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Database: PDB
Entry: 2N80
LinkDB: 2N80
Original site: 2N80 
HEADER    SIGNALING PROTEIN                       30-SEP-15   2N80              
TITLE     P75NTR DD:RHOGDI                                                      
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 16;      
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: UNP RESIDUES 334-427;                                      
COMPND   5 SYNONYM: GP80-LNGFR, LOW AFFINITY NEUROTROPHIN RECEPTOR P75NTR, LOW- 
COMPND   6 AFFINITY NERVE GROWTH FACTOR RECEPTOR, NGF RECEPTOR, P75 ICD;        
COMPND   7 ENGINEERED: YES;                                                     
COMPND   8 MOL_ID: 2;                                                           
COMPND   9 MOLECULE: RHO GDP-DISSOCIATION INHIBITOR 1;                          
COMPND  10 CHAIN: B;                                                            
COMPND  11 FRAGMENT: UNP RESIDUES 31-204;                                       
COMPND  12 SYNONYM: RHO GDI 1, RHO-GDI ALPHA;                                   
COMPND  13 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: NGFR, TNFRSF16;                                                
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;                               
SOURCE   9 EXPRESSION_SYSTEM_VECTOR: PET32A-DERIVED;                            
SOURCE  10 MOL_ID: 2;                                                           
SOURCE  11 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE  12 ORGANISM_COMMON: HUMAN;                                              
SOURCE  13 ORGANISM_TAXID: 9606;                                                
SOURCE  14 GENE: ARHGDIA, GDIA1;                                                
SOURCE  15 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE  16 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE  17 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR                                
KEYWDS    RHOGDI, P75NTR, DEATH DOMAIN, SIGNALING PROTEIN                       
EXPDTA    SOLUTION NMR                                                          
NUMMDL    10                                                                    
AUTHOR    Z.LIN,C.F.IBANEZ                                                      
REVDAT   1   23-DEC-15 2N80    0                                                
JRNL        AUTH   Z.LIN,J.Y.TANN,E.T.GOH,C.KELLY,K.B.LIM,J.F.GAO,C.F.IBANEZ    
JRNL        TITL   STRUCTURAL BASIS OF DEATH DOMAIN SIGNALING IN THE P75        
JRNL        TITL 2 NEUROTROPHIN RECEPTOR                                        
JRNL        REF    ELIFE                         V.   4 11692 2015              
JRNL        REFN                   ESSN 2050-084X                               
JRNL        PMID   26646181                                                     
JRNL        DOI    10.7554/ELIFE.11692                                          
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : AMBER                                                
REMARK   3   AUTHORS     : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG,       
REMARK   3                 DUKE, LUO, ... AND KOLLMAN                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2N80 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-OCT-15.                  
REMARK 100 THE RCSB ID CODE IS RCSB104537.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 301                                
REMARK 210  PH                             : 6.9                                
REMARK 210  IONIC STRENGTH                 : 10                                 
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 0.5 MM [U-99% 13C; U-99% 15N]      
REMARK 210                                   P75NTR DD-1, 1 MM [U-98% 2H] DTT-  
REMARK 210                                   2, 10 MM [U-98% 2H] HEPES-3, 1 MM  
REMARK 210                                   EDTA-4, 1 MM SODIUM AZIDE-5, 2 MM  
REMARK 210                                   RHOGDI-6, 95% H2O/5% D2O; 0.5 MM   
REMARK 210                                   [U-99% 13C; U-99% 15N] RHOGDI-7,   
REMARK 210                                   2 MM P75NTR DD-8, 1 MM [U-98% 2H]  
REMARK 210                                   DTT-9, 10 MM [U-98% 2H] HEPES-10,  
REMARK 210                                   1 MM EDTA-11, 1 MM SODIUM AZIDE-   
REMARK 210                                   12, 95% H2O/5% D2O                 
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 2D 1H-13C HSQC     
REMARK 210                                   ALIPHATIC; 2D 1H-13C HSQC          
REMARK 210                                   AROMATIC; 3D HNCA; 3D HN(CO)CA;    
REMARK 210                                   3D HCCH-TOCSY; 3D 13C,15N-         
REMARK 210                                   FILTERED NOESY; 4D 13C, 15N-       
