Calmodulin

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (19:03, 7 July 2023) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 3: Line 3:
==Function==
==Function==
-
[[Calmodulin]] (CaM) – calcium modulated protein – regulates various protein targets. It is used by various proteins as calcium sensor and signal transducer by binding to their calcium binding domain (CBD). It undergoes conformational change upon binding Ca++ via its 4 [[EF hand]] motives and can undergo post-translational modification. <scene name='39/398280/Cv/4'>Click here to see EF hand</scene> of Human calmodulin (PDB code [[1cll]]). <ref>PMID:1474585</ref> More details on apo-CaM<br />
+
[[Calmodulin]] (CaM) – calcium modulated protein – regulates various protein targets. It is used by various proteins as calcium sensor and signal transducer by binding to their calcium binding domain (CBD). It undergoes conformational change upon binding Ca++ via its 4 [[EF hand]] motives and can undergo post-translational modification. <scene name='39/398280/Cv/4'>Click here to see EF hand</scene> of Human calmodulin (PDB code [[1cll]]). <ref>PMID:1474585</ref> More details on apo-CaM [[Calcium-free Calmodulin]] and [[Calmodulin JMU]].
-
[[Calcium-free Calmodulin]]<br />
+
-
[[Calmodulin JMU]].
+
{{Clear}}
{{Clear}}
Line 17: Line 15:
== Calmodulin in Motion ==
== Calmodulin in Motion ==
-
The clip represents Calmodulin in motion. At the beginning it is shown moving in the unbound form (ApoCaM), and it changes its conformation when Calcium ions are present in the medium (CaCaM).
+
The buttons below allow you to explore morphs <ref>The [[Jmol/Storymorph|Storymorph Jmol scripts]] creates the interpolated coordinates of the morph on the fly.</ref> between structures [[1prw]] and [[1cll]].
-
<center><swf width="720" height="576">/flash/Apo_CaM_CaCaM.swf</swf></center>
+
<jmol>
 +
<jmolButton>
 +
<script>
 +
script "/wiki/images/a/a2/Storymorph.spt";
 +
load files "=1prw" "=1cll";
 +
delete water;
 +
delete protein and not backbone;
 +
select all;cartoon only;cartoon off;
 +
select 4-147;cartoon on;
 +
model 1;
 +
center visible;color group;
 +
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{4-138}{4-138} ROTATE TRANSLATE;
 +
</script>
 +
<text>Prepare Animation</text>
 +
</jmolButton>
 +
</jmol><jmol>
 +
<jmolButton>
 +
<script>
 +
model 2;
 +
display 4-147;
 +
backbone only;
 +
backbone 0.5
 +
structures = [{1.1}, {2.1}];
 +
my_recipe = [
 +
[{79-147},{79-147}, {(79-138) and alpha}],
 +
[{4-78}, {79}, {(8-78) and alpha}],
 +
];
 +
morph(20, structures, my_recipe);
 +
</script>
 +
<text>Open</text>
 +
</jmolButton>
 +
</jmol><jmol>
 +
<jmolButton>
 +
<script>
 +
model 1
 +
display 4-147;
 +
backbone only;
 +
backbone 0.5
 +
structures = [{2.1}, {1.1}];
 +
my_recipe = [
 +
[{79-147},{79-147}, {(79-138) and alpha}],
 +
[{4-78}, {79}, {(8-78) and alpha}],
 +
];
 +
morph(20, structures, my_recipe);
 +
</script>
 +
<text>Close</text>
 +
</jmolButton>
 +
</jmol>
-
Motion of ApoCaM is elaborated on the basis of 23 conformations derived from NMR file [[1cfc]], using the 3D animation program Blender, and according to a system to be published soon (Zini et al., manuscript in preparation). The transition from ApoCaM to CaCaM is elaborated with Blender starting with conformation 21 of 1cfc to arrive in conformation 11 of pdb file 1x02.
+
The following morph is between [[1prw]] and [[1cll]] after superposition of residues 79-138. This shows the subtle conformational changes in that domain more clearly.
 +
<jmol>
 +
<jmolButton>
 +
<script>
 +
script "/wiki/images/a/a2/Storymorph.spt";
