Ribosome Models


Model of putative helix from pufX protein, color-coded to show the hydropathy profile (Rainbow scale*). The coordinates of the model were generated using the Ribosome function of PSAAM. The model is seen as a stereo-pair (for crossed-eye viewing) displayed by PDVWIN (Protein Data Viewer for Windows).

*Rainbow scale, RedOrgYelGrnCyaBluVioGray with red indicating high values

The PufX helix model shown in the Render window of PDVWIN. The residues are color-coded according to the side-chain volume moment (Rainbow scale). Notice the patch of red-yellow residues showing a span in which the helix is lob-sided, with a cavity of small side-chains on one side among a patch of large side chains. We have suggested that the PufX protein sits in the ring of LH1 light-harvesting complexes surrounding the reaction center; a dimer would make a hole through which ubiquinone could diffuse between the volume inside the ring (to which the Qb-site of the reaction center has access), and the volume outside the ring (to which the bc-complex has access).

Example of the file generated by Ribosome.

The first putative transmembrane helix of pine LHCII. The Header file has been prepended to the coordinate data set (shown in truncated form here). Note that the SEQRES lines are taken from the sequence currently under analysis, and the secondary structural lines (HELIX, TURN, etc.) are taken from the current model. The ATOM lines are from the first few entries for the model generated by Ribosome.

SEQRES   1    266  MET ALA THR ALA SER ALA ILE GLN SER SER SER LEU ALA          
SEQRES   2    266  GLY GLN THR LEU LEU ARG PRO GLN GLN ASN GLU LEU VAL          
SEQRES   3    266  LYS LYS VAL GLY THR ALA GLN ALA ARG ILE THR MET ARG          
SEQRES   4    266  ARG THR VAL ARG SER ALA PRO GLU SER ILE TRP TYR GLY          
SEQRES   5    266  PRO ASP ARG PRO LYS TYR LEU GLY PRO PHE SER GLU GLY          
SEQRES   6    266  THR PRO SER TYR LEU THR GLY GLU PHE PRO GLY ASP TYR          
SEQRES   7    266  GLY TRP ASP THR ALA GLY LEU SER ALA ASP PRO GLU THR          
SEQRES   8    266  PHE ALA LYS ASN ARG GLU LEU GLU VAL ILE HIS CYS ARG          
SEQRES   9    266  TRP ALA MET LEU GLY ALA LEU GLY CYS LEU PHE PRO GLU          
SEQRES  10    266  LEU LEU ALA LYS ASN GLY VAL LYS PHE GLY GLU ALA VAL          
SEQRES  11    266  TRP PHE LYS ALA GLY ALA GLN ILE PHE SER GLU GLY GLY          
SEQRES  12    266  LEU ASP TYR LEU GLY ASN PRO ASN LEU ILE HIS ALA GLN          
SEQRES  13    266  SER ILE LEU ALA ILE TRP ALA CYS GLN VAL VAL LEU MET          
SEQRES  14    266  GLY LEU ILE GLU GLY TYR ARG VAL GLY GLY GLY PRO LEU          
SEQRES  15    266  GLY GLU GLY LEU ASP PRO LEU TYR PRO GLY GLY ALA PHE          
SEQRES  16    266  ASP PRO LEU GLY LEU ALA ASP ASP PRO GLU ALA PHE ALA          
SEQRES  17    266  GLU LEU LYS VAL LYS GLU ILE LYS ASN GLY ARG LEU ALA          
SEQRES  18    266  MET PHE SER MET PHE GLY PHE PHE VAL GLN ALA ILE VAL          
SEQRES  19    266  THR GLY LYS GLY PRO ILE GLU ASN LEU TYR ASP HIS LEU          
SEQRES  20    266  ALA ASP PRO VAL ALA ASN ASN ALA TRP ALA TYR ALA THR          
SEQRES  21    266  ASN PHE VAL PRO GLY LYS                                      
HET    CHL      1                                                               
HET    CHL      2                                                               
HET    CHL      3                                                               
HET    CHL      4                                                               
HET    CHL      5                                                               
HET    CHL      6                                                               
HET    CHL      7                                                               
HET    CHL      8                                                               
HET    CHL      9                                                               
HET    CHL     10                                                               
HET    CHL     11                                                               
HET    CHL     12                                                               
HET    CHL     13                                                               
HELIX    1     PRO     89  ALA    120                                           
HELIX    2     LEU    152  GLU    173                                           
HELIX    3     GLU    205  THR    235                                           
HELIX    4     ILE    240  ASN    254                                           
TURN     1     PRO    75  TYR    78                                             
TURN     2     LYS   121  VAL   124                                             
TURN     3     GLY   148  ASN   151                                             
TURN     4     GLY   178  PRO   181                                             
TURN     5     PRO   191  ALA   194                                             
TURN     6     ALA   201  PRO   204                                             
TURN     7     GLY   236  PRO   239                                             

ATOM    734  N   PRO    89       0.000   0.000   0.000                          
ATOM    735  CA  PRO    89       0.000  -1.325   0.765                          
ATOM    736  C   PRO    89      -1.118  -2.166   0.313                          
ATOM    737  O   PRO    89      -0.953  -3.389   0.189                          
ATOM    738  CB  PRO    89      -0.027  -1.144   2.294                          
ATOM    739  CG  PRO    89       0.002   0.359   2.618                          
ATOM    740  CD  PRO    89       0.046   1.149   1.301                          
ATOM    741  N   PRO    89       0.000   0.000   0.000                          
ATOM    742  N   GLU    90      -2.261  -1.558   0.059                          
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Sequence.....Side-chain volume moment.....Amphipathy.....Hydropathy

Model color-code using Rainbow scale.

Sequence is -89PETFAKNRELGVIHCRWAMLGALGCLFPELLA-