HEADER    SIGNALING PROTEIN                       11-JUN-18   6DRF              
TITLE     STRUCTURE OF HUMAN RETINAL DEGENERATION 3(RD3) PROTEIN                
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PROTEIN RD3;                                               
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: RESIDUES 19-153;                                           
COMPND   5 SYNONYM: RETINAL DEGENERATION PROTEIN 3;                             
COMPND   6 ENGINEERED: YES;                                                     
COMPND   7 MUTATION: YES                                                        
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: RD3, C1ORF36;                                                  
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    SENSORY TRANSDUCTION, VISION, SIGNALING PROTEIN                       
EXPDTA    SOLUTION NMR                                                          
NUMMDL    10                                                                    
AUTHOR    Q.YU,S.LIM,I.PESHENKO,D.CUDIA,A.M.DIZHOOR,J.B.AMES                    
REVDAT   5   15-MAY-24 6DRF    1       REMARK                                   
REVDAT   4   14-JUN-23 6DRF    1       REMARK                                   
REVDAT   3   11-DEC-19 6DRF    1       REMARK                                   
REVDAT   2   27-FEB-19 6DRF    1       JRNL   REMARK DBREF  SEQADV              
REVDAT   2 2                   1       HELIX  ATOM                              
REVDAT   1   06-FEB-19 6DRF    0                                                
JRNL        AUTH   I.V.PESHENKO,Q.YU,S.LIM,D.CUDIA,A.M.DIZHOOR,J.B.AMES         
JRNL        TITL   RETINAL DEGENERATION 3 (RD3) PROTEIN, A RETINAL GUANYLYL     
JRNL        TITL 2 CYCLASE REGULATOR, FORMS A MONOMERIC AND ELONGATED           
JRNL        TITL 3 FOUR-HELIX BUNDLE.                                           
JRNL        REF    J. BIOL. CHEM.                V. 294  2318 2019              
JRNL        REFN                   ESSN 1083-351X                               
JRNL        PMID   30559291                                                     
JRNL        DOI    10.1074/JBC.RA118.006106                                     
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR NIH 2.47                                      
REMARK   3   AUTHORS     : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE             
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 6DRF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-18.                  
REMARK 100 THE DEPOSITION ID IS D_1000234992.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 296                                
REMARK 210  PH                             : 7.4                                
REMARK 210  IONIC STRENGTH                 : 20                                 
REMARK 210  PRESSURE                       : 1 ATM                              
REMARK 210  SAMPLE CONTENTS                : 0.9 MM [U-15N] HUMAN RD3, 20 MM    
REMARK 210                                   D11 TRIS, 3 MM D10 DTT, 50 UM      
REMARK 210                                   D12 EDTA, 0.04 % W/V SODIUM        
REMARK 210                                   AZIDE, 93% H2O/7% D2O; 0.9 MM [U-  
REMARK 210                                   13C; U-15N] HUMAN RD3, 20 MM D11   
REMARK 210                                   TRIS, 3 MM D10 DTT, 50 UM D12      
REMARK 210                                   EDTA, 0.04 % W/V SODIUM AZIDE,     
REMARK 210                                   93% H2O/7% D2O                     
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 3D HNCA; 3D        
REMARK 210                                   HNCACB; 3D CBCA(CO)NH; 3D HNCO;    
REMARK 210                                   3D HCCH-TOCSY; 3D CCCONH; 3D       
REMARK 210                                   HCCCONH; 3D 1H-15N NOESY; 3D 1H-   
REMARK 210                                   13C NOESY; 3D 1H-15N TOCSY; 2D     
REMARK 210                                   1H-13C HSQC                        
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ                            
REMARK 210  SPECTROMETER MODEL             : AVANCE                             
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NMRPIPE 8.9, SPARKY 3.134, X       
REMARK 210                                   -PLOR NIH 2.47                     
REMARK 210   METHOD USED                   : DGSA-DISTANCE GEOMETRY SIMULATED   
REMARK 210                                   ANNEALING                          
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 200                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 10                                 
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: 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: 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  52     -152.71     64.80                                   
REMARK 500  1 LYS A  53      -22.03     78.20                                   
REMARK 500  1 THR A  56      -67.70     72.98                                   
REMARK 500  1 SER A  61       15.28   -178.47                                   
REMARK 500  1 ALA A  64       -8.26   -144.17                                   
REMARK 500  1 PRO A  67      -82.95    -84.09                                   
REMARK 500  1 ASP A  68      -61.69     69.84                                   
REMARK 500  1 GLU A 108      149.68     75.53                                   
REMARK 500  1 GLU A 110      124.11    175.83                                   
REMARK 500  1 ARG A 145       97.89   -163.53                                   