REMARK 210                                   EDITED NOESY                       
REMARK 210  SPECTROMETER FIELD STRENGTH    : 800 MHZ                            
REMARK 210  SPECTROMETER MODEL             : AVANCE                             
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NMRPIPE, NMRVIEW, CYANA            
REMARK 210   METHOD USED                   : MOLECULAR DYNAMICS                 
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 10                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST 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: 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: 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  2 ARG B 120   NE  -  CZ  -  NH1 ANGL. DEV. =   3.7 DEGREES          
REMARK 500  4 ARG A 410   NE  -  CZ  -  NH1 ANGL. DEV. =   3.2 DEGREES          
REMARK 500  9 ARG B 172   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 ALA A 396       40.75    -68.59                                   
REMARK 500  1 SER A 421       28.53    -74.44                                   
REMARK 500  1 ALA A 423       92.53    -66.36                                   
REMARK 500  1 SER A 425       68.37   -162.43                                   
REMARK 500  1 LYS B  33       47.60   -147.63                                   
REMARK 500  1 SER B  34      -38.50   -138.34                                   
REMARK 500  1 ARG B  58       45.47   -148.37                                   
REMARK 500  1 VAL B  59       10.11    -63.24                                   
REMARK 500  1 VAL B  61       17.10     53.24                                   
REMARK 500  1 VAL B  72      109.60    -59.95                                   
REMARK 500  1 ASP B  93       67.86    -69.42                                   
REMARK 500  1 ARG B 120      -65.99   -145.06                                   
REMARK 500  1 PRO B 151       49.14    -74.98                                   
REMARK 500  1 GLU B 154     -168.88   -100.08                                   
REMARK 500  1 TRP B 202       13.69   -158.88                                   
REMARK 500  1 LYS B 203      -32.70   -160.92                                   
REMARK 500  2 ALA A 396       38.31    -68.91                                   
REMARK 500  2 ILE B  35       49.52    -72.98                                   
REMARK 500  2 CYS B  79      101.15   -160.15                                   
REMARK 500  2 LEU B  90       29.64   -140.59                                   
REMARK 500  2 ASP B  93       96.81    -59.18                                   
REMARK 500  2 ARG B 120       41.24   -175.43                                   
REMARK 500  2 TRP B 202       13.02   -152.03                                   
REMARK 500  2 LYS B 203       54.63   -166.61                                   
REMARK 500  3 ALA A 355      159.46    169.41                                   
REMARK 500  3 ALA A 396       53.12    -68.29                                   
REMARK 500  3 SER A 421       49.65    -77.66                                   
REMARK 500  3 ILE B  38      -36.66   -149.76                                   
REMARK 500  3 GLU B  40        1.84    -66.24                                   
REMARK 500  3 ALA B  60       56.62    -90.67                                   
REMARK 500  3 SER B  62       50.95   -116.98                                   
REMARK 500  3 LEU B  90       36.56   -142.31                                   
REMARK 500  3 ASP B  93       85.23    -60.93                                   
REMARK 500  3 ARG B 120      -69.96   -147.60                                   
REMARK 500  3 GLU B 154     -167.77   -101.95                                   
REMARK 500  3 TRP B 202       11.81   -160.26                                   
REMARK 500  3 LYS B 203      -40.95   -169.41                                   
REMARK 500  4 SER A 354     -178.06    -62.57                                   
REMARK 500  4 ALA A 396       37.27    -68.51                                   
REMARK 500  4 SER A 421       32.12    -77.24                                   
REMARK 500  4 THR A 422       59.88    -69.94                                   
REMARK 500  4 GLN B  32      -21.21   -148.89                                   
REMARK 500  4 GLU B  40        1.75    -61.71                                   
REMARK 500  4 ASP B  44       24.93   -144.43                                   
REMARK 500  4 ARG B  58       44.76    -83.92                                   
REMARK 500  4 CYS B  79       97.88   -164.82                                   
REMARK 500  4 ARG B 120       40.36   -179.68                                   
REMARK 500  4 LYS B 203      -25.96   -163.41                                   
REMARK 500  5 SER A 354      170.35    -58.96                                   
