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Database: PDB
Entry: 2MJH
LinkDB: 2MJH
Original site: 2MJH 
HEADER    RNA BINDING PROTEIN                     09-JAN-14   2MJH              
TITLE     SOLUTION STRUCTURE OF THE GLD-1 RNA-BINDING DOMAIN IN COMPLEX WITH RNA
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: FEMALE GERMLINE-SPECIFIC TUMOR SUPPRESSOR GLD-1;           
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: KH-QUA2 DOMAIN OF GLD-1, UNP RESIDUES 195-336;             
COMPND   5 SYNONYM: DEFECTIVE IN GERM LINE DEVELOPMENT PROTEIN 1;               
COMPND   6 ENGINEERED: YES;                                                     
COMPND   7 MOL_ID: 2;                                                           
COMPND   8 MOLECULE: 5'-CUACUCAUAU-3';                                          
COMPND   9 CHAIN: B;                                                            
COMPND  10 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS;                         
SOURCE   3 ORGANISM_COMMON: NEMATODE;                                           
SOURCE   4 ORGANISM_TAXID: 6239;                                                
SOURCE   5 GENE: GLD-1, T23G11.3;                                               
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008;                                     
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);                                 
SOURCE   9 EXPRESSION_SYSTEM_VECTOR: PTYB1;                                     
SOURCE  10 OTHER_DETAILS: PURIFICATION VIA THE IMPACT SYSTEM (NEB) THAT RESULTS 
SOURCE  11 IN THE PROTEIN WITHOUT ANY ADDITIONAL RESIDUES;                      
SOURCE  12 MOL_ID: 2;                                                           
SOURCE  13 SYNTHETIC: YES                                                       
KEYWDS    GLD-1, KH-QUA2 DOMAIN, STAR PROTEIN FAMILY, RNA REGULATION, TRA-2,    
KEYWDS   2 RNA BINDING PROTEIN                                                  
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    G.M.DAUBNER,F.H.-T.ALLAIN                                             
REVDAT   5   14-JUN-23 2MJH    1       REMARK                                   
REVDAT   4   24-JAN-18 2MJH    1       AUTHOR                                   
REVDAT   3   30-JUL-14 2MJH    1       JRNL                                     
REVDAT   2   02-JUL-14 2MJH    1       JRNL                                     
REVDAT   1   28-MAY-14 2MJH    0                                                
JRNL        AUTH   G.M.DAUBNER,A.BRUMMER,C.TOCCHINI,S.GERHARDY,R.CIOSK,         
JRNL        AUTH 2 M.ZAVOLAN,F.H.ALLAIN                                         
JRNL        TITL   STRUCTURAL AND FUNCTIONAL IMPLICATIONS OF THE QUA2 DOMAIN ON 
JRNL        TITL 2 RNA RECOGNITION BY GLD-1.                                    
JRNL        REF    NUCLEIC ACIDS RES.            V.  42  8092 2014              
JRNL        REFN                   ISSN 0305-1048                               
JRNL        PMID   24838563                                                     
JRNL        DOI    10.1093/NAR/GKU445                                           
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : AMBER 9                                              
REMARK   3   AUTHORS     : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG,       
REMARK   3                 DUKE, LUO, ... AND KOLLMAN                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: FF99SB FORCE-FIELD/ IMPLICIT WATER        
REMARK   4                                                                      
REMARK   4 2MJH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-14.                  
REMARK 100 THE DEPOSITION ID IS D_1000103687.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 303                                
REMARK 210  PH                             : 6.5                                
REMARK 210  IONIC STRENGTH                 : 0.17                               
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 0.45 MM [U-15N] GLD-1 (AA 195      
REMARK 210                                   -336), 0.45 MM 5'-CUACUCAUAU-3',   
REMARK 210                                   50 MM SODIUM CHLORIDE, 20 MM       
REMARK 210                                   SODIUM PHOSPHATE, 3 MM DTT, 90%    
REMARK 210                                   H2O/10% D2O; 0.45 MM [U-13C; U-    
REMARK 210                                   15N] GLD-1 (AA 195-336), 0.45 MM   
REMARK 210                                   5'-CUACUCAUAU-3', 50 MM SODIUM     
REMARK 210                                   CHLORIDE, 20 MM SODIUM PHOSPHATE,  
REMARK 210                                   3 MM DTT, 90% H2O/10% D2O; 0.45    
REMARK 210                                   MM [U-15N] GLD-1 (AA 195-336),     
REMARK 210                                   0.45 MM 5'-CUACUCAUAU-3', 50 MM    
REMARK 210                                   SODIUM CHLORIDE, 20 MM SODIUM      
