farrah at nwnexus.wa.com@immunex.UUCP writes:
>From: NAME: Terry Farrah
> FUNC: Protein Chemistry
> TEL: 206-587-0430 x4206 <FARRAH AT A1 AT GENOME>
>To: UUCP%"peitsch at ncbi.nlm.nih.gov"@MRGATE
>>> Manuel,
>> It was generous of you to post your model for CD40 ligand to the net.
> Since we cloned that molecule here at Immunex, it won't be surprising
> that we are very interested in your model. This is the first time I've
> seen a molecular model posted to the net. I'm curious why you are
> willing to share your model with the world before publication. Can you
> also post the figure legend for the model (e.g. what are the colored
> bands on the ribbon diagram of the monomer?)? Would you consider
> posting alpha-carbon coordinates? It took us some time to figure out
> how to make use of the GIF file.
>> I'm writing to you directly because I currently have no means of
> posting (only reading). I hope others follow your example and that
> bionet becomes a forum for sharing interesting models.
> I think that sharing data, AS SOON AS you know they will be
published is a good for the advancment of science. It also
prevents people from spending time and money on things which
have already been done.
> Sincerely,
>> Terry Farrah, Immunex (farrah at immunex.com)
This is the first time I was posting something to the net. So I thought
that posting one of my pictures from a recent modelling project would
be a nice way to start. Nice pictures are in fact just the icing on the
cake, and are only of limited use. In this case however, the intention
was just to show that CD40L can adopt a trimeric structure, the same way
both known TNF structures do. Our paper (in Feb. 1993) gives the details
of the modelling procedure and the structural analysis which allow us to
make this hypothesis. More recently, another group cloned the human CD40L
and found that the expressed molecule with biological activity is in dimeric
and trimer form. These data seem to confirm our model.
-------------------------
Short legend for TNFs.gif
Ribbon models of TNF-alpha, TNF-beta and the ligand of CD40 (CD40L).
Both TNF-alpha and TNF-beta are known to form trimers, as deduced
from crystallographic analysis by S.R. Sprang (1,2). The structure
of CD40L was derived by knowledge-based molecular modelling using the
TNF structures as input data (3).
Each chain in the trimer is depicted in another color.
The disulfide bonds in TNF-alpha and CD40L are shown in ball and sticks.
The fourth pannel is a stereo representation of on CD40L monomer. The color
codes for the residues is given below.
Color code for the monomer of CD40L
Color Residues
RED : D,E
GREEN : A,F,I,L,V
YELLOW : C,M
BLUE : H,K,R
MAGENTA: N,Q
CYAN : G,P
WHITE : W
ORANGE : S,T,Y
1. Eck-M-J, Sprang-S-R. (1989): The structure of tumor necrosis
factor-alpha at 2.6 A resolution. Implications for receptor binding.
J.Biol.Chem. 264, 17595-605.
2. Eck-M-J, Ultsch-M, Rinderknecht-E, de-Vos-A-M, Sprang-S-R. (1992):
The structure of human lymphotoxin (tumor necrosis factor-beta) at
1.9-A resolution. J.Biol.Chem. 267, 2119-22.
3. Peitsch-M-C, Jongeneel-C-V. (1993): International Immunology, in press
(issue due in February).
