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Database: PDB
Entry: 2N97
LinkDB: 2N97
Original site: 2N97 
HEADER    SIGNALING PROTEIN                       07-NOV-15   2N97              
TITLE     DD HOMODIMER                                                          
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 16;      
COMPND   3 CHAIN: A, B;                                                         
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                                                      
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                             
KEYWDS    DEATH DOMAIN, P75NTR, SIGNALING PROTEIN                               
EXPDTA    SOLUTION NMR                                                          
NUMMDL    10                                                                    
AUTHOR    Z.LIN,C.F.IBANEZ                                                      
REVDAT   2   27-APR-16 2N97    1       ATOM   DBREF  REMARK SEQRES              
REVDAT   1   23-DEC-15 2N97    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 2N97 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-NOV-15.                  
REMARK 100 THE RCSB ID CODE IS RCSB104580.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 308                                
REMARK 210  PH                             : 6.9                                
REMARK 210  IONIC STRENGTH                 : NULL                               
REMARK 210  PRESSURE                       : AMBIENT                            
REMARK 210  SAMPLE CONTENTS                : 1 MM [U-99% 13C; U-99% 15N]        
REMARK 210                                   P75NTR DD-1, 10 MM [U-98% 2H] DTT  
REMARK 210                                   -2, 1 MM P75NTR DD-3, 50 MM        
REMARK 210                                   SODIUM PHOSPHATE-4, 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 HNCACB; 3D CBCA(CO)   
REMARK 210                                   NH; 3D HCCH-TOCSY; 3D 13C,15N-     
REMARK 210                                   FILTERED NOESY; 3D 13C, 15N-       
REMARK 210                                   EDITED NOESY; 3D HN(CO)CA; 4D      
REMARK 210                                   13C, 15N-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 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;                   
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                            
REMARK 465   MODELS 1-10                                                        
REMARK 465     RES C SSSEQI                                                     
REMARK 465     LYS A   330                                                      
REMARK 465     GLY A   331                                                      
REMARK 465     ASP A   332                                                      
REMARK 465     GLY A   333                                                      
REMARK 465     LYS B   330                                                      
REMARK 465     GLY B   331                                                      
REMARK 465     ASP B   332                                                      
REMARK 465     GLY B   333                                                      
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  3 ARG B 384   NE  -  CZ  -  NH1 ANGL. DEV. =   3.7 DEGREES          
REMARK 500  3 ARG B 407   NE  -  CZ  -  NH1 ANGL. DEV. =   3.1 DEGREES          
REMARK 500  3 ARG B 410   NE  -  CZ  -  NH1 ANGL. DEV. =   3.1 DEGREES          
REMARK 500  7 ARG B 410   NE  -  CZ  -  NH1 ANGL. DEV. =   3.2 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 SER A 354      -62.24    -99.46                                   
REMARK 500  1 CYS A 381       71.26   -112.84                                   
REMARK 500  1 ALA A 396       23.75    -69.64                                   
REMARK 500  1 THR A 424       32.65   -141.35                                   
REMARK 500  1 ALA B 355       92.12   -163.71                                   
REMARK 500  1 CYS B 381       67.17   -115.82                                   
REMARK 500  1 ALA B 396       26.33    -68.49                                   
REMARK 500  2 ALA A 355       93.63    -38.30                                   
REMARK 500  2 CYS A 381       70.66   -113.37                                   
REMARK 500  2 ALA A 396       25.44    -67.57                                   
REMARK 500  2 ALA B 355       60.68   -164.65                                   
REMARK 500  2 CYS B 381       68.04   -118.03                                   
REMARK 500  2 ALA B 396       25.41    -70.46                                   
REMARK 500  2 THR B 422       70.37     24.81                                   
REMARK 500  3 ALA A 355      109.91   -167.51                                   
REMARK 500  3 THR A 377        2.93    -69.15                                   
REMARK 500  3 CYS A 381       67.08   -117.68                                   
REMARK 500  3 ALA A 396       22.49    -69.88                                   
REMARK 500  3 THR A 424      -80.34   -134.92                                   
REMARK 500  3 CYS B 381       72.64   -112.34                                   
REMARK 500  3 ALA B 396       34.97    -69.27                                   
