HEADER PROTEIN BINDING 14-MAR-16 2NBW TITLE SOLUTION STRUCTURE OF THE RPN1 T1 SITE WITH THE RAD23 UBL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26S PROTEASOME REGULATORY SUBUNIT RPN1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 482-612; COMPND 5 SYNONYM: HMG-COA REDUCTASE DEGRADATION PROTEIN 2, PROTEASOME NON- COMPND 6 ATPASE SUBUNIT 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UV EXCISION REPAIR PROTEIN RAD23; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: RESIDUES 1-78; COMPND 12 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 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: RPN1, HRD2, NAS1, RPD1, YHR027C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX4T1; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 12 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 13 ORGANISM_TAXID: 559292; SOURCE 14 STRAIN: ATCC 204508 / S288C; SOURCE 15 GENE: RAD23, YEL037C, SYGP-ORF29; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PET23A KEYWDS PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR X.CHEN,K.J.WALTERS REVDAT 3 01-MAY-24 2NBW 1 REMARK REVDAT 2 17-AUG-16 2NBW 1 JRNL REVDAT 1 20-JUL-16 2NBW 0 JRNL AUTH X.CHEN,L.RANDLES,K.SHI,S.G.TARASOV,H.AIHARA,K.J.WALTERS JRNL TITL STRUCTURES OF RPN1 T1:RAD23 AND HRPN13:HPLIC2 REVEAL JRNL TITL 2 DISTINCT BINDING MECHANISMS BETWEEN SUBSTRATE RECEPTORS AND JRNL TITL 3 SHUTTLE FACTORS OF THE PROTEASOME. JRNL REF STRUCTURE V. 24 1257 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27396824 JRNL DOI 10.1016/J.STR.2016.05.018 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, X-PLOR NIH REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NBW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000104673. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM [U-100% 15N] PROTEIN_1, REMARK 210 0.04-1.2 MM PROTEIN_2, 50 MM REMARK 210 HEPES, 50 MM SODIUM CHLORIDE, 1 REMARK 210 MM EDTA, 2 MM DTT, 0.1 % SODIUM REMARK 210 AZIDE, 95% H2O/5% D2O; 0.04-0.6 REMARK 210 MM PROTEIN_1, 0.3 MM [U-100% 15N] REMARK 210 PROTEIN_2, 50 MM HEPES, 50 MM REMARK 210 SODIUM CHLORIDE, 1 MM EDTA, 2 MM REMARK 210 DTT, 0.1 % SODIUM AZIDE, 95% H2O/ REMARK 210 5% D2O; 0.6 MM [U-13C] PROTEIN_1, REMARK 210 0.6 MM PROTEIN_2, 50 MM HEPES, REMARK 210 50 MM SODIUM CHLORIDE, 1 MM EDTA, REMARK 210 2 MM DTT, 0.1 % SODIUM AZIDE, REMARK 210 100% D2O; 0.6 MM PROTEIN_1, 0.6 REMARK 210 MM [U-13C] PROTEIN_2, 50 MM REMARK 210 HEPES, 50 MM SODIUM CHLORIDE, 1 REMARK 210 MM EDTA, 2 MM DTT, 0.1 % SODIUM REMARK 210 AZIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 13C-HALF FILTER REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, XEASY, X-PLOR NIH, REMARK 210 TALOS, PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ALA A 489 -71.01 -72.81 REMARK 500 1 ALA A 498 -4.52 -58.01 REMARK 500 1 SER A 500 98.04 -171.80 REMARK 500 1 ALA A 514 56.55 -158.88 REMARK 500 1 SER A 515 -102.06 -80.20 REMARK 500 1 THR A 516 -86.89 -82.24 REMARK 500 1 ASP A 517 51.94 -157.83 REMARK 500 1 ILE A 520 2.80 -64.42 REMARK 500 1 GLU A 521 -74.23 -77.81 REMARK 500 1 THR A 537 -169.00 -64.01 REMARK 500 1 LEU A 551 -76.56 -74.84 REMARK 500 1 GLU A 552 -16.84 -46.28 REMARK 500 1 ALA A 555 6.02 55.20 REMARK 500 1 GLU A 557 -89.04 -78.44 REMARK 500 1 THR A 560 111.83 -163.52 REMARK 500 1 ASP A 561 93.43 55.53 REMARK 500 1 TRP A 562 -37.46 -159.79 REMARK 500 1 ALA A 569 -70.89 -44.11 REMARK 500 1 LEU A 570 -17.82 -43.59 REMARK 500 1 ILE A 572 -32.70 -36.94 REMARK 500 1 GLN A 577 80.57 45.62 REMARK 500 1 VAL A 584 -75.07 -68.46 REMARK 500 1 LEU A 585 -28.47 -39.84 REMARK 500 