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Sandbox Eric Martz
From Proteopedia
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| - | + | The <b>morph</b> | |
<ref>The 9-model [[Morphs|morph]] file can be downloaded from [[Image: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 [http://www.ebi.ac.uk/msd-srv/pqs/pqs-bin/macmol.pl?filename=3DQV PQS] as 3dqv_1.mmol. The morph was performed by the Yale Morph Server (beta server), ID [http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b899128-21508 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.</ref> | <ref>The 9-model [[Morphs|morph]] file can be downloaded from [[Image: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 [http://www.ebi.ac.uk/msd-srv/pqs/pqs-bin/macmol.pl?filename=3DQV PQS] as 3dqv_1.mmol. The morph was performed by the Yale Morph Server (beta server), ID [http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b899128-21508 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.</ref> | ||
| - | from a Cullin-RING ligase | + | button above shows the transition |
| + | from a Cullin-RING ligase <b>dimer</b> ([[3dpl]]) to the <b>trimer</b> 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.'' | ||
{{Clear}} | {{Clear}} | ||
==Notes and References== | ==Notes and References== | ||
<references /> | <references /> | ||
Revision as of 18:44, 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
|
Display chains as smoothed backbone traces colored by N->C Rainbow:
| N | C |
Color traces by chain:
RING (A) Cullin (C) NEDD8
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.
Notes and References
- ↑ The 9-model morph file can be downloaded from Image: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.