REMARK 500  3 SER B 421       51.04   -116.87                                   
REMARK 500  3 THR B 422       34.95    -70.75                                   
REMARK 500  3 SER B 425       59.85     32.66                                   
REMARK 500  4 ALA A 355      -55.60   -153.96                                   
REMARK 500  4 CYS A 381       71.06   -113.92                                   
REMARK 500  4 ALA A 396       24.28    -67.93                                   
REMARK 500  4 THR A 424       47.14   -144.28                                   
REMARK 500  4 SER A 425      158.07     74.83                                   
REMARK 500  4 SER B 354      -60.05   -108.02                                   
REMARK 500  4 CYS B 381       70.95   -116.12                                   
REMARK 500  4 ALA B 396       25.87    -69.56                                   
REMARK 500  5 ALA A 355       82.79   -163.11                                   
REMARK 500  5 CYS A 381       66.82   -117.66                                   
REMARK 500  5 ALA A 396       28.07    -67.21                                   
REMARK 500  5 ALA B 355      117.27   -164.46                                   
REMARK 500  5 CYS B 381       67.86   -112.08                                   
REMARK 500  5 ALA B 396       25.16    -68.10                                   
REMARK 500  6 ALA A 355      104.57   -163.36                                   
REMARK 500  6 CYS A 381       67.58   -110.54                                   
REMARK 500  6 ALA A 396       22.52    -70.79                                   
REMARK 500  6 SER A 421       24.89    -75.03                                   
REMARK 500  6 THR A 422       12.55   -146.94                                   
REMARK 500  6 THR A 424      -72.31   -151.47                                   
REMARK 500  6 SER B 354       21.90    -62.74                                   
REMARK 500  6 ALA B 355       11.28   -142.27                                   
REMARK 500  6 CYS B 381       67.82   -110.86                                   
REMARK 500  6 ALA B 396       25.38    -67.85                                   
REMARK 500  6 THR B 422       59.63     35.95                                   
REMARK 500  6 PRO B 426       98.88    -69.43                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS      84 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 25883   RELATED DB: BMRB                                 
REMARK 900 RELATED ID: 2N7Z   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 2N80   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 2N83   RELATED DB: PDB                                   
DBREF  2N97 A  330   427  UNP    P08138   TNR16_HUMAN    330    427             
DBREF  2N97 B  330   427  UNP    P08138   TNR16_HUMAN    330    427             
SEQRES   1 A   98  LYS GLY ASP GLY GLY LEU TYR SER SER LEU PRO PRO ALA          
SEQRES   2 A   98  LYS ARG GLU GLU VAL GLU LYS LEU LEU ASN GLY SER ALA          
SEQRES   3 A   98  GLY ASP THR TRP ARG HIS LEU ALA GLY GLU LEU GLY TYR          
SEQRES   4 A   98  GLN PRO GLU HIS ILE ASP SER PHE THR HIS GLU ALA CYS          
SEQRES   5 A   98  PRO VAL ARG ALA LEU LEU ALA SER TRP ALA THR GLN ASP          
SEQRES   6 A   98  SER ALA THR LEU ASP ALA LEU LEU ALA ALA LEU ARG ARG          
SEQRES   7 A   98  ILE GLN ARG ALA ASP LEU VAL GLU SER LEU CYS SER GLU          
SEQRES   8 A   98  SER THR ALA THR SER PRO VAL                                  
SEQRES   1 B   98  LYS GLY ASP GLY GLY LEU TYR SER SER LEU PRO PRO ALA          
SEQRES   2 B   98  LYS ARG GLU GLU VAL GLU LYS LEU LEU ASN GLY SER ALA          
SEQRES   3 B   98  GLY ASP THR TRP ARG HIS LEU ALA GLY GLU LEU GLY TYR          
SEQRES   4 B   98  GLN PRO GLU HIS ILE ASP SER PHE THR HIS GLU ALA CYS          
SEQRES   5 B   98  PRO VAL ARG ALA LEU LEU ALA SER TRP ALA THR GLN ASP          
SEQRES   6 B   98  SER ALA THR LEU ASP ALA LEU LEU ALA ALA LEU ARG ARG          
SEQRES   7 B   98  ILE GLN ARG ALA ASP LEU VAL GLU SER LEU CYS SER GLU          
SEQRES   8 B   98  SER THR ALA THR SER PRO VAL                                  
HELIX    1   1 LEU A  335  LEU A  339  5                                   5    
HELIX    2   2 PRO A  340  SER A  354  1                                  15    
HELIX    3   3 ASP A  357  LEU A  366  1                                  10    
HELIX    4   4 GLN A  369  THR A  377  1                                   9    
HELIX    5   5 CYS A  381  THR A  392  1                                  12    
HELIX    6   6 THR A  397  ILE A  408  1                                  12    
HELIX    7   7 ARG A  410  GLU A  420  1                                  11    
HELIX    8   8 LEU B  335  LEU B  339  5                                   5    
HELIX    9   9 PRO B  340  SER B  354  1                                  15    
HELIX   10  10 ASP B  357  GLY B  367  1                                  11    
HELIX   11  11 GLN B  369  THR B  377  1                                   9    
HELIX   12  12 CYS B  381  ALA B  391  1                                  11    
HELIX   13  13 THR B  397  ILE B  408  1                                  12    
HELIX   14  14 ARG B  410  GLU B  420  1                                  11    
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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