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Database: PDB
Entry: 2Z4D
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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                                                                  
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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