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Database: PDB
Entry: 3ZJ1
LinkDB: 3ZJ1
Original site: 3ZJ1 
HEADER    RNA BINDING PROTEIN                     16-JAN-13   3ZJ1              
TITLE     STRUCTURE OF NAB2P TANDEM ZINC FINGER 12                              
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN NAB2;           
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: ZINC FINGERS 1 AND 2, RESIDUES 253-333;                    
COMPND   5 SYNONYM: NAB2P;                                                      
COMPND   6 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;                       
SOURCE   3 ORGANISM_COMMON: BAKER'S YEAST;                                      
SOURCE   4 ORGANISM_TAXID: 4932;                                                
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);                                 
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE   9 EXPRESSION_SYSTEM_VECTOR: PET28                                      
KEYWDS    RNA BINDING PROTEIN, CCCH-TYPE ZINC FINGER, MRNA EXPORT, POLY(A)      
KEYWDS   2 LENGTH CONTROL, POLYADENOSINE RNA BINDING.                           
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    S.MARTINEZ-LUMBRERAS,C.M.SANTIVERI,Y.MIRASSOU,S.ZORRILLA,             
AUTHOR   2 J.M.PEREZ- CANADILLAS                                                
REVDAT   3   09-JUL-14 3ZJ1    1       AUTHOR JRNL                              
REVDAT   2   30-OCT-13 3ZJ1    1       JRNL                                     
REVDAT   1   11-SEP-13 3ZJ1    0                                                
JRNL        AUTH   S.MARTINEZ-LUMBRERAS,C.M.SANTIVERI,Y.MIRASSOU,S.ZORRILLA,    
JRNL        AUTH 2 J.M.PEREZ-CANADILLAS                                         
JRNL        TITL   TWO SINGULAR TYPES OF CCCH TANDEM ZINC FINGER IN NAB2P       
JRNL        TITL 2 CONTRIBUTE TO POLYADENOSINE RNA RECOGNITION.                 
JRNL        REF    STRUCTURE                     V.  21  1800 2013              
JRNL        REFN                   ISSN 0969-2126                               
JRNL        PMID   23994011                                                     
JRNL        DOI    10.1016/J.STR.2013.07.019                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : AMBER 7.0                                            
REMARK   3   AUTHORS     : CASE, D.A. ET AL                                     
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: REFINEMENT PROTOCOL AS DESCRIBED IN THE   
REMARK   3  PRIMARY CITATION                                                    
REMARK   4                                                                      
REMARK   4 3ZJ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUL-13.                  
REMARK 100 THE PDBE ID CODE IS EBI-55425.                                       
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298.0                              
REMARK 210  PH                             : 6.5                                
REMARK 210  IONIC STRENGTH                 : 25MM                               
REMARK 210  PRESSURE                       : 1.0 ATM                            
REMARK 210  SAMPLE CONTENTS                : 90% H2O/10% D2O, 100% D2O          
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 1H-15N HSQC, 1H-13C HSQC, HNCO,    
REMARK 210                                   HNCA, CBCA(CO)HN, H(C)CH-TOCSY,    
REMARK 210                                   15N HSQC- NOESY, NOESY, TOCSY      
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ, 800 MHZ                   
REMARK 210  SPECTROMETER MODEL             : AVANCE, DMX                        
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NMRPIPE, ANALYSIS, CYANA, AMBER    
REMARK 210   METHOD USED                   : CYANA, AMBER                       
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 50                                 
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : LOWEST TARGET FUNCTION             
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
REMARK 210                                                                      
REMARK 210 REMARK: NONE                                                         
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PQS                                                   
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: 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 ARG A 313   NE  -  CZ  -  NH1 ANGL. DEV. =   3.4 DEGREES          
REMARK 500  1 ARG A 313   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.4 DEGREES          
REMARK 500  6 ARG A 315   NE  -  CZ  -  NH1 ANGL. DEV. =   3.2 DEGREES          
REMARK 500  8 ARG A 315   NE  -  CZ  -  NH1 ANGL. DEV. =   3.0 DEGREES          
REMARK 500 10 ARG A 321   NE  -  CZ  -  NH1 ANGL. DEV. =   3.4 DEGREES          
REMARK 500 12 ARG A 313   NE  -  CZ  -  NH1 ANGL. DEV. =   3.1 DEGREES          
REMARK 500 16 ARG A 313   NE  -  CZ  -  NH1 ANGL. DEV. =   3.1 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 ARG A 261      125.25     71.51                                   
REMARK 500  1 HIS A 267       34.64    -83.52                                   
REMARK 500  1 ARG A 272      -33.46    176.25                                   
REMARK 500  1 SER A 273       -1.71   -146.81                                   
REMARK 500  1 ASN A 288       20.11    -78.68                                   
