HEADER NUCLEAR PROTEIN 15-JUN-07 2Z4D TITLE NMR STRUCTURES OF YEAST PROTEASOME COMPONENT RPN13 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26S PROTEASOME REGULATORY SUBUNIT RPN13; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 6-101; COMPND 5 SYNONYM: PROTEASOME COMPONENT RPN13, PROTEASOME NON-ATPASE SUBUNIT COMPND 6 13; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: RPN13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSET KEYWDS PROTEASOME, PH DOMAIN, NUCLEAR PROTEIN EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR N.ZHANG,K.J.WALTERS REVDAT 4 16-MAR-22 2Z4D 1 REMARK REVDAT 3 19-JAN-10 2Z4D 1 JRNL REVDAT 2 24-FEB-09 2Z4D 1 VERSN REVDAT 1 20-MAY-08 2Z4D 0 JRNL AUTH K.HUSNJAK,S.ELSASSER,N.ZHANG,X.CHEN,L.RANDLES,Y.SHI, JRNL AUTH 2 K.HOFMANN,K.J.WALTERS,D.FINLEY,I.DIKIC JRNL TITL PROTEASOME SUBUNIT RPN13 IS A NOVEL UBIQUITIN RECEPTOR. JRNL REF NATURE V. 453 481 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18497817 JRNL DOI 10.1038/NATURE06926 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2006, X-PLOR 3.851 REMARK 3 AUTHORS : FRANK DELAGLIO, STEPHAN GRZESIEK, GUANG ZHU, REMARK 3 GEERTEN W. VUISTER, JOHN PFEIFER AND AD BAX REMARK 3 (NMRPIPE), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 1084 RESTRAINTS, 949 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 79 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 56 DISTANCE RESTRAINTS FROM HYDROGEN REMARK 3 BONDS. REMARK 4 REMARK 4 2Z4D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000027505. 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 : 20MM PHOSPHATE, 50MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4MM RPN13 U-15N, 13C; U-70% REMARK 210 2H; 20MM PHOSPHATE BUFFER; 50MM REMARK 210 NACL; 4MM DTT; 90% H2O, 10% D2O; REMARK 210 0.5MM RPN13 U-15N; U-50% 2H; REMARK 210 20MM PHOSPHATE BUFFER; 50MM NACL; REMARK 210 4MM DTT; 90% H2O, 10% D2O; REMARK 210 0.5MM RPN13 U-13C; 20MM REMARK 210 PHOSPHATE BUFFER; 50MM NACL; 4MM REMARK 210 DTT; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCACB, HNCA/HN(CO)CA, REMARK 210 HNCO/HN(CA)CO; 3D_15N-SEPARATED_ REMARK 210 NOESY; 3D_13C-SEPARATED_NOESY; REMARK 210 HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1996, X-PLOR 3.851 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 35 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 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: 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 12 -158.65 -150.15 REMARK 500 1 VAL A 14 -142.27 -103.88 REMARK 500 1 CYS A 15 108.30 -163.75 REMARK 500 1 ASN A 38 164.63 65.02 REMARK 500 1 GLU A 40 38.33 -147.82 REMARK 500 1 ARG A 51 146.32 -177.50 REMARK 500 1 GLU A 54 -169.09 -116.20 REMARK 500 1 PRO A 56 -167.34 -78.29 REMARK 500 1 VAL A 57 49.88 -148.59 REMARK 500 1 LEU A 61 -162.15 -116.53 REMARK 500 1 GLU A 72 -68.29 -133.10 REMARK 500 1 LYS A 79 49.33 -104.67 REMARK 500 1 SER A 80 -173.61 53.27 REMARK 500 1 SER A 81 -168.08 52.43 REMARK 500 1 ARG A 85 94.06 -162.45 REMARK 500 1 PHE A 91 -79.65 -92.03 REMARK 500 1 SER A 92 -39.59 -172.82 REMARK 500 1 SER A 93 -81.58 -83.64 REMARK 500 1 ASN A 94 15.76 -150.82 REMARK 500 1 GLU A 95 49.53 -90.51 REMARK 500 2 ALA A 12 -155.04 -170.72 REMARK 500 2 VAL A 14 -141.51 -89.55 REMARK 500 2 CYS A 15 110.13 -162.99 REMARK 500 2 ASN A 38 150.16 62.45 REMARK 500 2 GLU A 40 -154.38 -133.74 REMARK 500 2 ARG A 51 146.20 -175.44 REMARK 500 2 GLU A 72 -76.87 -60.47 REMARK 500 2 THR A 73 -153.06 -71.71 REMARK 500 2 LYS A 79 50.38 -94.80 REMARK 500 2 ARG A 85 134.81 62.49 REMARK 500 2 PHE A 91 -61.62 -100.99 REMARK 500 2 SER A 92 -50.92 -142.53 REMARK 500 2 SER A 93 -29.23 -178.85 REMARK 500 3 VAL A 7 59.53 -111.20 REMARK 500 3 ALA A 12 -160.68 -161.81 REMARK 500 3 VAL A 14 -138.87 -95.53 REMARK 500 3 PRO A 37 55.41 -93.14 REMARK 500 3 ASN A 38 175.16 60.29 REMARK 500 3 TRP A 46 81.87 -66.78 REMARK 500 3 ARG A 51 146.89 179.55 REMARK 500 3 GLU A 54 -169.59 -100.62 REMARK 500 3 VAL A 57 30.69 -148.41 REMARK 500 3 LEU A 61 -163.46 -103.73 REMARK 500 3 GLU A 72 -80.55 -61.86 REMARK 500 3 SER A 81 -156.08 49.39 REMARK 500 3 LYS A 82 49.80 -98.99 REMARK 500 3 SER A 83 -76.26 -117.82 REMARK 500 3 ARG A 85 86.77 50.64 REMARK 500 3 PHE A 91 -70.85 -117.32 REMARK 500 3 SER A 92 -68.04 -133.94 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: 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 11 0.29 SIDE CHAIN REMARK 500 1 ARG A 22 0.32 SIDE CHAIN REMARK 500 1 ARG A 51 0.23 SIDE CHAIN REMARK 500 1 ARG A 59 0.23 SIDE CHAIN REMARK 500 1 ARG A 85 0.27 SIDE CHAIN REMARK 500 1 ARG A 96 0.28 SIDE CHAIN REMARK 500 2 ARG A 11 0.32 SIDE CHAIN REMARK 500 2 ARG A 22 0.31 SIDE CHAIN REMARK 500 2 ARG A 51 0.25 SIDE CHAIN REMARK 500 2 ARG A 59 0.32 SIDE CHAIN REMARK 500 2 ARG A 85 0.25 SIDE CHAIN REMARK 500 2 ARG A 96 0.32 SIDE CHAIN REMARK 500 3 ARG A 11 0.22 SIDE CHAIN REMARK 500 3 ARG A 22 0.31 SIDE CHAIN REMARK 500 3 ARG A 51 0.24 SIDE CHAIN REMARK 500 3 ARG A 59 0.31 SIDE CHAIN REMARK 500 3 ARG A 85 0.26 SIDE CHAIN REMARK 500 3 ARG A 96 0.27 SIDE CHAIN REMARK 500 4 ARG A 11 0.30 SIDE CHAIN REMARK 500 4 ARG A 22 0.26 SIDE CHAIN REMARK 500 4 ARG A 51 0.32 SIDE CHAIN REMARK 500 4 ARG A 59 0.25 SIDE CHAIN REMARK 500 4 ARG A 85 0.26 SIDE CHAIN REMARK 500 4 ARG A 96 0.16 SIDE CHAIN REMARK 500 5 ARG A 11 0.21 SIDE CHAIN REMARK 500 5 ARG A 22 0.25 SIDE CHAIN REMARK 500 5 ARG A 51 0.31 SIDE CHAIN REMARK 500 5 ARG A 59 0.32 SIDE CHAIN REMARK 500 5 ARG A 85 