HEADER PROTEIN BINDING 06-JUL-14 2MRI TITLE SOLUTION STRUCTURE OF A PROTEASOME RELATED SUBUNIT C TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26S PROTEASOME REGULATORY SUBUNIT RPN9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 181-356; COMPND 5 SYNONYM: PROTEASOME NON-ATPASE SUBUNIT 7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 GENE: RPN9, NAS7, YDR427W, D9461.14; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET21A KEYWDS HYDROLASE, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.WU,Y.HU,C.JIN REVDAT 3 01-MAY-24 2MRI 1 REMARK REVDAT 2 12-APR-17 2MRI 1 JRNL REVDAT 1 04-FEB-15 2MRI 0 JRNL AUTH Y.HU,Y.WU,Q.LI,W.ZHANG,C.JIN JRNL TITL SOLUTION STRUCTURE OF YEAST RPN9: INSIGHTS INTO PROTEASOME JRNL TITL 2 LID ASSEMBLY. JRNL REF J. BIOL. CHEM. V. 290 6878 2015 JRNL REFN ESSN 1083-351X JRNL PMID 25631053 JRNL DOI 10.1074/JBC.M114.626762 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MRI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000103965. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 0.07 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM [U-100% 13C, U-100% 15N] REMARK 210 PROTEIN-1, 20MM TRIS-2, 50MM REMARK 210 SODIUM CHLORIDE-3, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D HNCA; REMARK 210 3D HNCACB; 3D HBHA(CO)NH; 3D 1H- REMARK 210 15N NOESY; 3D HCCH-COSY; 3D CCH- REMARK 210 TOCSY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 1 ARG A 356 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES 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 PHE A 230 -28.54 53.41 REMARK 500 1 VAL A 272 -51.29 -127.58 REMARK 500 2 LYS A 182 48.80 -79.26 REMARK 500 2 THR A 203 -38.88 -140.24 REMARK 500 2 SER A 204 -104.67 21.80 REMARK 500 2 LYS A 226 10.57 -152.24 REMARK 500 2 TYR A 228 -20.76 -150.21 REMARK 500 2 ASN A 229 40.74 -77.26 REMARK 500 2 VAL A 272 -56.54 -123.04 REMARK 500 2 HIS A 283 31.25 -140.41 REMARK 500 3 TYR A 228 -33.64 57.13 REMARK 500 3 PHE A 230 -23.82 56.80 REMARK 500 3 VAL A 272 -51.81 -127.18 REMARK 500 4 THR A 203 -44.93 -138.43 REMARK 500 4 SER A 204 -151.32 39.26 REMARK 500 4 ASN A 229 64.18 -160.36 REMARK 500 4 ILE A 238 -41.71 -145.10 REMARK 500 4 SER A 246 -7.69 71.70 REMARK 500 4 VAL A 272 -54.41 -126.62 REMARK 500 4 GLU A 346 31.83 84.47 REMARK 500 5 ASN A 183 -40.87 66.00 REMARK 500 5 PRO A 201 -16.27 -49.93 REMARK 500 5 LYS A 226 23.35 -153.04 REMARK 500 5 HIS A 283 37.37 -141.95 REMARK 500 5 GLU A 346 32.53 71.90 REMARK 500 5 PRO A 355 -173.71 -62.86 REMARK 500 6 THR A 203 50.12 -152.64 REMARK 500 6 ASP A 225 41.62 -84.06 REMARK 500 6 LYS A 226 -51.86 -168.00 REMARK 500 6 PHE A 230 -26.98 50.10 REMARK 500 6 ASN A 244 -2.33 60.44 REMARK 500 6 VAL A 272 -50.85 -129.23 REMARK 500 6 PRO