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Database: PDB
Entry: 2NEF
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Original site: 2NEF 
HEADER    REGULATORY FACTOR                       12-FEB-97   2NEF              
TITLE     HIV-1 NEF (REGULATORY FACTOR), NMR, 40 STRUCTURES                     
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: NEGATIVE FACTOR (F-PROTEIN);                               
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: HIV-1 NEF;                                                  
COMPND   5 ENGINEERED: YES;                                                     
COMPND   6 MUTATION: YES                                                        
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1;            
SOURCE   3 ORGANISM_TAXID: 11678;                                               
SOURCE   4 STRAIN: BH10;                                                        
SOURCE   5 GENE: HIV-1 NEF;                                                     
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: DE3;                                       
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PET11A;                                   
SOURCE  10 EXPRESSION_SYSTEM_GENE: HIV-1 NEF                                    
KEYWDS    REGULATORY FACTOR, AIDS, MYRISTYLATION, GTP-BINDING                   
EXPDTA    SOLUTION NMR                                                          
NUMMDL    40                                                                    
AUTHOR    S.GRZESIEK,A.BAX,G.M.CLORE,A.M.GRONENBORN,J.S.HU,J.KAUFMAN,I.PALMER,  
AUTHOR   2 S.J.STAHL,N.TJANDRA,P.T.WINGFIELD                                    
REVDAT   4   29-NOV-17 2NEF    1       HELIX                                    
REVDAT   3   13-JUL-11 2NEF    1       VERSN                                    
REVDAT   2   24-FEB-09 2NEF    1       VERSN                                    
REVDAT   1   07-JUL-97 2NEF    0                                                
SPRSDE     07-JUL-97 2NEF      1NEF                                             
JRNL        AUTH   S.GRZESIEK,A.BAX,J.S.HU,J.KAUFMAN,I.PALMER,S.J.STAHL,        
JRNL        AUTH 2 N.TJANDRA,P.T.WINGFIELD                                      
JRNL        TITL   REFINED SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF HIV-1    
JRNL        TITL 2 NEF.                                                         
JRNL        REF    PROTEIN SCI.                  V.   6  1248 1997              
JRNL        REFN                   ISSN 0961-8368                               
JRNL        PMID   9194185                                                      
REMARK   1                                                                      
REMARK   1 REFERENCE 1                                                          
REMARK   1  AUTH   S.GRZESIEK,A.BAX,G.M.CLORE,A.M.GRONENBORN,J.S.HU,J.KAUFMAN,  
REMARK   1  AUTH 2 I.PALMER,S.J.STAHL,P.T.WINGFIELD                             
REMARK   1  TITL   THE SOLUTION STRUCTURE OF HIV-1 NEF REVEALS AN UNEXPECTED    
REMARK   1  TITL 2 FOLD AND PERMITS DELINEATION OF THE BINDING SURFACE FOR THE  
REMARK   1  TITL 3 SH3 DOMAIN OF HCK TYROSINE PROTEIN KINASE                    
REMARK   1  REF    NAT.STRUCT.BIOL.              V.   3   340 1996              
REMARK   1  REFN                   ISSN 1072-8368                               
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.1                                           
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS:                                           
REMARK   3  THE STRUCTURES WERE CALCULATED USING THE SIMULATED                  
REMARK   3   ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT.              
REMARK   3   229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER)              
REMARK   3   MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL.          
REMARK   3   (1984) J. MAGN. RESON. SERIES B 104, 99 - 103) AND CARBON          
REMARK   3   CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON.            
REMARK   3   SERIES B 106, 92 - 96) RESTRAINTS.                                 
REMARK   3                                                                      
REMARK   3  THE COORDINATES OF THE 40 FINAL SIMULATED ANNEALING                 
REMARK   3  STRUCTURES ARE PRESENTED IN THIS ENTRY.  THE B FACTOR               
REMARK   3  FIELD PRESENTS THE AVERAGE RMS OF THE 40 INDIVIDUAL                 
REMARK   3  STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS OBTAINED BY          
REMARK   3  BEST FITTING RESIDUES 76 - 94, 97 - 102, 106 -147, 181 -            
REMARK   3  191, AND 194 -199.  THESE RESIDUES CORRESPOND TO THE                
REMARK   3  NON-MOBILE CORE OF THE PROTEIN AS EVIDENCED BY 15N                  
REMARK   3  RELAXATION DATA.                                                    
REMARK   4                                                                      
REMARK   4 2NEF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.                                
