REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0075AL156_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : BENNER-COHEN 
REMARK  ---------------------------------------------------------- 
TARGET T0075  
AUTHOR 5529-3140-9255  
REMARK Prediction team BENNER-COHEN has two group leaders,  
REMARK but we will consistently use Steven Benner's predictor  
REMARK number to avoid confusion concerning a second team  
REMARK connected with Fred Cohen (called Cohen, Fred).  
REMARK (Fred Cohen's number as a group leader is 6140-7890-6093).  
REMARK Prediction team members: D.L.Gerloff, G.Cannarozzi,  
REMARK M.Joachimiak, F.E.Cohen & S.A.Benner.  
REMARK  
REMARK This threading alignment prediction is accompanied by  
REMARK a separate secondary structure submission !!  
METHOD  
METHOD IMPORTANT REMARK: THIS STRUCTURE WAS MODELLED UNDER THE   
METHOD ASSUMPTION THAT THE STRUCTURE IS MONOMERIC.  
METHOD HOWEVER, AS THE C-TERMINAL PART HAS SOME SEQUENCE SIMILARITY TO THE  
METHOD HELIX-LOOP-HELIX PROTEINS (SETH & PAPAS, ONCOGENE (1990), 5:1761-1767)   
METHOD WE ARE SUBMITTING THE SUGGESTED THREADING ALIGNMENT WITH A MEMBER OF  
METHOD THE bHLH PROTEINS (1AN4, USF1) AS A SECOND ALTERNATIVE. IF THE TARGET  
METHOD PROTEIN OCCURRED AT A DIMER, ONE WOULD HAVE TO START FROM THE HLH-  
METHOD FRAGMENT AND PACK A FRAGMENT SIMILAR TO A PART OF MODEL1:75-100   
METHOD AGAINST THE SIDE NOT OCCUPIED BY DIMER-INTERACTIONS. DUE TO TIME  
METHOD PRESSURE, WE WILL NOT BE ABLE TO MODEL THIS ALTERNATIVE IN COORDINATE  
METHOD FORMAT.  
METHOD OUR FAVORITE MODEL IS NUMBER ONE, AND WE HAVE NO INDICATIONS FROM THE  
METHOD LITERATURE THAT T0075 IS A MANDATORY OLIGOMER. IN FACT, WE FOUND THE  
METHOD SOME REMARKS IN THE LITERATURE THAT THE ETS1 PROTEIN (FULL PROTEIN)  
METHOD APPEARS TO BE CAPABLE OF BINDING TO DNA AS A MONOMER.  
METHOD  
METHOD This model was assembled based on our secondary structure prediction  
METHOD which is submitted separately. Due to the absence of significant hits  
METHOD in the UCLA-DOE and ProCyon standard results, we attempted to assemble    
METHOD a core model ab initio, first, based on sequence analysis (Surf/Int/  
METHOD Parse prediction) and three central assumptions specific to this problem.  
METHOD (A), The target is a monomer and forms a small core, starting approxi-  
METHOD mately at residue 54, or even 69. This conclusion is based on the lack  
METHOD of sequence similarity throughout the protein family in the N-terminal  
METHOD segment (which is consistent with the PRODOM domain assignment in this  
METHOD case), and on the occurrence of a strongly charged region 58-67 which   
METHOD is reminiscent of the "basic" regions found in DNA-binding proteins.  
METHOD (Our secondary structure prediction includes the N-terminus, however.)  
METHOD (B) Consistent with what is found in small protein cores, we attribute  
METHOD the high conservation of hydrophobic residues W72, V77, W80, W83, L90,  
METHOD L105, L125, L129, and possibly F113 to core packing. This was used  
METHOD to assemble our model together with (C), the prediction of a functional  
METHOD site including the highly conserved C106, H128; possible other candi-  
METHOD dates to complement this site are E111, H76, or E78.  
METHOD (we suspect a zinc-binding site, either monomeric or functioning  
METHOD as composite site between monomeric subunits in an oligomer).  
METHOD  
METHOD After restricting the number of plausible conformations based on the  
METHOD assumptions listed above, we noted that the folding topology of a   
METHOD winged DNA-binding domain might be helpful as a scaffold in the  
METHOD modeling, as the orientation of the secondary structure elements  
METHOD around a hydrophobic core seemed to fit the constraint of one of  
METHOD our favorite topologies, approximately.  
