Sandbox Eric Martz: Difference between revisions
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<jmolButton> | <jmolButton> | ||
<script>set backgroundmodel none; spin off; anim off; frame | <script>set backgroundmodel none; spin off; anim off; frame 0;</script> | ||
<text>Dimer</text> | <text>Dimer</text> | ||
</jmolButton> | </jmolButton> | ||
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<jmolButton> | <jmolButton> | ||
<script>spin off; set backgroundmodel 1.9; anim mode palindrome; frame range 1.1 1.8;frame play;</script> | <script>spin off; set backgroundmodel 1.9; anim mode palindrome; frame range 1.1 1.8;frame play;</script> | ||
<text>Morph</text> | <text>Animate Morph</text> | ||
</jmolButton> | </jmolButton> | ||
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<font color='#a03000'>NEDD8 (A)</font></b> | <font color='#a03000'>NEDD8 (A)</font></b> | ||
Display chains as smoothed backbone traces colored by N->C Rainbow: | Display chains A/C/R as smoothed backbone traces colored by N->C Rainbow: | ||
<jmol> | <jmol> | ||
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{{Template:ColorKey_Element_N}} | {{Template:ColorKey_Element_N}} | ||
</center> | </center> | ||
Use the buttons above to show Cullin as a trace in order to see these contacting atoms, then animate the morph. This shows that although the same long alpha helix contacts both RING and NEDD8, the Cullin atoms contacting RING do not, for the most part, contact NEDD8. | Use the buttons above to show Cullin as a trace in order to see these contacting atoms, then animate the morph. This shows that although the same long alpha helix contacts both RING and NEDD8, the Cullin atoms contacting RING do not, for the most part, contact NEDD8. <b>Important Caveat:</b> The dimer model [http://oca.weizmann.ac.il/oca-bin/send-s2c?w=1&id=3dpl lacks coordinates] for residues 64-66 of RING (<font color='#00e000'><b>green</b></font> in the N->C Rainbow), which are likely part of the Culllin-RING contact. | ||
==Flexibility of Trimer== | |||
<scene name='Sandbox_Eric_Martz/Trimer_morph/1'>Load and Animate Trimer Morph</scene>. | |||
The model [[3dqv]] contains two copies of the trimer in the asymmetric unit. Morphing<ref>The trimer morph [[Image:3dqv_trimer1_trimer2_morph.pdb.gz]] was generated from 3dqv_1.mmol and 3dqv_2.mmol (obtained from [http://www.ebi.ac.uk/msd-srv/pqs/pqs-bin/macmol.pl?filename=3DQV PQS]) with the Yale Morph Server (beta version), ID [http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b318728-3599 b318728-3599]. The chains B, D, and Y in 3dqv_2.mmol were first renamed to A, C, and R in order to match up with those in 3dqv_1.mmol, using [[DeepView]].</ref> one to the other shows flexibility of the trimer. The position of RING changes the most because of its flexible tether to Cullin. The two positions of RING in the crystal structure are undoubtedly stabilized by different crystal contacts (not shown here, but [http://proteinexplorer.org/xtlcon.htm could be shown]). | |||
To reload the NEDD8ylation morph into Jmol above, simply reload this page. | |||
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==Notes and References== | ==Notes and References== | ||
<references /> | <references /> | ||