REMARK 100 THE DEPOSITION ID IS D_1000178400.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : NULL                               
REMARK 210  PH                             : NULL                               
REMARK 210  IONIC STRENGTH                 : NULL                               
REMARK 210  PRESSURE                       : NULL                               
REMARK 210  SAMPLE CONTENTS                : NULL                               
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : NULL                               
REMARK 210  SPECTROMETER FIELD STRENGTH    : NULL                               
REMARK 210  SPECTROMETER MODEL             : NULL                               
REMARK 210  SPECTROMETER MANUFACTURER      : NULL                               
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NULL                               
REMARK 210   METHOD USED                   : NULL                               
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : NULL                               
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 40                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : NULL                               
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL                
REMARK 210                                                                      
REMARK 210 REMARK:                                                              
REMARK 210  THE 3D STRUCTURE OF THE HIV-1 NEF (DELTA2 - 39, DELTA 159 -         
REMARK 210  173) SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND           
REMARK 210  -FILTERED NMR IS BASED ON 1250 EXPERIMENTAL RESTRAINTS:             
REMARK 210  338 SEQUENTIAL (|I-J|=1), 101 MEDIUM RANGE (1 < |I-J| <=5)          
REMARK 210  AND 245 LONG RANGE (|I-J| >5) INTERRESIDUES AND 70                  
REMARK 210  INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS;           
REMARK 210  64 DISTANCE RESTRAINTS FOR 32 HYDROGEN BONDS; 157 TORSION           
REMARK 210  ANGLE (78 PHI, 10 PSI, 55 CHI1 AND 14 CHI2) RESTRAINTS; 91          
REMARK 210  THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; AND 184 (93          
REMARK 210  CALPHA AND 91 CBETA) 13C SHIFT RESTRAINTS.                          
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   HG   SER A    88     HD1  HIS A    89              1.32            
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 GLU A  62      -83.59   -147.98                                   
REMARK 500  1 GLU A  64      155.34    -45.17                                   
REMARK 500  1 VAL A  66       31.27    -81.13                                   
REMARK 500  1 PHE A  68       43.36   -155.79                                   
REMARK 500  1 GLN A  73       98.06    -53.11                                   
REMARK 500  1 PRO A  75      108.43    -34.05                                   
REMARK 500  1 LEU A  76       97.85    -61.80                                   
REMARK 500  1 LYS A  94       28.58    -77.49                                   
REMARK 500  1 SER A 103      -75.93    -66.39                                   
REMARK 500  1 GLN A 104      -41.51   -170.82                                   
REMARK 500  1 HIS A 116       11.69    -62.72                                   
REMARK 500  1 THR A 117      -82.72   -126.03                                   
REMARK 500  1 PRO A 122       40.33    -75.32                                   
REMARK 500  1 PRO A 129     -168.61    -71.27                                   
REMARK 500  1 PRO A 131     -167.45    -76.95                                   
REMARK 500  1 ILE A 133      175.82    -48.80                                   
REMARK 500  1 ARG A 134      102.34   -165.90                                   
REMARK 500  1 CYS A 142       49.55    -80.28                                   
REMARK 500  1 GLU A 151       79.94    -61.24                                   
REMARK 500  1 LEU A 153       41.85    -82.55                                   
REMARK 500  1 ALA A 156      -58.43   -173.58                                   
REMARK 500  1 LYS A 158       38.46    -92.56                                   
REMARK 500  1 ASP A 174     -121.18    -93.96                                   
REMARK 500  1 ASP A 186       67.79   -154.67                                   
REMARK 500  1 SER A 187      -11.19    -44.33                                   
REMARK 500  1 PHE A 191      -33.41   -141.48                                   
REMARK 500  1 HIS A 193       75.12   -157.92                                   
REMARK 500  1 LEU A 198      -70.58    -76.48                                   
REMARK 500  1 ASN A 205      -84.68    -79.98                                   
REMARK 500  2 LEU A  58      -73.12    -81.30                                   
REMARK 500  2 GLN A  61     -106.64    -63.62                                   
REMARK 500  2 GLU A  62      -69.45   -170.52                                   
REMARK 500  2 GLU A  63      -75.43    -83.71                                   
REMARK 500  2 GLU A  64      107.49    -56.39                                   