METHOD If we model onto this scaffold, residue H76 seems to be involved  
METHOD in the functional site (zinc?), while E87 is not -- note that   
METHOD these presence of these two residues at the functional site is  
METHOD mutually exclusive due to the predicted alpha helix inbetween.  
METHOD Accordingly, another plausible topology would have the buried  
METHOD helix V77-V85, and the loop/strand hairpin, rotated by 180 deg.   
METHOD and allow E87 to participate. We slightly prefer the first to-  
METHOD pology because of packing. However, we cannot assign a role to  
METHOD conserved position E87 -- this might indicate a problem in this  
METHOD prediction.   
METHOD  
METHOD Therefore, and because the search for plausible topologies was  
METHOD not exhaustive, we submit this model at LOW CONFIDENCE LEVEL.  
METHOD (Also, we cannot see any indication for similarity in functional  
METHOD sites between our target structure, 2stw_A (DBD) and the upstream  
METHOD fragment, T0075. This further weakens our prediction.) In addition,  
METHOD we did not search actively to find the best possible scaffold.   
METHOD Interesting in this context, the homolog to 2stw_A, 1pue_E was  
METHOD listed among the UCLA-DOE FR-server hits below significance level,  
METHOD so were a number of other members of the so-called winged DNA-  
METHOD binding proteins.   
METHOD  
METHOD In summary, it should be noted that we have insufficient grounds  
METHOD for predicting an evolutionary relationship between our scaffold  
METHOD ETS-domain and the T0075 fragment. However, the geometrical   
METHOD arrangement of the secondary structure elements seems plausible,  
METHOD while it is probably not the only plausible arrangement.  
METHOD  
REMARK   
REMARK WE HAVE GENERATED A COORDINATE MODEL FOR T0075 ALSO (WHICH IS MODEL1).  
REMARK WHERE THE MISSING PARTS HAVE BEEN FILLED IN (AT VERY LOW RESOLUTION).  
REMARK THE COORDINATE MODEL 1 WILL SUPERSEDE THIS ENTRY (AL-FORMAT MODEL1).  
REMARK   
MODEL  1  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 2stw_A 
ATOM      1  N   THR    75     -93.778  20.442 -10.384  1.00  0.00              
ATOM      2  CA  THR    75     -93.357  19.430  -9.399  1.00  0.00              
ATOM      3  C   THR    75     -93.201  18.126 -10.173  1.00  0.00              
ATOM      4  O   THR    75     -94.016  17.795 -11.013  1.00  0.00              
ATOM      5  N   HIS    76     -92.150  17.406  -9.930  1.00  0.00              
ATOM      6  CA  HIS    76     -91.919  16.144 -10.682  1.00  0.00              
ATOM      7  C   HIS    76     -93.213  15.331 -10.821  1.00  0.00              
ATOM      8  O   HIS    76     -93.803  15.268 -11.882  1.00  0.00              
ATOM      9  N   VAL    77     -93.616  14.650  -9.788  1.00  0.00              
ATOM     10  CA  VAL    77     -94.813  13.773  -9.900  1.00  0.00              
ATOM     11  C   VAL    77     -96.059  14.534 -10.360  1.00  0.00              
ATOM     12  O   VAL    77     -96.825  14.023 -11.151  1.00  0.00              
ATOM     13  N   ARG    78     -96.300  15.730  -9.891  1.00  0.00              
ATOM     14  CA  ARG    78     -97.532  16.436 -10.355  1.00  0.00              
ATOM     15  C   ARG    78     -97.551  16.427 -11.884  1.00  0.00              
ATOM     16  O   ARG    78     -98.539  16.088 -12.493  1.00  0.00              
ATOM     17  N   ASP    79     -96.451  16.759 -12.506  1.00  0.00              
ATOM     18  CA  ASP    79     -96.393  16.734 -13.997  1.00  0.00              
ATOM     19  C   ASP    79     -96.669  15.302 -14.484  1.00  0.00              
ATOM     20  O   ASP    79     -97.569  15.058 -15.263  1.00  0.00              
ATOM     21  N   TRP    80     -95.890  14.360 -14.023  1.00  0.00              