1 ILE A 588 -74.27 -41.57 REMARK 500 1 ILE A 591 78.95 -54.84 REMARK 500 1 GLU A 592 -167.59 42.56 REMARK 500 1 MET A 595 56.83 -155.13 REMARK 500 1 ALA A 607 -101.01 -161.19 REMARK 500 1 TYR A 608 90.38 -63.31 REMARK 500 1 ASN B 8 -115.79 -92.88 REMARK 500 1 ASN B 22 137.10 -27.03 REMARK 500 1 SER B 36 29.19 85.79 REMARK 500 1 LEU B 44 98.84 -68.72 REMARK 500 1 VAL B 50 108.64 -34.62 REMARK 500 1 LEU B 51 -167.00 -62.59 REMARK 500 1 THR B 56 -150.89 -78.13 REMARK 500 1 ASP B 66 -152.94 -118.62 REMARK 500 1 SER B 77 125.42 59.93 REMARK 500 2 THR A 483 -17.90 -162.40 REMARK 500 2 LEU A 491 -76.17 -54.45 REMARK 500 2 ILE A 495 0.84 -69.29 REMARK 500 2 ALA A 496 -72.22 -83.86 REMARK 500 2 PHE A 497 27.48 -73.28 REMARK 500 2 ALA A 498 -79.81 -43.00 REMARK 500 2 SER A 500 -58.62 -164.09 REMARK 500 2 ASP A 503 -2.27 -58.56 REMARK 500 2 ALA A 513 -9.14 -55.33 REMARK 500 2 ALA A 514 58.34 -150.59 REMARK 500 2 SER A 515 -75.18 -81.89 REMARK 500 2 THR A 516 -46.55 -160.41 REMARK 500 REMARK 500 THIS ENTRY HAS 399 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 553 0.17 SIDE CHAIN REMARK 500 1 ARG A 564 0.31 SIDE CHAIN REMARK 500 2 ARG A 564 0.30 SIDE CHAIN REMARK 500 3 ARG A 564 0.19 SIDE CHAIN REMARK 500 4 ARG A 553 0.27 SIDE CHAIN REMARK 500 4 ARG A 564 0.30 SIDE CHAIN REMARK 500 5 ARG A 564 0.22 SIDE CHAIN REMARK 500 6 ARG A 553 0.21 SIDE CHAIN REMARK 500 6 ARG A 564 0.27 SIDE CHAIN REMARK 500 7 ARG A 553 0.30 SIDE CHAIN REMARK 500 7 ARG A 564 0.30 SIDE CHAIN REMARK 500 8 ARG A 553 0.31 SIDE CHAIN REMARK 500 8 ARG A 564 0.09 SIDE CHAIN REMARK 500 9 ARG A 564 0.16 SIDE CHAIN REMARK 500 10 ARG A 553 0.16 SIDE CHAIN REMARK 500 10 ARG A 564 0.19 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25825 RELATED DB: BMRB REMARK 900 RELATED ID: 2NBU RELATED DB: PDB REMARK 900 RELATED ID: 2NBV RELATED DB: PDB DBREF 2NBW A 482 612 UNP P38764 RPN1_YEAST 482 612 DBREF 2NBW B 1 78 UNP P32628 RAD23_YEAST 1 78 SEQRES 1 A 131 ASP THR LYS ILE SER SER ALA ALA ILE LEU GLY LEU GLY SEQRES 2 A 131 ILE ALA PHE ALA GLY SER LYS ASN ASP GLU VAL LEU GLY SEQRES 3 A 131 LEU LEU LEU PRO ILE ALA ALA SER THR ASP LEU PRO ILE SEQRES 4 A 131 GLU THR ALA ALA MET ALA SER LEU ALA LEU ALA HIS VAL SEQRES 5 A 131 PHE VAL GLY THR CYS ASN GLY ASP ILE THR THR SER ILE SEQRES 6 A 131 MET ASP ASN PHE LEU GLU ARG THR ALA ILE GLU LEU LYS SEQRES 7 A 131 THR ASP TRP VAL ARG PHE LEU ALA LEU ALA LEU GLY ILE SEQRES 8 A 131 LEU TYR MET GLY GLN GLY GLU GLN VAL ASP ASP VAL LEU SEQRES 9 A 131 GLU THR ILE SER ALA ILE GLU HIS PRO MET THR SER ALA SEQRES 10 A 131 ILE GLU VAL LEU VAL GLY SER CYS ALA TYR THR GLY THR SEQRES 11 A 131 GLY SEQRES 1 B 78 MET VAL SER LEU THR PHE LYS ASN PHE LYS LYS GLU LYS SEQRES 2 B 78 VAL PRO LEU ASP LEU GLU PRO SER ASN THR ILE LEU GLU SEQRES 3 B 78 THR LYS THR LYS LEU ALA GLN SER ILE SER CYS GLU GLU SEQRES 4 B 78 SER GLN ILE LYS LEU ILE TYR SER GLY LYS VAL LEU GLN SEQRES 5 B 78 ASP SER LYS THR VAL SER GLU CYS GLY LEU LYS ASP GLY SEQRES 6 B 78 ASP GLN VAL VAL PHE MET VAL SER GLN LYS LYS SER THR HELIX 1 1 LYS A 484 ALA A 498 1 15 HELIX 2 2 ASN A 502 ALA A 514 1 13 HELIX 3 3 PRO A 519 PHE A 534 1 16 HELIX 4 4 GLY A 540 ARG A 553 1 14 HELIX 5 5 TRP A 562 LEU A 573 1 12 HELIX 6 6 GLU A 579 ILE A 591 1 13 HELIX 7 7 THR A 596 CYS A 606 1 11 HELIX 8 8 THR B 23 SER B 36 1 14 HELIX 9 9 THR B 56 GLY B 61 1 6 SHEET 1 A 4 LYS B 13 LEU B 18 0 SHEET 2 A 4 VAL B 2 LYS B 7 -1 N VAL B 2 O LEU B 18 SHEET 3 A 4 GLN B 67 MET B 71 1 O VAL B 68 N THR B 5 SHEET 4 A 4 LYS B 43 ILE B 45 -1 N LYS B 43 O MET B 71 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