REMARK 210                                   PHOSPHATE, 3 MM DTT, 100% D2O;     
REMARK 210                                   0.45 MM [U-13C; U-15N] GLD-1 (AA   
REMARK 210                                   195-336), 0.45 MM 5'-CUACUCAUAU-   
REMARK 210                                   3', 50 MM SODIUM CHLORIDE, 20 MM   
REMARK 210                                   SODIUM PHOSPHATE, 3 MM DTT, 100%   
REMARK 210                                   D2O; 0.45 MM [U-10% 13C; U-100%    
REMARK 210                                   15N] GLD-1 (AA 195-336), 0.45 MM   
REMARK 210                                   5'-CUACUCAUAU-3', 50 MM SODIUM     
REMARK 210                                   CHLORIDE, 20 MM SODIUM PHOSPHATE,  
REMARK 210                                   3 MM DTT, 90% H2O/10% D2O; 0.45    
REMARK 210                                   MM [U-15N] GLD-1 (AA 195-336),     
REMARK 210                                   0.45 MM 5'-CUACUCAUAU-3', 50 MM    
REMARK 210                                   SODIUM CHLORIDE, 20 MM SODIUM      
REMARK 210                                   PHOSPHATE, 3 MM DTT, 14 MG/ML      
REMARK 210                                   PF1 PHAGE, 90% H2O/10% D2O         
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 2D 1H-13C HSQC;    
REMARK 210                                   3D HNCA; 3D HN(CO)CA; 3D HNCO;     
REMARK 210                                   3D HN(CA)CO; 3D CBCA(CO)NH; 3D     
REMARK 210                                   HCCH-TOCSY; 3D 1H-15N NOESY; 3D    
REMARK 210                                   1H-13C NOESY; 2D 1H-1H TOCSY; 2D   
REMARK 210                                   1H-1H NOESY; 2D F1F F2F 1H-1H      
REMARK 210                                   NOESY; 2D F2F 1H-1H NOESY; 3D      
REMARK 210                                   F1F F2E 1H-1H NOESY; LONG-RANGE    
REMARK 210                                   1H-15N HSQC; 3D HNHA; 2D 1H-15N    
REMARK 210                                   IPAP HSQC                          
REMARK 210  SPECTROMETER FIELD STRENGTH    : 500 MHZ; 600 MHZ; 700 MHZ; 750     
REMARK 210                                   MHZ; 900 MHZ                       
REMARK 210  SPECTROMETER MODEL             : AVANCE                             
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : CYANA 3.0, SPARKY 3.114, TOPSPIN   
REMARK 210                                   3.0, TALOS +, PROCHECKNMR 3.5.4,   
REMARK 210                                   ATNOSCANDID 2.1, PALES 2.1, WHAT   
REMARK 210                                   IF 10.1.1                          
REMARK 210   METHOD USED                   : SIMULATED ANNEALING                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 250                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : LOWEST ENERGY AND NOE VIOLATIONS   
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: CLOSE CONTACTS                                             
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
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   C B  21   O4' -  C1' -  N1  ANGL. DEV. =   6.0 DEGREES          
REMARK 500  3   C B  21   O4' -  C1' -  N1  ANGL. DEV. =   4.4 DEGREES          
REMARK 500  5   C B  21   O4' -  C1' -  N1  ANGL. DEV. =   4.2 DEGREES          
REMARK 500  6   C B  21   O4' -  C1' -  N1  ANGL. DEV. =   4.6 DEGREES          
REMARK 500  7   C B  21   O4' -  C1' -  N1  ANGL. DEV. =   4.6 DEGREES          
REMARK 500  8   C B  21   O4' -  C1' -  N1  ANGL. DEV. =   6.0 DEGREES          
REMARK 500 11   C B  21   O4' -  C1' -  N1  ANGL. DEV. =   4.7 DEGREES          
REMARK 500 12   U B  17   C5' -  C4' -  C3' ANGL. DEV. =  -8.5 DEGREES          
REMARK 500 15   C B  21   O4' -  C1' -  N1  ANGL. DEV. =   5.1 DEGREES          
REMARK 500 17   C B  21   O4' -  C1' -  N1  ANGL. DEV. =   5.1 DEGREES          
REMARK 500 18   C B  21   O4' -  C1' -  N1  ANGL. DEV. =   4.7 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 ALA A 199     -158.63    -97.69                                   
REMARK 500  1 PRO A 212       32.95    -75.28                                   
REMARK 500  1 ARG A 229       25.61     47.95                                   
REMARK 500  1 SER A 256       -3.30     64.09                                   
REMARK 500  1 ALA A 260       15.09     52.41                                   
REMARK 500  1 ARG A 262       87.98     55.49                                   
REMARK 500  1 TRP A 267       35.49    -80.59                                   
REMARK 500  1 GLU A 268     -143.76     54.07                                   
REMARK 500  1 GLU A 284       -8.66    -59.74                                   
REMARK 500  1 MET A 330      179.85     53.51                                   
REMARK 500  2 PRO A 212       32.50    -75.02                                   
REMARK 500  2 LYS A 213       -8.23    -59.08                                   
REMARK 500  2 ARG A 229       23.33     49.13                                   