0.32 SIDE CHAIN REMARK 500 5 ARG A 96 0.23 SIDE CHAIN REMARK 500 6 ARG A 11 0.25 SIDE CHAIN REMARK 500 6 ARG A 22 0.28 SIDE CHAIN REMARK 500 6 ARG A 51 0.31 SIDE CHAIN REMARK 500 6 ARG A 59 0.32 SIDE CHAIN REMARK 500 6 ARG A 85 0.23 SIDE CHAIN REMARK 500 6 ARG A 96 0.22 SIDE CHAIN REMARK 500 7 ARG A 11 0.30 SIDE CHAIN REMARK 500 7 ARG A 22 0.27 SIDE CHAIN REMARK 500 7 ARG A 51 0.23 SIDE CHAIN REMARK 500 7 ARG A 59 0.32 SIDE CHAIN REMARK 500 7 ARG A 85 0.25 SIDE CHAIN REMARK 500 7 ARG A 96 0.27 SIDE CHAIN REMARK 500 8 ARG A 11 0.28 SIDE CHAIN REMARK 500 8 ARG A 22 0.29 SIDE CHAIN REMARK 500 8 ARG A 51 0.28 SIDE CHAIN REMARK 500 8 ARG A 59 0.25 SIDE CHAIN REMARK 500 8 ARG A 85 0.25 SIDE CHAIN REMARK 500 8 ARG A 96 0.24 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UBQ RELATED DB: PDB REMARK 900 STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION REMARK 900 RELATED ID: 2COC RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE C-TERMINAL PH DOMAIN OF FYVE, RHOGEF AND REMARK 900 PH DOMAIN CONTAINING PROTEIN 3 (FGD3) FROM HUMAN REMARK 900 RELATED ID: 2DHK RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PH DOMAIN OF TBC1 DOMAIN FAMILY MEMBER 2 REMARK 900 PROTEIN FROM HUMAN REMARK 900 RELATED ID: 2HTH RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR UBIQUITIN RECOGNITION BY THE HUMAN EAP45/ESCRT- REMARK 900 II GLUE DOMAIN REMARK 900 RELATED ID: 1FHO RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PH DOMAIN FROM THE C. ELEGANS MUSCLE REMARK 900 PROTEIN UNC-89 REMARK 900 RELATED ID: 2D9V RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PH DOMAIN OF PLECKSTRIN HOMOLOGY DOMAIN- REMARK 900 CONTAINING PROTEIN FAMILY B MEMBER 1 FROM MOUSE DBREF 2Z4D A 6 101 UNP O13563 RPN13_YEAST 6 101 SEQRES 1 A 96 THR VAL ILE LYS PHE ARG ALA GLY VAL CYS GLU TYR ASN SEQRES 2 A 96 GLU ASP SER ARG LEU CYS THR PRO ILE PRO VAL GLN GLY SEQRES 3 A 96 GLU ILE GLU ILE LYS PRO ASN GLU GLU GLU GLU LEU GLY SEQRES 4 A 96 PHE TRP ASP PHE GLU TRP ARG PRO THR GLU LYS PRO VAL SEQRES 5 A 96 GLY ARG GLU LEU ASP PRO ILE SER LEU ILE LEU ILE PRO SEQRES 6 A 96 GLY GLU THR MET TRP VAL PRO ILE LYS SER SER LYS SER SEQRES 7 A 96 GLY ARG ILE PHE ALA LEU VAL PHE SER SER ASN GLU ARG SEQRES 8 A 96 TYR PHE PHE TRP LEU SHEET 1 A 4 ILE A 8 PHE A 10 0 SHEET 2 A 4 ILE A 33 PRO A 37 -1 O ILE A 33 N PHE A 10 SHEET 3 A 4 TRP A 46 TRP A 50 -1 O GLU A 49 N GLU A 34 SHEET 4 A 4 ILE A 64 LEU A 66 -1 O LEU A 66 N PHE A 48 SHEET 1 B 2 CYS A 15 ASN A 18 0 SHEET 2 B 2 LEU A 23 PRO A 26 -1 O LEU A 23 N ASN A 18 SHEET 1 C 3 MET A 74 VAL A 76 0 SHEET 2 C 3 ILE A 86 VAL A 90 -1 O VAL A 90 N MET A 74 SHEET 3 C 3 TYR A 97 TRP A 100 -1 O TYR A 97 N LEU A 89 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