-------------------------
For those who have problems with the GIF format, here is a site where you can
get a GIF-viewer for SGI's: vab02.larc.nasa.gov
how to operate:
1. ftp vab02.larc.nasa.gov, login as anonymous/passwd=user at host.domain
2. binary
3. cd sgi
4. get igif2.1.tar.Z
5. quit
6. uncompress igif2.1.tar.Z
7. tar -xvf igif2.1.tar
8. cd ./igif2.1
9. make
to view a file: igif xxxx.gif
-------------------------
CA atom coordinates of the CD40L trimer as submitted to the Brookhaven
Protein DataBank:
ATOM 5 CA GLY A 1 31.618 48.672 62.763 0.00 0.00
ATOM 10 CA ASP A 2 33.601 45.787 61.309 0.00 0.00
ATOM 19 CA GLU A 3 32.647 42.218 60.477 0.00 0.00
ATOM 29 CA ASP A 4 35.251 40.147 58.597 0.00 0.00
ATOM 38 CA PRO A 5 38.536 41.421 56.949 0.00 0.00
ATOM 45 CA GLN A 6 37.258 42.203 53.482 0.00 0.00
ATOM 57 CA ILE A 7 37.857 45.811 52.368 0.00 0.00
ATOM 66 CA ALA A 8 34.683 47.818 52.744 0.00 0.00
ATOM 72 CA ALA A 9 33.555 51.249 51.648 0.00 0.00
ATOM 78 CA HIS A 10 30.353 53.224 51.577 0.00 0.00
ATOM 90 CA VAL A 11 30.650 57.065 51.166 0.00 0.00
ATOM 98 CA VAL A 12 27.835 59.635 50.999 0.00 0.00
ATOM 106 CA SER A 13 27.565 63.000 49.191 0.00 0.00
ATOM 114 CA GLU A 14 28.257 65.774 51.686 0.00 0.00
ATOM 124 CA ALA A 15 25.740 68.528 52.581 0.00 0.00
ATOM 130 CA ASN A 16 25.526 70.498 49.339 0.00 0.00
ATOM 141 CA SER A 17 24.719 73.743 51.109 0.00 0.00
ATOM 149 CA ASN A 18 28.466 73.631 51.974 0.00 0.00
ATOM 160 CA ALA A 19 29.745 71.737 48.903 0.00 0.00
ATOM 166 CA ALA A 20 28.365 74.544 46.704 0.00 0.00
ATOM 172 CA SER A 21 27.661 72.772 43.412 0.00 0.00
ATOM 180 CA VAL A 22 30.289 70.121 44.334 0.00 0.00
ATOM 188 CA LEU A 23 30.054 66.319 44.435 0.00 0.00
ATOM 197 CA GLN A 24 32.028 65.875 47.637 0.00 0.00
ATOM 209 CA TRP A 25 31.984 62.351 49.004 0.00 0.00
ATOM 225 CA ALA A 26 32.294 61.965 52.807 0.00 0.00
ATOM 231 CA LYS A 27 32.442 59.374 55.605 0.00 0.00
ATOM 244 CA LYS A 28 31.472 59.694 59.401 0.00 0.00
ATOM 257 CA GLY A 29 27.688 60.040 58.805 0.00 0.00
ATOM 262 CA TYR A 30 26.370 56.959 60.653 0.00 0.00
ATOM 276 CA TYR A 31 26.485 54.290 57.872 0.00 0.00
ATOM 290 CA THR A 32 29.314 55.455 55.628 0.00 0.00
ATOM 299 CA MET A 33 31.986 52.856 56.265 0.00 0.00
ATOM 308 CA LYS A 34 35.462 53.753 55.094 0.00 0.00
ATOM 321 CA SER A 35 37.207 50.853 56.914 0.00 0.00
ATOM 329 CA ASN A 36 39.646 47.866 56.404 0.00 0.00
ATOM 340 CA LEU A 37 42.331 49.984 54.837 0.00 0.00
ATOM 349 CA VAL A 38 39.939 52.185 52.722 0.00 0.00
ATOM 357 CA MET A 39 41.328 55.522 51.952 0.00 0.00
ATOM 366 CA LEU A 40 38.811 57.752 50.261 0.00 0.00
ATOM 375 CA GLU A 41 41.411 60.298 49.146 0.00 0.00
ATOM 385 CA ASN A 42 43.139 61.142 45.694 0.00 0.00
ATOM 396 CA GLY A 43 40.595 63.789 44.646 0.00 0.00
ATOM 401 CA LYS A 44 37.329 62.376 45.856 0.00 0.00
ATOM 414 CA GLN A 45 38.616 59.057 44.699 0.00 0.00
ATOM 426 CA LEU A 46 38.476 55.843 46.670 0.00 0.00
ATOM 435 CA THR A 47 41.831 54.008 46.280 0.00 0.00
ATOM 444 CA VAL A 48 42.148 50.182 45.921 0.00 0.00
ATOM 452 CA LYS A 49 44.477 48.149 48.179 0.00 0.00
