Proteopedia

Sandbox Eric Martz: Difference between revisions

← Older edit
Eric Martz (talk | contribs)
ConfirmAccount, Editor, Tester, Administrators
27,351 edits
x
Eric Martz (talk | contribs)
ConfirmAccount, Editor, Tester, Administrators
27,351 edits
x
 
(26 intermediate revisions by the same user not shown)
Line 2: Line 2:


Proposed article title: <big><b>Release of
Proposed article title: <big><b>Release of
<font color='#a04090'>RING</font>
RING
from
from
<font color='#b0a090'>Cullin</font>
Cullin
by
by
<font color='#a03000'>NEDD8ylation</font></b></big>
NEDD8ylation</b></big>


<applet load='3dpl_3dqv_acr_morph.pdb' size='500' frame='true' align='right' caption='NEDD8ylation of Cullin-RING'  
<applet load='3dpl_3dqv_acr_morph.pdb' size='500' frame='true' align='right' caption='NEDD8ylation of Cullin-RING'  
scene='Sandbox_Eric_Martz/Three_chains/1' />
scene='Sandbox_Eric_Martz/Three_chains/1' />


<!--
<jmol>
<jmolButton>
<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>
</jmolButton>
</jmol>
-->
<jmol>
<jmol>


<jmolButton>
<jmolButton>
<script>set background model none; spin off; anim off; frame 1;</script>
<script>set backgroundmodel none; spin off; anim off; frame 0;</script>
<text>Dimer</text>
<text>Dimer</text>
</jmolButton>
</jmolButton>


<jmolButton>
<jmolButton>
<script>set background model none; spin off; anim off; frame 7-8;</script>
<script>set backgroundmodel none; spin off; anim off; frame 7-8;</script>
<text>Trimer</text>
<text>Trimer</text>
</jmolButton>
</jmolButton>
Line 25: Line 33:
<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>


</jmol>
</jmol>
<b><font color='#a04090'>RING (A)</font>
&nbsp;
<font color='#b0a090'>Cullin (C)</font>
&nbsp;
<font color='#a03000'>NEDD8 (A)</font></b>


<!--
Display chains A/C/R as smoothed backbone traces colored by N->C Rainbow:
<jmol>
<jmol>
<jmolButton>
<jmolButton>
<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>
<script>select *a; spacefill off; trace 0.5; color trace group;</script>
<text>Toggle Animation</text>
<text>NEDD8 (A)</text>
</jmolButton>
 
<jmolButton>
<script>select *c; spacefill off; trace 0.5; color trace group;</script>
<text>Cullin (C)</text>
</jmolButton>
 
<jmolButton>
<script>select *r; spacefill off; trace 0.5; color trace group;</script>
<text>RING (R)</text>
</jmolButton>
 
<jmolButton>
<script>select protein; spacefill;</script>
<text>Spacefill All</text>
</jmolButton>
</jmolButton>
</jmol>
</jmol>
-->
{{Template:ColorKey_N2CRainbow}}
 
Color traces by chain:
<jmol>
 
<jmolButton>
<script>select *a; spacefill off; trace 0.5; color trace [xa03000];</script>
<text>NEDD8 (A)</text>
</jmolButton>
 
<jmolButton>
<script>select *c; spacefill off; trace 0.5; color trace [xb08090];</script>
<text>Cullin (C)</text>
</jmolButton>
 
<jmolButton>
<script>select *r; spacefill off; trace 0.5; color trace [xa04090];</script>
<text>RING (R)</text>
</jmolButton>


</jmol>
<center>
<b><font color='#a04090'>RING (A)</font>
&nbsp;
<font color='#b0a090'>Cullin (C)</font>
&nbsp;
<font color='#a03000'>NEDD8 (A)</font></b>
</center>


At right is a morph
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 complex ([[3dpl]]) to the same complex after NEDD8ylation (covalent addition of the NEDD8 ubiquitin-like chain to LysXXX 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.
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.''
 
Cullin atoms within 4.0 &Aring; of:
<jmol>
 
<jmolButton>
<script>select leu713:c.cd1, lys492:c.nz, arg495:c.ne, arg495:c.nh2; select selected or glu762:c, his763:c.cd2, his763:c.ce1, his763:c.ne2; spacefill; color cpk;</script>
<text>RING (R) in dimer</text>
</jmolButton>
 
</jmol>
<center>
Colored by Element:
{{Template:ColorKey_Element_C}}
{{Template:ColorKey_Element_O}}
{{Template:ColorKey_Element_N}}
</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. <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.
 
<!--
INCLUDING THIS APPLET CAUSES THE REFERENCES TO FAIL TO DISPLAY.
{{Clear}}
&nbsp;
<applet load='3dqv_trimer1_trimer2_morph.pdb.gz' size='500' frame='true' align='right'
caption='Two trimers in the asymmetric unit of 3dqv.' />
 
Hello
-->


{{Clear}}
==Notes and References==
==Notes and References==
<references />
<references />

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz
Retrieved from "https://proteopedia.openfox.io/w/Sandbox_Eric_Martz"