU A 187 N VAL A 129 SHEET 4 AA1 4 VAL A 177 THR A 179 -1 N VAL A 177 O THR A 188 SHEET 1 AA2 3 ALA A 146 THR A 148 0 SHEET 2 AA2 3 ASP A 151 VAL A 154 -1 O ASP A 151 N THR A 148 SHEET 3 AA2 3 TRP A 162 VAL A 165 -1 O TRP A 162 N VAL A 154 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