ATOM 465 CA ARG A 50 44.232 44.367 47.613 0.00 0.00
ATOM 482 CA GLU A 51 43.482 42.879 44.164 0.00 0.00
ATOM 492 CA GLY A 52 40.186 41.194 43.404 0.00 0.00
ATOM 497 CA LEU A 53 36.536 40.964 42.502 0.00 0.00
ATOM 506 CA TYR A 54 35.066 44.190 43.955 0.00 0.00
ATOM 520 CA TYR A 55 31.354 45.059 43.928 0.00 0.00
ATOM 534 CA VAL A 56 31.235 48.730 43.006 0.00 0.00
ATOM 542 CA TYR A 57 28.033 50.692 43.214 0.00 0.00
ATOM 556 CA THR A 58 26.783 54.225 43.071 0.00 0.00
ATOM 565 CA GLN A 59 23.446 55.959 43.305 0.00 0.00
ATOM 577 CA VAL A 60 22.293 59.604 42.963 0.00 0.00
ATOM 585 CA THR A 61 19.130 61.844 42.709 0.00 0.00
ATOM 594 CA PHE A 62 17.927 65.017 40.874 0.00 0.00
ATOM 606 CA CYS A 63 15.333 67.810 40.994 0.00 0.00
ATOM 613 CA SER A 64 14.917 71.079 39.167 0.00 0.00
ATOM 621 CA ASN A 65 11.904 73.213 39.981 0.00 0.00
ATOM 632 CA ARG A 66 11.010 73.655 36.318 0.00 0.00
ATOM 649 CA GLU A 67 12.562 72.515 33.087 0.00 0.00
ATOM 659 CA PRO A 68 15.106 74.918 31.426 0.00 0.00
ATOM 666 CA SER A 69 15.923 75.529 27.704 0.00 0.00
ATOM 674 CA SER A 70 16.078 72.719 25.113 0.00 0.00
ATOM 682 CA GLN A 71 17.955 69.988 27.036 0.00 0.00
ATOM 694 CA ARG A 72 19.350 69.174 30.445 0.00 0.00
ATOM 711 CA PRO A 73 20.463 65.410 30.251 0.00 0.00
ATOM 718 CA PHE A 74 22.024 64.212 33.461 0.00 0.00
ATOM 730 CA ILE A 75 25.052 62.055 32.747 0.00 0.00
ATOM 739 CA VAL A 76 26.437 60.219 35.718 0.00 0.00
ATOM 747 CA GLY A 77 29.490 57.993 35.420 0.00 0.00
ATOM 752 CA LEU A 78 32.017 55.915 37.284 0.00 0.00
ATOM 761 CA TRP A 79 35.620 56.161 36.172 0.00 0.00
ATOM 777 CA LEU A 80 38.711 54.121 37.057 0.00 0.00
ATOM 786 CA LYS A 81 42.348 55.163 37.218 0.00 0.00
ATOM 799 CA PRO A 82 44.830 52.229 37.610 0.00 0.00
ATOM 806 CA SER A 83 48.259 51.098 36.477 0.00 0.00
ATOM 814 CA ILE A 84 47.359 52.247 32.919 0.00 0.00
ATOM 823 CA GLY A 85 47.168 55.746 34.359 0.00 0.00
ATOM 828 CA SER A 86 44.171 57.181 32.499 0.00 0.00
ATOM 836 CA GLU A 87 40.611 57.608 33.662 0.00 0.00
ATOM 846 CA ARG A 88 38.735 54.804 31.987 0.00 0.00
ATOM 863 CA ILE A 89 34.975 54.407 32.421 0.00 0.00
ATOM 872 CA LEU A 90 33.478 51.335 34.137 0.00 0.00
ATOM 881 CA LEU A 91 29.864 52.351 34.786 0.00 0.00
ATOM 890 CA LYS A 92 27.485 54.909 33.246 0.00 0.00
ATOM 903 CA ALA A 93 23.971 56.248 33.479 0.00 0.00
ATOM 909 CA ALA A 94 22.319 58.946 31.374 0.00 0.00
ATOM 915 CA ASN A 95 18.929 60.566 31.981 0.00 0.00
ATOM 926 CA THR A 96 16.791 63.201 30.321 0.00 0.00
ATOM 935 CA HIS A 97 14.951 65.823 32.358 0.00 0.00
ATOM 947 CA SER A 98 11.325 65.335 31.271 0.00 0.00
ATOM 955 CA SER A 99 9.460 66.972 28.433 0.00 0.00
ATOM 963 CA SER A 100 8.280 70.119 30.132 0.00 0.00
ATOM 971 CA GLN A 101 7.897 69.610 33.884 0.00 0.00
ATOM 983 CA LEU A 102 8.124 71.341 37.310 0.00 0.00
ATOM 992 CA CYS A 103 10.334 69.545 39.820 0.00 0.00
ATOM 999 CA GLU A 104 11.911 67.129 37.432 0.00 0.00
ATOM 1009 CA GLN A 105 12.556 64.734 40.232 0.00 0.00
ATOM 1021 CA GLN A 106 14.794 61.976 39.227 0.00 0.00
ATOM 1033 CA SER A 107 17.137 59.365 40.680 0.00 0.00
ATOM 1041 CA VAL A 108 19.702 56.965 39.198 0.00 0.00
ATOM 1049 CA
