HEADER HYDROLASE 30-JUN-14 2MR3 TITLE A SUBUNIT OF 26S PROTEASOME LID COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26S PROTEASOME REGULATORY SUBUNIT RPN9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-393; 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: PET21A KEYWDS HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.WU,Y.HU,C.JIN REVDAT 3 12-APR-17 2MR3 1 JRNL REVDAT 2 27-APR-16 2MR3 1 DBREF SEQRES REVDAT 1 04-FEB-15 2MR3 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, SIMMERLING, WANG, DUKE, REMARK 3 LUO, AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MR3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000103951. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.21 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN-1, 100 MM SODIUM REMARK 210 CHLORIDE-2, 50 MM SODIUM REMARK 210 PHOSPHATE-3, 90% H2O/10% D2O; REMARK 210 0.5 MM [U-13C; U-15N; U-2H] REMARK 210 PROTEIN-4, 100 MM SODIUM REMARK 210 CHLORIDE-5, 50 MM SODIUM REMARK 210 PHOSPHATE-6, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 CCH-TOCSY; 3D HCCH-COSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D HN(COCA)CB REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 ILE A 357 REMARK 465 ILE A 358 REMARK 465 SER A 359 REMARK 465 GLY A 360 REMARK 465 ASP A 361 REMARK 465 GLN A 362 REMARK 465 ILE A 363 REMARK 465 THR A 364 REMARK 465 LYS A 365 REMARK 465 MET A 366 REMARK 465 LYS A 367 REMARK 465 ASP A 368 REMARK 465 ARG A 369 REMARK 465 LEU A 370 REMARK 465 VAL A 371 REMARK 465 GLU A 372 REMARK 465 TRP A 373 REMARK 465 ASN A 374 REMARK 465 ASP A 375 REMARK 465 GLN A 376 REMARK 465 VAL A 377 REMARK 465 GLU A 378 REMARK 465 LYS A 379 REMARK 465 LEU A 380 REMARK 465 GLY A 381 REMARK 465 LYS A 382 REMARK 465 LYS A 383 REMARK 465 MET A 384 REMARK 465 GLU A 385 REMARK 465 ALA A 386 REMARK 465 ARG A 387 REMARK 465 GLY A 388 REMARK 465 GLN A 389 REMARK 465 SER A 390 REMARK 465 ILE A 391 REMARK 465 TRP A 392 REMARK 465 VAL A 393 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 OD1 ASP A 19 HG SER A 21 1.60 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 TYR A 70 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 16 ARG A 356 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 18 PRO A 56 C - N - CA ANGL. DEV. = 9.7 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 LEU A 37 63.63 -101.34 REMARK 500 1 PHE A 65 -63.27 -132.26 REMARK 500 1 ASP A 93 -41.51 -134.17 REMARK 500 1 SER A 111 -40.55 -140.28 REMARK 500 1 ASN A 117 41.39 -149.44 REMARK 500 1 ASP A 124 59.59 -69.93 REMARK 500 1 LYS A 159 18.72 -67.60 REMARK 500 1 SER A 162 48.93 -74.24 REMARK 500 1 PRO A 201 108.99 -47.97 REMARK 500 1 TYR A 228 -45.43 -133.77 REMARK 500 1 ASN A 229 84.02 -69.72 REMARK 500 1 ASP A 245 -48.01 -152.70 REMARK 500 1 VAL A 272 -61.88 -130.72 REMARK 500 1 TRP A 352 168.33 60.28 REMARK 500 2 GLU A 6 -90.80 -136.53 REMARK 500 