A 355 -6.11 -59.07 REMARK 500 7 VAL A 272 -55.74 -128.56 REMARK 500 8 ILE A 238 -41.22 -151.26 REMARK 500 8 VAL A 272 -59.31 -128.33 REMARK 500 8 HIS A 283 34.94 -140.72 REMARK 500 8 PRO A 355 163.02 -48.99 REMARK 500 9 THR A 203 -0.85 -141.19 REMARK 500 9 TYR A 248 13.06 -140.38 REMARK 500 9 VAL A 272 -56.58 -128.37 REMARK 500 10 TYR A 228 -31.56 -146.68 REMARK 500 10 PHE A 230 -4.48 -141.16 REMARK 500 10 VAL A 272 -57.64 -124.93 REMARK 500 11 TYR A 228 -20.64 -140.71 REMARK 500 11 ASP A 245 -36.15 -138.53 REMARK 500 11 VAL A 272 -55.34 -120.73 REMARK 500 11 HIS A 283 36.77 -141.98 REMARK 500 12 TYR A 228 -13.90 -141.91 REMARK 500 12 PHE A 230 -27.84 49.76 REMARK 500 REMARK 500 THIS ENTRY HAS 98 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 1 TYR A 228 0.09 SIDE CHAIN REMARK 500 5 TYR A 228 0.07 SIDE CHAIN REMARK 500 6 ARG A 330 0.10 SIDE CHAIN REMARK 500 10 TYR A 228 0.08 SIDE CHAIN REMARK 500 13 TYR A 228 0.07 SIDE CHAIN REMARK 500 14 TYR A 228 0.07 SIDE CHAIN REMARK 500 15 TYR A 248 0.07 SIDE CHAIN REMARK 500 16 ARG A 356 0.08 SIDE CHAIN REMARK 500 20 TYR A 228 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19221 RELATED DB: BMRB DBREF 2MRI A 181 356 UNP Q04062 RPN9_YEAST 181 356 SEQRES 1 A 176 PHE LYS ASN ASP PHE ASN SER PHE TYR TYR THR SER LEU SEQRES 2 A 176 LEU TYR LEU SER THR LEU GLU PRO SER THR SER ILE THR SEQRES 3 A 176 LEU ALA GLU ARG GLN GLN LEU ALA TYR ASP LEU SER ILE SEQRES 4 A 176 SER ALA LEU LEU GLY ASP LYS ILE TYR ASN PHE GLY GLU SEQRES 5 A 176 LEU LEU HIS HIS PRO ILE MET GLU THR ILE VAL ASN ASP SEQRES 6 A 176 SER ASN TYR ASP TRP LEU PHE GLN LEU LEU ASN ALA LEU SEQRES 7 A 176 THR VAL GLY ASP PHE ASP LYS PHE ASP SER LEU ILE LYS SEQRES 8 A 176 VAL GLN ILE SER LYS ILE PRO ILE LEU ALA GLN HIS GLU SEQRES 9 A 176 SER PHE LEU ARG GLN LYS ILE CYS LEU MET THR LEU ILE SEQRES 10 A 176 GLU THR VAL PHE VAL LYS ASN ILE ARG MET LEU SER PHE SEQRES 11 A 176 GLU ASP ILE SER LYS ALA THR HIS LEU PRO LYS ASP ASN SEQRES 12 A 176 VAL GLU HIS LEU VAL MET ARG ALA ILE SER LEU GLY LEU SEQRES 13 A 176 LEU LYS GLY SER ILE ASP GLN VAL ASN GLU LEU VAL THR SEQRES 14 A 176 ILE SER TRP VAL GLN PRO ARG HELIX 1 1 ASP A 184 LEU A 199 1 16 HELIX 2 2 THR A 206 LEU A 223 1 18 HELIX 3 3 PHE A 230 HIS A 236 1 7 HELIX 4 4 MET A 239 ASN A 244 1 6 HELIX 5 5 TYR A 248 GLY A 261 1 14 HELIX 6 6 ASP A 262 ILE A 277 1 16 HELIX 7 7 ILE A 277 HIS A 283 1 7 HELIX 8 8 HIS A 283 LYS A 303 1 21 HELIX 9 9 PHE A 310 ALA A 316 1 7 HELIX 10 10 PRO A 320 LEU A 334 1 15 HELIX 11 11 GLN A 343 ASN A 345 5 3 SHEET 1 A 3 MET A 307 SER A 309 0 SHEET 2 A 3 LEU A 347 VAL A 353 -1 O VAL A 348 N LEU A 308 SHEET 3 A 3 LEU A 337 ASP A 342 -1 N LYS A 338 O SER A 351 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