REMARK 500  1 GLU A 158     -177.50     63.90                                   
REMARK 500  2 ARG A  52     -155.90     67.79                                   
REMARK 500  2 ALA A  64      -14.69     69.59                                   
REMARK 500  2 SER A  65      127.87     62.24                                   
REMARK 500  2 ASP A  68       67.85     61.52                                   
REMARK 500  2 LEU A  73       73.62   -105.65                                   
REMARK 500  2 GLU A 108      145.90     75.04                                   
REMARK 500  2 GLU A 110      108.62   -175.84                                   
REMARK 500  2 ARG A 140      -87.57    -94.43                                   
REMARK 500  2 GLN A 141      -92.82     73.44                                   
REMARK 500  2 TRP A 142      -82.80     57.83                                   
REMARK 500  2 SER A 149      -44.64     70.79                                   
REMARK 500  2 ALA A 157      111.26   -160.56                                   
REMARK 500  3 THR A  56      -44.55     66.76                                   
REMARK 500  3 LEU A  63      -65.43   -132.52                                   
REMARK 500  3 ASP A  68      -67.83    -90.72                                   
REMARK 500  3 GLU A 108      129.93     77.62                                   
REMARK 500  3 GLU A 110      102.50   -168.58                                   
REMARK 500  3 ARG A 140      140.10     81.80                                   
REMARK 500  3 TRP A 142      -63.85     70.81                                   
REMARK 500  3 ARG A 145      104.75   -164.73                                   
REMARK 500  3 ARG A 147     -150.73   -122.58                                   
REMARK 500  3 THR A 152       10.26   -152.62                                   
REMARK 500  3 GLU A 156      103.20     60.52                                   
REMARK 500  4 ARG A  52      -66.33     69.71                                   
REMARK 500  4 VAL A  58      126.17     71.87                                   
REMARK 500  4 ALA A  64      -40.22     82.44                                   
REMARK 500  4 PRO A  67      -72.91    -62.97                                   
REMARK 500  4 GLU A 108      161.10     72.91                                   
REMARK 500  4 GLU A 110       95.78   -163.69                                   
REMARK 500  4 ARG A 140       36.75    -97.26                                   
REMARK 500  4 TRP A 142      -56.85   -125.23                                   
REMARK 500  4 ARG A 147      -59.01   -174.92                                   
REMARK 500  4 LEU A 150      107.96     69.25                                   
REMARK 500  4 THR A 152      -60.15     74.81                                   
REMARK 500  4 GLU A 158      151.61     72.70                                   
REMARK 500  5 ARG A  52      177.88     74.21                                   
REMARK 500  5 LYS A  53       69.89     63.90                                   
REMARK 500  5 TYR A  60      -34.22   -174.98                                   
REMARK 500  5 ASP A  68      -55.17     74.34                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     110 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 27305   RELATED DB: BMRB                                 
DBREF  6DRF A   19   153  UNP    Q7Z3Z2   RD3_HUMAN       19    153             
SEQADV 6DRF ALA A   18  UNP  Q7Z3Z2              EXPRESSION TAG                 
SEQADV 6DRF ASP A   68  UNP  Q7Z3Z2    ARG    68 ENGINEERED MUTATION            
SEQADV 6DRF GLU A  154  UNP  Q7Z3Z2              EXPRESSION TAG                 
SEQADV 6DRF THR A  155  UNP  Q7Z3Z2              EXPRESSION TAG                 
SEQADV 6DRF GLU A  156  UNP  Q7Z3Z2              EXPRESSION TAG                 
SEQADV 6DRF ALA A  157  UNP  Q7Z3Z2              EXPRESSION TAG                 
SEQADV 6DRF GLU A  158  UNP  Q7Z3Z2              EXPRESSION TAG                 
SEQADV 6DRF ILE A  159  UNP  Q7Z3Z2              EXPRESSION TAG                 
SEQADV 6DRF ASP A  160  UNP  Q7Z3Z2              EXPRESSION TAG                 
SEQRES   1 A  143  ALA ARG SER PRO ALA GLU MET VAL LEU GLU THR LEU MET          
SEQRES   2 A  143  MET GLU LEU THR GLY GLN MET ARG GLU ALA GLU ARG GLN          
SEQRES   3 A  143  GLN ARG GLU ARG SER ASN ALA VAL ARG LYS VAL CYS THR          
SEQRES   4 A  143  GLY VAL ASP TYR SER TRP LEU ALA SER THR PRO ASP SER          
SEQRES   5 A  143  THR TYR ASP LEU SER PRO ILE GLU ARG LEU GLN LEU GLU          
SEQRES   6 A  143  ASP VAL CYS VAL LYS ILE HIS PRO SER TYR CYS GLY PRO          
SEQRES   7 A  143  ALA ILE LEU ARG PHE ARG GLN LEU LEU ALA GLU GLN GLU          
SEQRES   8 A  143  PRO GLU VAL GLN GLU VAL SER GLN LEU PHE ARG SER VAL          
SEQRES   9 A  143  LEU GLN GLU VAL LEU GLU ARG MET LYS GLN GLU GLU GLU          
SEQRES  10 A  143  ALA HIS LYS LEU THR ARG GLN TRP SER LEU ARG PRO ARG          
SEQRES  11 A  143  GLY SER LEU ALA THR PHE GLU THR GLU ALA GLU ILE ASP          
HELIX    1 AA1 SER A   20  ARG A   52  1                                  33    
HELIX    2 AA2 SER A   74  LYS A   87  1                                  14    
HELIX    3 AA3 HIS A   89  SER A   91  5                                   3    
HELIX    4 AA4 TYR A   92  GLU A  108  1                                  17    
HELIX    5 AA5 GLU A  110  ARG A  140  1                                  31    
HELIX    6 AA6 GLN A  141  LEU A  144  5                                   4    
HELIX    7 AA7 ALA A  151  THR A  155  5                                   5    
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