2 SER A 54 54.96 -147.66 REMARK 500 2 PHE A 65 -56.89 -125.75 REMARK 500 2 ASP A 71 1.28 58.34 REMARK 500 2 LEU A 109 45.99 -84.20 REMARK 500 2 LYS A 113 -108.32 35.42 REMARK 500 2 LYS A 159 -132.18 -149.18 REMARK 500 2 LYS A 160 -174.03 57.20 REMARK 500 2 LEU A 199 -141.17 41.90 REMARK 500 2 PRO A 201 -7.03 -56.30 REMARK 500 2 SER A 202 -111.10 52.47 REMARK 500 2 LEU A 233 -61.32 -98.15 REMARK 500 2 ASN A 244 -4.01 58.91 REMARK 500 2 LYS A 271 -8.96 -59.21 REMARK 500 2 VAL A 272 -53.84 -132.26 REMARK 500 2 ASN A 304 74.39 45.98 REMARK 500 2 SER A 351 -37.42 -134.34 REMARK 500 3 PHE A 65 -72.68 -149.24 REMARK 500 3 PHE A 69 30.58 -140.80 REMARK 500 3 ASP A 71 -18.40 62.62 REMARK 500 3 ASP A 124 -45.99 -149.61 REMARK 500 3 LYS A 159 -22.20 -158.07 REMARK 500 3 PHE A 179 175.83 63.15 REMARK 500 3 PHE A 181 -36.34 -155.85 REMARK 500 3 THR A 203 20.67 -74.17 REMARK 500 3 ASN A 229 58.21 -144.97 REMARK 500 3 VAL A 272 -55.55 -140.24 REMARK 500 3 ASN A 304 53.53 39.82 REMARK 500 3 THR A 317 -21.69 -140.36 REMARK 500 4 ASN A 3 15.67 53.96 REMARK 500 4 HIS A 5 -31.82 -149.38 REMARK 500 4 LEU A 37 47.49 -87.00 REMARK 500 4 ALA A 52 35.76 -64.46 REMARK 500 4 SER A 54 83.28 -151.65 REMARK 500 4 PHE A 65 -69.51 -146.43 REMARK 500 4 ASP A 93 -37.68 -141.93 REMARK 500 REMARK 500 THIS ENTRY HAS 303 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 ARG A 58 0.08 SIDE CHAIN REMARK 500 1 ARG A 166 0.08 SIDE CHAIN REMARK 500 2 TYR A 62 0.09 SIDE CHAIN REMARK 500 2 TYR A 172 0.07 SIDE CHAIN REMARK 500 2 TYR A 228 0.08 SIDE CHAIN REMARK 500 3 ARG A 58 0.09 SIDE CHAIN REMARK 500 4 TYR A 189 0.07 SIDE CHAIN REMARK 500 5 ARG A 15 0.09 SIDE CHAIN REMARK 500 5 TYR A 172 0.08 SIDE CHAIN REMARK 500 6 TYR A 33 0.07 SIDE CHAIN REMARK 500 6 ARG A 58 0.17 SIDE CHAIN REMARK 500 8 TYR A 62 0.07 SIDE CHAIN REMARK 500 10 ARG A 166 0.09 SIDE CHAIN REMARK 500 10 TYR A 228 0.07 SIDE CHAIN REMARK 500 11 TYR A 33 0.07 SIDE CHAIN REMARK 500 11 TYR A 62 0.07 SIDE CHAIN REMARK 500 11 ARG A 330 0.09 SIDE CHAIN REMARK 500 12 ARG A 60 0.08 SIDE CHAIN REMARK 500 12 TYR A 62 0.07 SIDE CHAIN REMARK 500 12 TYR A 172 0.07 SIDE CHAIN REMARK 500 13 TYR A 62 0.07 SIDE CHAIN REMARK 500 13 TYR A 70 0.07 SIDE CHAIN REMARK 500 14 TYR A 62 0.16 SIDE CHAIN REMARK 500 15 ARG A 15 0.08 SIDE CHAIN REMARK 500 15 TYR A 62 0.08 SIDE CHAIN REMARK 500 18 ARG A 15 0.10 SIDE CHAIN REMARK 500 18 PHE A 29 0.08 SIDE CHAIN REMARK 500 18 TYR A 172 0.08 SIDE CHAIN REMARK 500 18 ARG A 356 0.09 SIDE CHAIN REMARK 500 19 ARG A 135 0.10 SIDE CHAIN REMARK 500 19 TYR A 228 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19219 RELATED DB: BMRB REMARK 900 RELATED ID: 2MQW RELATED DB: PDB REMARK 900 RELATED ID: 2MQX RELATED DB: PDB DBREF 2MR3 A 1 393 UNP Q04062 RPN9_YEAST 1 393 SEQRES 1 A 393 MET PHE ASN ASN HIS GLU ILE ASP THR ILE LEU SER THR SEQRES 2 A 393 LEU ARG MET GLU ALA ASP PRO SER LEU HIS PRO LEU