10 20 30 40 50 60 70 80 2Z4D - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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 COMPND 6 SUBUNIT 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, NMR, PH DOMAIN, NUCLEAR PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 8
AUTHOR N.ZHANG,K.J.WALTERS
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, JRNL AUTH 2 Y.SHI,K.HOFMANN,K.J.WALTERS,D.FINLEY,I.DIKIC JRNL TITL PROTEASOME SUBUNIT RPN13 IS A NOVEL UBIQUITIN JRNL TITL 2 RECEPTOR. JRNL REF NATURE V. 453 481 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18497817 JRNL DOI 10.1038/NATURE06926
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 1084 RESTRAINTS, 949 ARE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 79 DIHEDRAL ANGLE RESTRAINTS, 56 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN 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 19-JUN-07. REMARK 100 THE RCSB ID CODE IS RCSB027505.
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; REMARK 210 50MM NACL; 4MM DTT; 90% H2O, REMARK 210 10% D2O; 0.5MM RPN13 U-15N; U- REMARK 210 50% 2H; 20MM PHOSPHATE BUFFER; REMARK 210 50MM NACL; 4MM DTT; 90% H2O, REMARK 210 10% D2O; 0.5MM RPN13 U-13C; REMARK 210 20MM PHOSPHATE BUFFER; 50MM REMARK 210 NACL; 4MM DTT; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCACB, HNCA/HN(CO)CA, HNCO/ REMARK 210 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 : NMRPIPE 2006, XEASY 1996, X- REMARK 210 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 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, REMARK 900 RHOGEF AND 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 REMARK 900 MEMBER 2 PROTEIN FROM HUMAN REMARK 900 RELATED ID: 2HTH RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR UBIQUITIN RECOGNITION BY THE HUMAN REMARK 900 EAP45/ESCRT-II GLUE DOMAIN REMARK 900 RELATED ID: 1FHO RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PH DOMAIN FROM THE C. ELEGANS REMARK 900 MUSCLE PROTEIN UNC-89 REMARK 900 RELATED ID: 2D9V RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE PH DOMAIN OF PLECKSTRIN HOMOLOGY REMARK 900 DOMAIN-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