REMARK 500  1 THR A 295      -31.27   -138.54                                   
REMARK 500  1 PRO A 301       48.48    -76.20                                   
REMARK 500  1 ASN A 302      -59.20   -161.02                                   
REMARK 500  1 LYS A 329       14.03     59.74                                   
REMARK 500  2 ARG A 261      123.01     62.09                                   
REMARK 500  2 HIS A 267       34.40    -84.17                                   
REMARK 500  2 ARG A 272      -33.95    175.81                                   
REMARK 500  2 SER A 273       -2.20   -149.17                                   
REMARK 500  2 ASN A 288       22.36    -79.58                                   
REMARK 500  2 THR A 295      -29.05   -140.14                                   
REMARK 500  2 ASN A 302      -65.57   -167.32                                   
REMARK 500  2 ASP A 304       20.89    -77.23                                   
REMARK 500  3 ARG A 261      158.09     59.14                                   
REMARK 500  3 HIS A 267       39.03    -85.96                                   
REMARK 500  3 PRO A 301       48.51    -77.41                                   
REMARK 500  3 ASN A 302      -62.99   -164.04                                   
REMARK 500  3 ALA A 328      147.98     79.95                                   
REMARK 500  4 THR A 256      114.04     75.17                                   
REMARK 500  4 LYS A 258     -176.64    -69.27                                   
REMARK 500  4 ARG A 261      118.33     64.70                                   
REMARK 500  4 HIS A 267       41.24    -85.39                                   
REMARK 500  4 ASN A 288       20.43    -78.71                                   
REMARK 500  4 ASN A 302      -66.25   -162.70                                   
REMARK 500  4 ALA A 328     -152.87   -145.52                                   
REMARK 500  5 SER A 252      165.94     71.15                                   
REMARK 500  5 GLU A 259     -146.56   -104.57                                   
REMARK 500  5 ARG A 261      123.25     65.72                                   
REMARK 500  5 HIS A 267       35.95    -84.84                                   
REMARK 500  5 ASN A 288       31.18    -84.18                                   
REMARK 500  5 THR A 295      -35.59   -161.58                                   
REMARK 500  5 ASN A 302      -67.40   -163.94                                   
REMARK 500  5 ALA A 327     -133.42    -96.09                                   
REMARK 500  6 SER A 252      168.77     69.64                                   
REMARK 500  6 LYS A 258     -161.90    -69.37                                   
REMARK 500  6 GLU A 259     -153.36    -74.68                                   
REMARK 500  6 ARG A 261      123.14     64.08                                   
REMARK 500  6 HIS A 267       38.82    -84.93                                   
REMARK 500  6 THR A 295      -32.57   -137.63                                   
REMARK 500  6 ASN A 302      -52.08   -164.57                                   
REMARK 500  6 GLU A 303      -64.25    -96.20                                   
REMARK 500  6 ASP A 304       23.36    -75.60                                   
REMARK 500  6 LYS A 329      -30.95   -143.59                                   
REMARK 500  7 THR A 254      155.59     68.89                                   
REMARK 500  7 ARG A 261      121.43     64.47                                   
REMARK 500  7 HIS A 267       33.43    -83.65                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     165 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 12 ARG A 261         0.08    SIDE CHAIN                              
REMARK 500 17 ARG A 313         0.09    SIDE CHAIN                              
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                           1  ZN A 401  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 268   SG                                                     
REMARK 620 2 CYS A 262   SG  113.0                                              
REMARK 620 3 CYS A 274   SG  114.0 112.7                                        
REMARK 620 4 HIS A 278   NE2 104.2 104.8 107.2                                  
REMARK 620 N                    1     2     3                                   
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                           1  ZN A 402  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 CYS A 289   SG                                                     
REMARK 620 2 HIS A 300   NE2 105.7                                              
REMARK 620 3 CYS A 283   SG  115.1 104.5                                        
REMARK 620 4 CYS A 296   SG  111.5 103.9 114.7                                  
REMARK 620 N                    1     2     3                                   
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  ZN A 401                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  ZN A 402                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 3ZJ2   RELATED DB: PDB                                   
REMARK 900  STRUCTURE OF NAB2P TANDEM ZINC FINGER 34                            
REMARK 999                                                                      
REMARK 999 SEQUENCE                                                             