REMARK 500  2 GLU A  65     -165.43    -79.34                                   
REMARK 500  2 PHE A  68       52.33   -153.04                                   
REMARK 500  2 PRO A  69     -178.49    -68.98                                   
REMARK 500  2 VAL A  70     -159.79    -84.35                                   
REMARK 500  2 PRO A  72     -160.22    -77.89                                   
REMARK 500  2 GLN A  73       97.38    -38.90                                   
REMARK 500  2 PRO A  75      136.79    -33.90                                   
REMARK 500  2 GLU A  93      -72.91    -72.07                                   
REMARK 500  2 ILE A 101      107.45    -58.80                                   
REMARK 500  2 SER A 103      -81.51    -67.14                                   
REMARK 500  2 GLN A 104      -27.48   -156.94                                   
REMARK 500  2 THR A 117      -94.89    -99.21                                   
REMARK 500  2 PRO A 122       95.02    -42.92                                   
REMARK 500  2 ASP A 123       18.96   -154.81                                   
REMARK 500  2 PRO A 129       38.39    -76.04                                   
REMARK 500  2 PRO A 131     -118.48    -85.25                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS    1240 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 999                                                                      
REMARK 999 SEQUENCE                                                             
REMARK 999 THE MATERIAL USED WAS A DELETION MUTANT:  DELTA 2 - 39 AND           
REMARK 999 DELTA 159 - 173, WHICH REMOVES THE DISORDERED N-TERMINUS             
REMARK 999 AND REDUCES THE SIZE OF A LONG DISORDERED SOLVENT EXPOSED            
REMARK 999 LOOP.  IT ALSO CONTAINS A CYS 206 TO ALA MUTATION TO                 
REMARK 999 PREVENT THE FORMATION OF INTERMOLECULAR DISULFIDES.  THE             
REMARK 999 HIV-1 STRAIN FROM WHICH THE PROTEIN WAS DERIVED IS STRAIN            
REMARK 999 BH10.                                                                
DBREF  2NEF A   56   205  UNP    Q70627   NEF_HV1LW       56    205             
SEQADV 2NEF GLU A   65  UNP  Q70627    LYS    65 CONFLICT                       
SEQADV 2NEF     A       UNP  Q70627    GLY   159 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    GLU   160 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    ASN   161 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    THR   162 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    SER   163 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    LEU   164 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    LEU   165 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    HIS   166 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    PRO   167 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    VAL   168 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    SER   169 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    LEU   170 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    HIS   171 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    GLY   172 DELETION                       
SEQADV 2NEF     A       UNP  Q70627    MET   173 DELETION                       
SEQADV 2NEF MET A  194  UNP  Q70627    VAL   194 CONFLICT                       
SEQRES   1 A  136  ALA TRP LEU GLU ALA GLN GLU GLU GLU GLU VAL GLY PHE          
SEQRES   2 A  136  PRO VAL THR PRO GLN VAL PRO LEU ARG PRO MET THR TYR          
SEQRES   3 A  136  LYS ALA ALA VAL ASP LEU SER HIS PHE LEU LYS GLU LYS          
SEQRES   4 A  136  GLY GLY LEU GLU GLY LEU ILE HIS SER GLN ARG ARG GLN          
SEQRES   5 A  136  ASP ILE LEU ASP LEU TRP ILE TYR HIS THR GLN GLY TYR          
SEQRES   6 A  136  PHE PRO ASP TRP GLN ASN TYR THR PRO GLY PRO GLY ILE          
SEQRES   7 A  136  ARG TYR PRO LEU THR PHE GLY TRP CYS TYR LYS LEU VAL          
SEQRES   8 A  136  PRO VAL GLU PRO GLU LYS LEU GLU GLU ALA ASN LYS ASP          
SEQRES   9 A  136  ASP PRO GLU ARG GLU VAL LEU GLU TRP ARG PHE ASP SER          
SEQRES  10 A  136  ARG LEU ALA PHE HIS HIS MET ALA ARG GLU LEU HIS PRO          
SEQRES  11 A  136  GLU TYR PHE LYS ASN ALA                                      
HELIX    1   1 PRO A   69  PRO A   78 10                                  10    
HELIX    2   2 TYR A   81  LYS A   94  1                                  14    
HELIX    3   3 ARG A  105  ILE A  114  1                                  10    
HELIX    4   4 SER A  187  ALA A  190  5                                   4    
HELIX    5   5 MET A  194  LEU A  198  1                                   5    
SHEET    1   A 5 LEU A 100  HIS A 102  0                                        
SHEET    2   A 5 LEU A 181  ASP A 186 -1                                        
SHEET    3   A 5 TYR A 143  PRO A 147 -1                                        
SHEET    4   A 5 ILE A 133  LEU A 137 -1                                        
SHEET    5   A 5 ASN A 126  THR A 128 -1                                        
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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