ATOM     22  CA  TRP    80     -96.079  12.941 -14.443  1.00  0.00              
ATOM     23  C   TRP    80     -97.502  12.507 -14.112  1.00  0.00              
ATOM     24  O   TRP    80     -98.165  11.869 -14.904  1.00  0.00              
ATOM     25  N   VAL    81     -97.981  12.850 -12.950  1.00  0.00              
ATOM     26  CA  VAL    81     -99.364  12.454 -12.579  1.00  0.00              
ATOM     27  C   VAL    81    -100.367  13.177 -13.485  1.00  0.00              
ATOM     28  O   VAL    81    -101.386  12.626 -13.851  1.00  0.00              
ATOM     29  N   MET    82    -100.094  14.403 -13.861  1.00  0.00              
ATOM     30  CA  MET    82    -101.052  15.123 -14.752  1.00  0.00              
ATOM     31  C   MET    82    -101.025  14.449 -16.131  1.00  0.00              
ATOM     32  O   MET    82    -102.047  14.253 -16.758  1.00  0.00              
ATOM     33  N   TRP    83     -99.860  14.083 -16.594  1.00  0.00              
ATOM     34  CA  TRP    83     -99.758  13.407 -17.918  1.00  0.00              
ATOM     35  C   TRP    83    -100.328  11.993 -17.800  1.00  0.00              
ATOM     36  O   TRP    83    -100.714  11.383 -18.777  1.00  0.00              
ATOM     37  N   ALA    84    -100.373  11.464 -16.615  1.00  0.00              
ATOM     38  CA  ALA    84    -100.903  10.085 -16.438  1.00  0.00              
ATOM     39  C   ALA    84    -102.411  10.069 -16.736  1.00  0.00              
ATOM     40  O   ALA    84    -102.851   9.550 -17.742  1.00  0.00              
ATOM     41  N   VAL    85    -103.199  10.650 -15.872  1.00  0.00              
ATOM     42  CA  VAL    85    -104.672  10.689 -16.103  1.00  0.00              
ATOM     43  C   VAL    85    -104.925  11.719 -17.191  1.00  0.00              
ATOM     44  O   VAL    85    -105.605  12.703 -16.970  1.00  0.00              
ATOM     45  N   SER    89     -99.474   2.036 -21.926  1.00  0.00              
ATOM     46  CA  SER    89    -100.640   1.162 -21.553  1.00  0.00              
ATOM     47  C   SER    89    -101.294   1.648 -20.245  1.00  0.00              
ATOM     48  O   SER    89    -100.702   1.626 -19.183  1.00  0.00              
ATOM     49  N   LEU    90    -102.529   2.071 -20.340  1.00  0.00              
ATOM     50  CA  LEU    90    -103.298   2.559 -19.151  1.00  0.00              
ATOM     51  C   LEU    90    -104.474   1.583 -18.923  1.00  0.00              
ATOM     52  O   LEU    90    -105.479   1.657 -19.602  1.00  0.00              
ATOM     53  N   LYS    91    -104.378   0.672 -17.986  1.00  0.00              
ATOM     54  CA  LYS    91    -105.528  -0.260 -17.780  1.00  0.00              
ATOM     55  C   LYS    91    -106.774   0.579 -17.495  1.00  0.00              
ATOM     56  O   LYS    91    -106.684   1.718 -17.080  1.00  0.00              
ATOM     57  N   ASP    94    -109.168  -0.097 -15.158  1.00  0.00              
ATOM     58  CA  ASP    94    -109.766  -0.750 -13.948  1.00  0.00              
ATOM     59  C   ASP    94    -109.468   0.099 -12.686  1.00  0.00              
ATOM     60  O   ASP    94    -109.983   1.190 -12.544  1.00  0.00              
ATOM     61  N   PHE    95    -108.670  -0.383 -11.764  1.00  0.00              
ATOM     62  CA  PHE    95    -108.388   0.402 -10.529  1.00  0.00              
ATOM     63  C   PHE    95    -107.294   1.434 -10.792  1.00  0.00              
ATOM     64  O   PHE    95    -107.559   2.523 -11.259  1.00  0.00              
ATOM     65  N   GLN    96    -106.061   1.112 -10.487  1.00  0.00              
ATOM     66  CA  GLN    96    -104.963   2.097 -10.716  1.00  0.00              
ATOM     67  C   GLN    96    -103.651   1.373 -11.019  1.00  0.00              