REMARK 999 THE TWO N-TERMINAL RESIDUES (GS) ARE NOT FROM WILD TYPE              
REMARK 999 SEQUENCE                                                             
DBREF  3ZJ1 A  253   333  UNP    P32505   NAB2_YEAST     253    333             
SEQADV 3ZJ1 GLY A  251  UNP  P32505              EXPRESSION TAG                 
SEQADV 3ZJ1 SER A  252  UNP  P32505              EXPRESSION TAG                 
SEQRES   1 A   83  GLY SER PHE THR PRO THR LYS LYS GLU GLY ARG CYS ARG          
SEQRES   2 A   83  LEU PHE PRO HIS CYS PRO LEU GLY ARG SER CYS PRO HIS          
SEQRES   3 A   83  ALA HIS PRO THR LYS VAL CYS ASN GLU TYR PRO ASN CYS          
SEQRES   4 A   83  PRO LYS PRO PRO GLY THR CYS GLU PHE LEU HIS PRO ASN          
SEQRES   5 A   83  GLU ASP GLU GLU LEU MET LYS GLU MET GLU ARG THR ARG          
SEQRES   6 A   83  GLU GLU PHE GLN LYS ARG LYS ALA ASP LEU LEU ALA ALA          
SEQRES   7 A   83  LYS ARG LYS PRO VAL                                          
HET     ZN  A 401       1                                                       
HET     ZN  A 402       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   2   ZN    2(ZN 2+)                                                     
HELIX    1   1 ASP A  304  ALA A  327  1                                  24    
LINK        ZN    ZN A 401                 SG  CYS A 268     1555   1555  2.46  
LINK        ZN    ZN A 401                 SG  CYS A 262     1555   1555  2.45  
LINK        ZN    ZN A 401                 SG  CYS A 274     1555   1555  2.44  
LINK        ZN    ZN A 401                 NE2 HIS A 278     1555   1555  2.33  
LINK        ZN    ZN A 402                 NE2 HIS A 300     1555   1555  2.30  
LINK        ZN    ZN A 402                 SG  CYS A 283     1555   1555  2.43  
LINK        ZN    ZN A 402                 SG  CYS A 296     1555   1555  2.45  
LINK        ZN    ZN A 402                 SG  CYS A 289     1555   1555  2.44  
CISPEP   1 PHE A  265    PRO A  266          1         6.17                     
CISPEP   2 TYR A  286    PRO A  287          1         2.10                     
CISPEP   3 PHE A  265    PRO A  266          2         5.08                     
CISPEP   4 TYR A  286    PRO A  287          2         3.27                     
CISPEP   5 PHE A  265    PRO A  266          3         2.17                     
CISPEP   6 TYR A  286    PRO A  287          3         3.56                     
CISPEP   7 PHE A  265    PRO A  266          4         2.33                     
CISPEP   8 TYR A  286    PRO A  287          4         3.19                     
CISPEP   9 PHE A  265    PRO A  266          5         4.87                     
CISPEP  10 TYR A  286    PRO A  287          5         2.79                     
CISPEP  11 PHE A  265    PRO A  266          6         5.26                     
CISPEP  12 TYR A  286    PRO A  287          6         2.44                     
CISPEP  13 PHE A  265    PRO A  266          7         3.76                     
CISPEP  14 TYR A  286    PRO A  287          7         2.32                     
CISPEP  15 PHE A  265    PRO A  266          8         7.72                     
CISPEP  16 TYR A  286    PRO A  287          8         2.76                     
CISPEP  17 PHE A  265    PRO A  266          9         4.28                     
CISPEP  18 TYR A  286    PRO A  287          9         3.27                     
CISPEP  19 PHE A  265    PRO A  266         10         5.66                     
CISPEP  20 TYR A  286    PRO A  287         10         2.95                     
CISPEP  21 PHE A  265    PRO A  266         11         5.05                     
CISPEP  22 TYR A  286    PRO A  287         11         3.58                     
CISPEP  23 PHE A  265    PRO A  266         12         2.86                     
CISPEP  24 TYR A  286    PRO A  287         12         3.82                     
CISPEP  25 PHE A  265    PRO A  266         13        11.46                     
CISPEP  26 TYR A  286    PRO A  287         13         0.74                     
CISPEP  27 PHE A  265    PRO A  266         14         7.50                     
CISPEP  28 TYR A  286    PRO A  287         14         1.69                     
CISPEP  29 PHE A  265    PRO A  266         15         4.69                     
CISPEP  30 TYR A  286    PRO A  287         15         1.85                     
CISPEP  31 PHE A  265    PRO A  266         16         5.29                     
CISPEP  32 TYR A  286    PRO A  287         16         2.53                     
CISPEP  33 PHE A  265    PRO A  266         17         7.80                     
CISPEP  34 TYR A  286    PRO A  287         17         2.95                     
CISPEP  35 PHE A  265    PRO A  266         18         5.37                     
CISPEP  36 TYR A  286    PRO A  287         18        -0.38                     
CISPEP  37 PHE A  265    PRO A  266         19         4.36                     
CISPEP  38 TYR A  286    PRO A  287         19         4.79                     
CISPEP  39 PHE A  265    PRO A  266         20         3.97                     
CISPEP  40 TYR A  286    PRO A  287         20         1.82                     
SITE     1 AC1  4 CYS A 262  CYS A 268  CYS A 274  HIS A 278                    
SITE     1 AC2  4 CYS A 283  CYS A 289  CYS A 296  HIS A 300                    
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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