HEADER HYDROLASE 19-AUG-19 6KQV TITLE SOLUTION STRUCTURE OF THE UBL DOMAIN OF USP19 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 19; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 19,UBIQUITIN THIOESTERASE 19, COMPND 5 UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 19,ZINC FINGER MYND DOMAIN- COMPND 6 CONTAINING PROTEIN 9; COMPND 7 EC: 3.4.19.12; 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 GENE: USP19, KIAA0891, ZMYND9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBL DOMAIN, AUTOINHIBITORY REGULATION, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR W.XUE,H.Y.HU REVDAT 3 14-JUN-23 6KQV 1 REMARK REVDAT 2 23-DEC-20 6KQV 1 JRNL REVDAT 1 19-AUG-20 6KQV 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 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6KQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1300013485. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.6 REMARK 210 IONIC STRENGTH : 0.06 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 UBL(679-766), 10 MM SODIUM REMARK 210 ACETATE, 50 MM SODIUM CHLORIDE, REMARK 210 0.05 MM SODIUM AZIDE, 1 MM DTT, REMARK 210 90 % V/V H2O, 10 % V/V [U-99% 2H] REMARK 210 D2O, 90% H2O/10% D2O; 1 MM [U- REMARK 210 99% 15N] UBL(679-766), 10 MM REMARK 210 SODIUM ACETATE, 50 MM SODIUM REMARK 210 CHLORIDE, 0.05 MM SODIUM AZIDE, REMARK 210 1 MM DTT, 90 % V/V H2O, 10 % V/V REMARK 210 [U-99% 2H] D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNHA; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D H(CCO) REMARK 210 NH; 3D HNCO; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA, SPARKY 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 HB3 SER A 704 HB2 ASP A 749 1.21 REMARK 500 HH TYR A 687 HB2 PHE A 699 1.35 REMARK 500 O LEU A 730 HA LEU A 758 1.60 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 3 TYR A 687 CE1 TYR A 687 CZ -0.104 REMARK 500 3 TYR A 687 CZ TYR A 687 CE2 0.102 REMARK 500 4 TYR A 687 CE1 TYR A 687 CZ -0.100 REMARK 500 4 TYR A 687 CZ TYR A 687 CE2 0.088 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 PRO A 692 3.06 -40.23 REMARK 500 1 HIS A 693 52.97 76.49 REMARK 500 1 GLU A 706 -177.69 -68.94 REMARK 500 1 ASN A 707 1.51 -60.22 REMARK 500 1 SER A 708 -63.96 -109.43 REMARK 500 1 LYS A 735 -154.81 156.86 REMARK 500 1 HIS A 739 179.58 65.26 REMARK 500 1 ARG A 740 -162.46 155.92 REMARK 500 1 SER A 745 107.23 -37.91 REMARK 500 1 LEU A 748 12.78 -69.57 REMARK 500 1 ASP A 749 25.60 -76.79 REMARK 500 1 THR A 756 115.18 -30.70 REMARK 500 2 PRO A 692 4.53 -42.80 REMARK 500 2 HIS A 693 51.20 77.07 REMARK 500 2 ASN A 707 4.90 -63.89 REMARK 500 2 SER A 708 -61.42 -90.59 REMARK 500 2 LYS A 735 -152.75 156.62 REMARK 500 2 ARG A 737 -75.10 -64.19 REMARK 500 2 PHE A 738 82.69 61.34 REMARK 500 2 ARG A 740 -11.50 -142.26 REMARK 500 2 SER A 745 123.23 -39.07 REMARK 500 2 LEU A 748 13.41 -68.05 REMARK 500 2 THR A 756 123.70 -27.67 REMARK 500 3 PRO A 692 4.10 -42.05 REMARK 500 3 HIS A 693 52.48 77.87 REMARK 500 3 ASN A 707 2.61 -62.34 REMARK 500 3 SER A 708 -63.09 -90.05 REMARK 500 3 ILE A 734 -149.83 -107.54 REMARK 500 3 LYS A 735 -145.14 11.21 REMARK 500 3 ARG A 740 -6.25 -147.04 REMARK 500 3 SER A 745 124.23 -38.12 REMARK 500 3 THR A 756 128.41 -27.78 REMARK 500 4 PRO A 692 4.31 -41.15 REMARK 500 4 HIS A 693 52.97 78.36 REMARK 500 4 GLU A 706 -175.22 -66.76 REMARK 500 4 ASN A 707 1.76 -56.51 REMARK 500 4 LYS A 735 -151.12 161.92 REMARK 500 4 SER A 745 122.03 -37.68 REMARK 500 4 ASP A 749 30.56 -75.35 REMARK 500 4 SER A 752 -52.05 -12.49 REMARK 500 4 PRO A 753 -9.25 -47.67 REMARK 500 4 ASP A 755 108.15 -19.41 REMARK 500 5 PRO A 692 6.84 -40.10 REMARK 500 5 HIS A 693 47.93 79.56 REMARK 500 5 ASN A 707 4.23 -63.97 REMARK 500 5 SER A 708 -61.32 -105.70 REMARK 500 5 LYS A 735 -151.99 159.54 REMARK 500 5 PHE A 738 90.60 67.72 REMARK 500 5 HIS A 739 178.66 71.35 REMARK 500 5 ARG A 740 -162.30 151.05 REMARK 500 REMARK 500 THIS ENTRY HAS 128 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 706 ASN A 707 7 130.59 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 5 TYR A 687 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36283 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE UBL DOMAIN OF USP19 DBREF 6KQV A 679 766 UNP O94966 UBP19_HUMAN 679 766 SEQRES 1 A 88 LYS GLN LYS VAL LEU PRO VAL PHE TYR PHE ALA ARG GLU SEQRES 2 A 88 PRO HIS SER LYS PRO ILE LYS PHE LEU VAL SER VAL SER SEQRES 3 A 88 LYS GLU ASN SER THR ALA SER GLU VAL LEU ASP SER LEU SEQRES 4 A 88 SER GLN SER VAL HIS VAL LYS PRO GLU ASN LEU ARG LEU SEQRES 5 A 88 ALA GLU VAL ILE LYS ASN ARG PHE HIS ARG VAL PHE LEU SEQRES 6 A 88 PRO SER HIS SER LEU ASP THR VAL SER PRO SER ASP THR SEQRES 7 A 88 LEU LEU CYS PHE GLU LEU LEU SER SER GLU HELIX 1 AA1 ALA A 710 VAL A 721 1 12 HELIX 2 AA2 LYS A 724 LEU A 728 5 5 SHEET 1 AA1 2 VAL A 682 TYR A 687 0 SHEET 2 AA1 2 ILE A 697 SER A 702 -1 O PHE A 699 N VAL A 685 SHEET 1 AA2 2 ALA A 731 GLU A 732 0 SHEET 2 AA2 2 LEU A 757 LEU A 758 -1 O LEU A 757 N GLU A 732 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