ATOM     68  O   GLN    96    -102.771   1.292 -10.186  1.00  0.00              
ATOM     69  N   LYS    97    -103.505   0.878 -12.217  1.00  0.00              
ATOM     70  CA  LYS    97    -102.240   0.189 -12.620  1.00  0.00              
ATOM     71  C   LYS    97    -101.694   0.931 -13.839  1.00  0.00              
ATOM     72  O   LYS    97    -102.423   1.265 -14.747  1.00  0.00              
ATOM     73  N   PHE    98    -100.429   1.239 -13.850  1.00  0.00              
ATOM     74  CA  PHE    98     -99.856   1.999 -15.002  1.00  0.00              
ATOM     75  C   PHE    98     -98.535   1.373 -15.443  1.00  0.00              
ATOM     76  O   PHE    98     -97.578   1.357 -14.693  1.00  0.00              
ATOM     77  N   CYS    99     -98.460   0.880 -16.666  1.00  0.00              
ATOM     78  CA  CYS    99     -97.176   0.281 -17.162  1.00  0.00              
ATOM     79  C   CYS    99     -96.622   1.129 -18.298  1.00  0.00              
ATOM     80  O   CYS    99     -97.344   1.677 -19.114  1.00  0.00              
ATOM     81  N   MET   100     -95.327   1.207 -18.355  1.00  0.00              
ATOM     82  CA  MET   100     -94.656   1.978 -19.422  1.00  0.00              
ATOM     83  C   MET   100     -94.286   1.035 -20.571  1.00  0.00              
ATOM     84  O   MET   100     -93.244   0.411 -20.565  1.00  0.00              
ATOM     85  N   GLY   102     -92.326   4.372 -23.719  1.00  0.00              
ATOM     86  CA  GLY   102     -92.169   5.795 -23.363  1.00  0.00              
ATOM     87  C   GLY   102     -91.194   6.453 -24.354  1.00  0.00              
ATOM     88  O   GLY   102     -90.223   7.074 -23.974  1.00  0.00              
ATOM     89  N   ALA   103     -91.441   6.319 -25.626  1.00  0.00              
ATOM     90  CA  ALA   103     -90.520   6.933 -26.624  1.00  0.00              
ATOM     91  C   ALA   103     -90.683   8.457 -26.596  1.00  0.00              
ATOM     92  O   ALA   103     -89.719   9.195 -26.661  1.00  0.00              
ATOM     93  N   ALA   104     -91.890   8.934 -26.498  1.00  0.00              
ATOM     94  CA  ALA   104     -92.106  10.406 -26.468  1.00  0.00              
ATOM     95  C   ALA   104     -91.931  10.906 -25.042  1.00  0.00              
ATOM     96  O   ALA   104     -91.386  11.965 -24.801  1.00  0.00              
ATOM     97  N   LEU   105     -92.382  10.144 -24.095  1.00  0.00              
ATOM     98  CA  LEU   105     -92.242  10.557 -22.679  1.00  0.00              
ATOM     99  C   LEU   105     -90.759  10.590 -22.318  1.00  0.00              
ATOM    100  O   LEU   105     -90.261  11.552 -21.769  1.00  0.00              
ATOM    101  N   CYS   106     -90.058   9.531 -22.606  1.00  0.00              
ATOM    102  CA  CYS   106     -88.617   9.479 -22.257  1.00  0.00              
ATOM    103  C   CYS   106     -87.865  10.648 -22.888  1.00  0.00              
ATOM    104  O   CYS   106     -87.025  11.248 -22.248  1.00  0.00              
ATOM    105  N   ALA   107     -88.120  10.993 -24.134  1.00  0.00              
ATOM    106  CA  ALA   107     -87.344  12.133 -24.719  1.00  0.00              
ATOM    107  C   ALA   107     -87.893  13.468 -24.201  1.00  0.00              
ATOM    108  O   ALA   107     -87.153  14.416 -24.078  1.00  0.00              
ATOM    109  N   LEU   108     -89.147  13.558 -23.834  1.00  0.00              
ATOM    110  CA  LEU   108     -89.628  14.857 -23.269  1.00  0.00              
ATOM    111  C   LEU   108     -88.936  15.055 -21.922  1.00  0.00              
ATOM    112  O   LEU   108     -88.531  16.144 -21.565  1.00  0.00              
ATOM    113  N   GLY   109     -88.810  13.999 -21.171  1.00  0.00              
ATOM    114  CA  GLY   109     -88.160  14.097 -19.838  1.00  0.00              
