Sandbox Eric Martz: Difference between revisions
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scene='Sandbox_Eric_Martz/Three_chains/1' /> | scene='Sandbox_Eric_Martz/Three_chains/1' /> | ||
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<script>if (~animation); if (_animating); anim pause;set echo bottom left; color echo white; font echo 20 sansserif;echo Animation Paused; else; anim resume; set echo off;endif;endif;</script> | |||
<text>Toggle Animation</text> | |||
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<font color='#a03000'>NEDD8</font></b> | <font color='#a03000'>NEDD8</font></b> | ||
</center> | </center> | ||
Contacts to: | |||
<jmol> | <jmol> | ||
<jmolButton> | <jmolButton> | ||
<script> | <script>select *a; spacefill off; trace 0.5; color trace [xa03000];</script> | ||
<text> | <text>NEDD8 (A)</text> | ||
</jmolButton> | </jmolButton> | ||
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{{Clear}} | {{Clear}} | ||
<applet load='3dqv_trimer1_trimer2_morph.pdb.gz' size='500' frame='true' align='right' caption='Two trimers in the asymmetric unit of 3dqv.' | |||
scene='' /> | |||
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==Notes and References== | ==Notes and References== | ||
<references /> | <references /> | ||
Revision as of 21:49, 22 February 2009
This article is under collaborative development by Eric Martz (UMass) and Raymond J. Deshaies and his team (CalTech). Please do not edit this page unless you are a member of the development team. Once completed, this page may be moved to a permanent article title.
Proposed article title: Release of RING from Cullin by NEDD8ylation
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Display chains as smoothed backbone traces colored by N->C Rainbow:
| N | C |
Color traces by chain:
RING (A) Cullin (C) NEDD8
Contacts to:
The morph
[1]
button above shows the transition
from a Cullin-RING ligase dimer (3dpl) to the trimer resulting from NEDD8ylation (covalent addition of the NEDD8 ubiquitin-like chain to Lys724 of Cullin; 3dqv). NEDD8 binds and rotates the C-terminal domain of Cullin, releasing the folded RING domain from its Cullin-binding site. RING remains attached to Cullin by the RING N-terminus which remains embedded in Cullin. The contraction and re-expansion of the C-terminal domain during rotation is an artifact of the morphing algorithm.
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Notes and ReferencesNotes and References
- ↑ The 9-model morph file can be downloaded from File:3dpl 3dqv acr morph.pdb. The morph represents the change from 3dpl to 3dqv, and only chains C and R which are common to these two models. Only one trimer was used from 3dqv (which contains 2 trimers in the asymmetric unit), namely, the one with chains named A, C, and R. This trimer was obtained from PQS as 3dqv_1.mmol. The morph was performed by the Yale Morph Server (beta server), ID b899128-21508. This produced 8 models numbered 0-7. In the product morph, the orientation of the final chains was not changed. Hence, chain A (NEDD8) from 3dqv.pdb was added as model number 8 (9th model) without the need for special alignment. Morph done by Eric Martz at the request of Raymond J. Deshaies of CalTech.