PHE SEQRES 3 A 393 GLU GLN PHE GLU LYS PHE TYR GLU GLU LYS LEU TRP PHE SEQRES 4 A 393 GLN LEU SER GLU SER LEU THR LYS PHE PHE ASP ASP ALA SEQRES 5 A 393 LYS SER THR PRO LEU ARG LEU ARG LEU TYR ASP ASN PHE SEQRES 6 A 393 VAL SER LYS PHE TYR ASP LYS ILE ASN GLN LEU SER VAL SEQRES 7 A 393 VAL LYS TYR LEU LEU ALA SER LEU LYS ASP SER LYS ASP SEQRES 8 A 393 PHE ASP GLU SER LEU LYS TYR LEU ASP ASP LEU LYS ALA SEQRES 9 A 393 GLN PHE GLN GLU LEU ASP SER LYS LYS GLN ARG ASN ASN SEQRES 10 A 393 GLY SER LYS ASP HIS GLY ASP GLY ILE LEU LEU ILE ASP SEQRES 11 A 393 SER GLU ILE ALA ARG THR TYR LEU LEU LYS ASN ASP LEU SEQRES 12 A 393 VAL LYS ALA ARG ASP LEU LEU ASP ASP LEU GLU LYS THR SEQRES 13 A 393 LEU ASP LYS LYS ASP SER ILE PRO LEU ARG ILE THR ASN SEQRES 14 A 393 SER PHE TYR SER THR ASN SER GLN TYR PHE LYS PHE LYS SEQRES 15 A 393 ASN ASP PHE ASN SER PHE TYR TYR THR SER LEU LEU TYR SEQRES 16 A 393 LEU SER THR LEU GLU PRO SER THR SER ILE THR LEU ALA SEQRES 17 A 393 GLU ARG GLN GLN LEU ALA TYR ASP LEU SER ILE SER ALA SEQRES 18 A 393 LEU LEU GLY ASP LYS ILE TYR ASN PHE GLY GLU LEU LEU SEQRES 19 A 393 HIS HIS PRO ILE MET GLU THR ILE VAL ASN ASP SER ASN SEQRES 20 A 393 TYR ASP TRP LEU PHE GLN LEU LEU ASN ALA LEU THR VAL SEQRES 21 A 393 GLY ASP PHE ASP LYS PHE ASP SER LEU ILE LYS VAL GLN SEQRES 22 A 393 ILE SER LYS ILE PRO ILE LEU ALA GLN HIS GLU SER PHE SEQRES 23 A 393 LEU ARG GLN LYS ILE CYS LEU MET THR LEU ILE GLU THR SEQRES 24 A 393 VAL PHE VAL LYS ASN ILE ARG MET LEU SER PHE GLU ASP SEQRES 25 A 393 ILE SER LYS ALA THR HIS LEU PRO LYS ASP ASN VAL GLU SEQRES 26 A 393 HIS LEU VAL MET ARG ALA ILE SER LEU GLY LEU LEU LYS SEQRES 27 A 393 GLY SER ILE ASP GLN VAL ASN GLU LEU VAL THR ILE SER SEQRES 28 A 393 TRP VAL GLN PRO ARG ILE ILE SER GLY ASP GLN ILE THR SEQRES 29 A 393 LYS MET LYS ASP ARG LEU VAL GLU TRP ASN ASP GLN VAL SEQRES 30 A 393 GLU LYS LEU GLY LYS LYS MET GLU ALA ARG GLY GLN SER SEQRES 31 A 393 ILE TRP VAL HELIX 1 1 HIS A 5 ALA A 18 1 14 HELIX 2 2 ASP A 19 HIS A 23 5 5 HELIX 3 3 PRO A 24 GLU A 35 1 12 HELIX 4 4 LEU A 37 ASP A 50 1 14 HELIX 5 5 PRO A 56 PHE A 65 1 10 HELIX 6 6 VAL A 66 PHE A 69 5 4 HELIX 7 7 ASN A 74 SER A 89 1 16 HELIX 8 8 ASP A 93 ASP A 110 1 18 HELIX 9 9 GLY A 125 LEU A 139 1 15 HELIX 10 10 ASP A 142 LYS A 155 1 14 HELIX 11 11 PRO A 164 GLN A 177 1 14 HELIX 12 12 ASP A 184 LEU A 199 1 16 HELIX 13 13 THR A 206 LEU A 223 1 18 HELIX 14 14 PHE A 230 HIS A 236 1 7 HELIX 15 15 PRO A 237 ASP A 245 5 9 HELIX 16 16 TYR A 248 GLY A 261 1 14 HELIX 17 17 ASP A 262 ILE A 277 1 16 HELIX 18 18 ILE A 277 HIS A 283 1 7 HELIX 19 19 HIS A 283 LYS A 303 1 21 HELIX 20 20 PHE A 310 HIS A 318 1 9 HELIX 21 21 ASN A 323 GLY A 335 1 13 HELIX 22 22 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 THR A 349 -1 O VAL A 348 N LEU A 308 SHEET 3 A 3 SER A 340 ASP A 342 -1 N ASP A 342 O LEU A 347 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