ATOM    115  C   GLY   109     -86.771  14.732 -19.974  1.00  0.00              
ATOM    116  O   GLY   109     -86.392  15.593 -19.205  1.00  0.00              
ATOM    117  N   ASP   123     -83.080   4.399 -18.494  1.00  0.00              
ATOM    118  CA  ASP   123     -82.378   3.989 -17.249  1.00  0.00              
ATOM    119  C   ASP   123     -82.440   5.137 -16.243  1.00  0.00              
ATOM    120  O   ASP   123     -82.525   4.930 -15.051  1.00  0.00              
ATOM    121  N   ILE   124     -82.393   6.343 -16.726  1.00  0.00              
ATOM    122  CA  ILE   124     -82.440   7.528 -15.825  1.00  0.00              
ATOM    123  C   ILE   124     -83.634   7.459 -14.898  1.00  0.00              
ATOM    124  O   ILE   124     -83.530   7.563 -13.698  1.00  0.00              
ATOM    125  N   LEU   125     -84.782   7.340 -15.465  1.00  0.00              
ATOM    126  CA  LEU   125     -85.995   7.329 -14.638  1.00  0.00              
ATOM    127  C   LEU   125     -85.861   6.218 -13.602  1.00  0.00              
ATOM    128  O   LEU   125     -86.039   6.444 -12.429  1.00  0.00              
ATOM    129  N   TRP   126     -85.461   5.051 -13.992  1.00  0.00              
ATOM    130  CA  TRP   126     -85.248   3.986 -12.975  1.00  0.00              
ATOM    131  C   TRP   126     -84.209   4.515 -11.974  1.00  0.00              
ATOM    132  O   TRP   126     -84.041   4.002 -10.887  1.00  0.00              
ATOM    133  N   GLU   127     -83.500   5.533 -12.375  1.00  0.00              
ATOM    134  CA  GLU   127     -82.427   6.133 -11.525  1.00  0.00              
ATOM    135  C   GLU   127     -83.001   7.242 -10.623  1.00  0.00              
ATOM    136  O   GLU   127     -83.134   7.082  -9.426  1.00  0.00              
ATOM    137  N   HIS   128     -83.306   8.375 -11.199  1.00  0.00              
ATOM    138  CA  HIS   128     -83.830   9.515 -10.401  1.00  0.00              
ATOM    139  C   HIS   128     -85.213   9.197  -9.850  1.00  0.00              
ATOM    140  O   HIS   128     -85.553   9.591  -8.753  1.00  0.00              
ATOM    141  N   LEU   129     -86.029   8.510 -10.597  1.00  0.00              
ATOM    142  CA  LEU   129     -87.390   8.214 -10.081  1.00  0.00              
ATOM    143  C   LEU   129     -87.247   7.302  -8.866  1.00  0.00              
ATOM    144  O   LEU   129     -87.912   7.463  -7.866  1.00  0.00              
ATOM    145  N   GLU   130     -86.354   6.359  -8.935  1.00  0.00              
ATOM    146  CA  GLU   130     -86.141   5.461  -7.772  1.00  0.00              
ATOM    147  C   GLU   130     -85.790   6.333  -6.560  1.00  0.00              
ATOM    148  O   GLU   130     -86.532   6.409  -5.611  1.00  0.00              
ATOM    149  N   ILE   131     -84.674   7.008  -6.593  1.00  0.00              
ATOM    150  CA  ILE   131     -84.293   7.877  -5.437  1.00  0.00              
ATOM    151  C   ILE   131     -85.472   8.771  -5.031  1.00  0.00              
ATOM    152  O   ILE   131     -85.424   9.459  -4.031  1.00  0.00              
ATOM    153  N   LEU   132     -86.516   8.791  -5.813  1.00  0.00              
ATOM    154  CA  LEU   132     -87.681   9.664  -5.489  1.00  0.00              
ATOM    155  C   LEU   132     -88.540   9.065  -4.360  1.00  0.00              
ATOM    156  O   LEU   132     -89.623   9.546  -4.089  1.00  0.00              
ATOM    157  N   GLN   133     -88.083   8.039  -3.688  1.00  0.00              
ATOM    158  CA  GLN   133     -88.913   7.467  -2.581  1.00  0.00              
ATOM    159  C   GLN   133     -88.816   8.388  -1.359  1.00  0.00              
ATOM    160  O   GLN   133     -88.912   7.944  -0.232  1.00  0.00              
END