REMARK 500  5 ALA A 396       33.27    -67.74                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     120 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  3 TYR B 175         0.08    SIDE CHAIN                              
REMARK 500  4 TYR B 175         0.09    SIDE CHAIN                              
REMARK 500  5 ARG A 384         0.09    SIDE CHAIN                              
REMARK 500  6 TYR B 175         0.07    SIDE CHAIN                              
REMARK 500  8 TYR B 175         0.08    SIDE CHAIN                              
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 25829   RELATED DB: BMRB                                 
REMARK 900 RELATED ID: 2N7Z   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 2N83   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 2N97   RELATED DB: PDB                                   
DBREF  2N80 A  334   427  UNP    P08138   TNR16_HUMAN    334    427             
DBREF  2N80 B   31   204  UNP    P52565   GDIR1_HUMAN     31    204             
SEQRES   1 A   94  GLY LEU TYR SER SER LEU PRO PRO ALA LYS ARG GLU GLU          
SEQRES   2 A   94  VAL GLU LYS LEU LEU ASN GLY SER ALA GLY ASP THR TRP          
SEQRES   3 A   94  ARG HIS LEU ALA GLY GLU LEU GLY TYR GLN PRO GLU HIS          
SEQRES   4 A   94  ILE ASP SER PHE THR HIS GLU ALA CYS PRO VAL ARG ALA          
SEQRES   5 A   94  LEU LEU ALA SER TRP ALA THR GLN ASP SER ALA THR LEU          
SEQRES   6 A   94  ASP ALA LEU LEU ALA ALA LEU ARG ARG ILE GLN ARG ALA          
SEQRES   7 A   94  ASP LEU VAL GLU SER LEU CYS SER GLU SER THR ALA THR          
SEQRES   8 A   94  SER PRO VAL                                                  
SEQRES   1 B  174  ALA GLN LYS SER ILE GLN GLU ILE GLN GLU LEU ASP LYS          
SEQRES   2 B  174  ASP ASP GLU SER LEU ARG LYS TYR LYS GLU ALA LEU LEU          
SEQRES   3 B  174  GLY ARG VAL ALA VAL SER ALA ASP PRO ASN VAL PRO ASN          
SEQRES   4 B  174  VAL VAL VAL THR GLY LEU THR LEU VAL CYS SER SER ALA          
SEQRES   5 B  174  PRO GLY PRO LEU GLU LEU ASP LEU THR GLY ASP LEU GLU          
SEQRES   6 B  174  SER PHE LYS LYS GLN SER PHE VAL LEU LYS GLU GLY VAL          
SEQRES   7 B  174  GLU TYR ARG ILE LYS ILE SER PHE ARG VAL ASN ARG GLU          
SEQRES   8 B  174  ILE VAL SER GLY MET LYS TYR ILE GLN HIS THR TYR ARG          
SEQRES   9 B  174  LYS GLY VAL LYS ILE ASP LYS THR ASP TYR MET VAL GLY          
SEQRES  10 B  174  SER TYR GLY PRO ARG ALA GLU GLU TYR GLU PHE LEU THR          
SEQRES  11 B  174  PRO VAL GLU GLU ALA PRO LYS GLY MET LEU ALA ARG GLY          
SEQRES  12 B  174  SER TYR SER ILE LYS SER ARG PHE THR ASP ASP ASP LYS          
SEQRES  13 B  174  THR ASP HIS LEU SER TRP GLU TRP ASN LEU THR ILE LYS          
SEQRES  14 B  174  LYS ASP TRP LYS ASP                                          
HELIX    1   1 LEU A  335  LEU A  339  5                                   5    
HELIX    2   2 PRO A  340  ASN A  352  1                                  13    
HELIX    3   3 ASP A  357  GLY A  367  1                                  11    
HELIX    4   4 GLN A  369  HIS A  378  1                                  10    
HELIX    5   5 CYS A  381  ALA A  391  1                                  11    
HELIX    6   6 THR A  397  ILE A  408  1                                  12    
HELIX    7   7 ARG A  410  CYS A  418  1                                   9    
HELIX    8   8 SER B   34  GLN B   39  5                                   6    
HELIX    9   9 GLU B   40  SER B   47  1                                   8    
HELIX   10  10 LEU B   48  ALA B   54  1                                   7    
HELIX   11  11 LEU B   55  VAL B   59  5                                   5    
HELIX   12  12 GLY B  168  ARG B  172  5                                   5    
SHEET    1   A 4 LEU B  86  ASP B  89  0                                        
SHEET    2   A 4 VAL B  70  VAL B  78 -1  N  LEU B  75   O  LEU B  88           
SHEET    3   A 4 GLU B 109  VAL B 118 -1  O  LYS B 113   N  THR B  76           
SHEET    4   A 4 GLU B 155  LEU B 159 -1  O  TYR B 156   N  PHE B 116           
SHEET    1   B 4 LEU B  86  ASP B  89  0                                        
SHEET    2   B 4 VAL B  70  VAL B  78 -1  N  LEU B  75   O  LEU B  88           
SHEET    3   B 4 GLU B 109  VAL B 118 -1  O  LYS B 113   N  THR B  76           
SHEET    4   B 4 GLU B 163  GLU B 164 -1  O  GLU B 163   N  TYR B 110           
SHEET    1   C 5 SER B 101  LYS B 105  0                                        
SHEET    2   C 5 LEU B 190  LYS B 199  1  O  LYS B 199   N  LEU B 104           
SHEET    3   C 5 SER B 174  THR B 182 -1  N  ILE B 177   O  TRP B 194           
SHEET    4   C 5 VAL B 123  ARG B 134 -1  N  ILE B 129   O  ARG B 180           
SHEET    5   C 5 VAL B 137  TYR B 149 -1  O  TYR B 144   N  TYR B 128           
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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