REMARK 500  2 ARG A 253      -21.54   -145.06                                   
REMARK 500  2 ASP A 254        9.58   -152.33                                   
REMARK 500  2 ARG A 262       28.42   -145.80                                   
REMARK 500  2 GLU A 268      -23.01   -148.57                                   
REMARK 500  2 LEU A 270        2.33    -68.46                                   
REMARK 500  2 PRO A 306      170.92    -56.40                                   
REMARK 500  2 THR A 309       11.14   -141.88                                   
REMARK 500  3 PRO A 212       31.05    -67.46                                   
REMARK 500  3 LYS A 213       -5.42    -59.51                                   
REMARK 500  3 ARG A 229       21.37     49.35                                   
REMARK 500  3 ARG A 253       11.15   -143.19                                   
REMARK 500  3 LYS A 255     -149.92   -147.82                                   
REMARK 500  3 LYS A 257       15.19   -149.61                                   
REMARK 500  3 TRP A 267       22.92   -142.65                                   
REMARK 500  3 ASP A 282     -170.51   -172.75                                   
REMARK 500  4 PRO A 212       34.74    -76.76                                   
REMARK 500  4 ARG A 229       27.38     47.82                                   
REMARK 500  4 ASP A 254       13.74     54.45                                   
REMARK 500  4 ARG A 262       13.44     56.98                                   
REMARK 500  4 TRP A 267       17.68   -141.99                                   
REMARK 500  4 PRO A 306      171.79    -56.03                                   
REMARK 500  4 THR A 309       19.95   -143.22                                   
REMARK 500  4 MET A 330       29.40     46.57                                   
REMARK 500  4 SER A 332      158.01     60.56                                   
REMARK 500  5 PRO A 212       43.24    -82.55                                   
REMARK 500  5 ARG A 229       22.80     49.54                                   
REMARK 500  5 TRP A 267       43.89   -145.96                                   
REMARK 500  5 LEU A 270       37.71    -75.05                                   
REMARK 500  5 THR A 309       -1.88   -141.32                                   
REMARK 500  6 PRO A 212       33.07    -75.33                                   
REMARK 500  6 ARG A 229       23.64     49.32                                   
REMARK 500  6 SER A 251       32.21    -89.68                                   
REMARK 500  6 ALA A 260       15.00     54.56                                   
REMARK 500  6 THR A 309       20.45   -146.66                                   
REMARK 500  6 SER A 332      139.93     62.49                                   
REMARK 500  7 ALA A 199     -142.43   -127.36                                   
REMARK 500  7 ASP A 201     -177.10     63.93                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     167 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 19726   RELATED DB: BMRB                                 
DBREF  2MJH A  195   336  UNP    Q17339   GLD1_CAEEL     195    336             
DBREF  2MJH B   16    25  PDB    2MJH     2MJH            16     25             
SEQRES   1 A  142  LEU PRO GLU PRO ALA GLY ASP MET ILE SER ILE THR GLU          
SEQRES   2 A  142  LYS ILE TYR VAL PRO LYS ASN GLU TYR PRO ASP TYR ASN          
SEQRES   3 A  142  PHE VAL GLY ARG ILE LEU GLY PRO ARG GLY MET THR ALA          
SEQRES   4 A  142  LYS GLN LEU GLU GLN ASP THR GLY CYS LYS ILE MET VAL          
SEQRES   5 A  142  ARG GLY LYS GLY SER MET ARG ASP LYS SER LYS GLU SER          
SEQRES   6 A  142  ALA HIS ARG GLY LYS ALA ASN TRP GLU HIS LEU GLU ASP          
SEQRES   7 A  142  ASP LEU HIS VAL LEU VAL GLN CYS GLU ASP THR GLU ASN          
SEQRES   8 A  142  ARG VAL HIS ILE LYS LEU GLN ALA ALA LEU GLU GLN VAL          
SEQRES   9 A  142  LYS LYS LEU LEU ILE PRO ALA PRO GLU GLY THR ASP GLU          
SEQRES  10 A  142  LEU LYS ARG LYS GLN LEU MET GLU LEU ALA ILE ILE ASN          
SEQRES  11 A  142  GLY THR TYR ARG PRO MET LYS SER PRO ASN PRO ALA              
SEQRES   1 B   10    C   U   A   C   U   C   A   U   A   U                      
HELIX    1   1 ASN A  220  GLY A  227  1                                   8    
HELIX    2   2 GLY A  230  THR A  240  1                                  11    
HELIX    3   3 GLY A  248  MET A  252  5                                   5    
HELIX    4   4 ARG A  286  LEU A  302  1                                  17    
HELIX    5   5 ASP A  310  ASN A  324  1                                  15    
SHEET    1   A 3 MET A 202  TYR A 210  0                                        
SHEET    2   A 3 HIS A 275  THR A 283 -1  O  CYS A 280   N  ILE A 205           
SHEET    3   A 3 LYS A 243  ARG A 247 -1  N  MET A 245   O  LEU A 277           
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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