 +
load files "=1prw" "=1cll";
 +
delete water;
 +
delete protein and not backbone;
 +
select all;cartoon only;cartoon off;
 +
select 4-147;cartoon on;
 +
model 1;
 +
center visible;color group;
 +
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{79-138}{79-138} ROTATE TRANSLATE;
 +
</script>
 +
<text>Prepare Animation</text>
 +
</jmolButton>
 +
</jmol><jmol>
 +
<jmolButton>
 +
<script>
 +
model 2;
 +
display 4-147;
 +
backbone only;
 +
backbone 0.5
 +
structures = [{1.1}, {2.1}];
 +
my_recipe = [
 +
[{79-147},{79-147}, {(79-138) and alpha}],
 +
[{4-78}, {79}, {(8-78) and alpha}],
 +
];
 +
morph(20, structures, my_recipe);
 +
</script>
 +
<text>Open</text>
 +
</jmolButton>
 +
</jmol><jmol>
 +
<jmolButton>
 +
<script>
 +
model 1
 +
display 4-147;
 +
backbone only;
 +
backbone 0.5
 +
structures = [{2.1}, {1.1}];
 +
my_recipe = [
 +
[{79-147},{79-147}, {(79-138) and alpha}],
 +
[{4-78}, {79}, {(8-78) and alpha}],
 +
];
 +
morph(20, structures, my_recipe);
 +
</script>
 +
<text>Close</text>
 +
</jmolButton>
 +
</jmol>
-
Surface rendering is also elaborated using Blender, and shows the lipophilic potential as a scale of white-black and smooth-rough, form the most lipophilic to the hydrophilic. Electrostatic potential is represented as a series of lines moving in the direction Positive to Negative, elaborated according to a scheme to be published soon (Andrei et al., in preparation). As most lines are moving towards Calmodulin, one can learn that the protein is slightly acidic (negative partial charges on its surface).
+
The following morph is between [[1prw]] and [[1cll]] after superposition of residues 8-78. This shows the subtle conformational changes in that domain more clearly.
 +
<jmol>
 +
<jmolButton>
 +
<script>
 +
script "/wiki/images/a/a2/Storymorph.spt";
 +
load files "=1prw" "=1cll";
 +
delete water;
 +
delete protein and not backbone;
 +
select all;cartoon only;cartoon off;
 +
select 4-147;cartoon on;
 +
model 1;
 +
center visible;color group;
 +
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{8-78}{8-78} ROTATE TRANSLATE;
 +
</script>
 +
<text>Prepare Animation</text>
 +
</jmolButton>
 +
</jmol><jmol>
 +
<jmolButton>
 +
<script>
 +
model 2;
 +
display 4-147;
 +
backbone only;
 +
backbone 0.5
 +
structures = [{1.1}, {2.1}];
 +
my_recipe = [
 +
[{4-78}, {4-78}, {(8-78) and alpha}],
 +
[{79-147},{78}, {(79-138) and alpha}],
 +
];
 +
morph(20, structures, my_recipe);
 +
</script>
 +
<text>Open</text>
 +
</jmolButton>
 +
</jmol><jmol>
 +
<jmolButton>
 +
<script>
 +
model 1
 +
display 4-147;
 +
backbone only;
 +
backbone 0.5
 +
structures = [{2.1}, {1.1}];
 +
my_recipe = [
 +
[{4-78}, {4-78}, {(8-78) and alpha}],
 +
[{79-147},{78}, {(79-138) and alpha}],
 +
];
 +
morph(20, structures, my_recipe);
 +
</script>
 +
<text>Close</text>
 +
</jmolButton>
 +
</jmol>
-
This movie was created by Andrei, Zini et al., of the
 
-
[http://www.scivis.ifc.cnr.it Scientific Visualization Unit],
 
-
Institute of Clinical Physiology - CNR of Itlay.
 
-
[http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b097743-28520 Conformational change of Calmodulin]
 
 +
== 3D Structures of Calmodulin ==
 +
[[Calmodulin 3D structures]]
- 
-
<scene name='Calmodulin/Inicio/1'>Unbound</scene>,
 
-
<scene name='Calmodulin/Bound/4'>Bound</scene>
 
- 
-
{{Clear}}
 
</StructureSection>
</StructureSection>
-
== 3D Structures of Calmodulin ==
 
- 
-
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
 
-
{{#tree:id=OrganizedByTopic|openlevels=0|
 
- 
-
* Native CaM
 
- 
-
**[[1prw]], [[1deg]] – bCaM - bovine<br />
 
-
**[[1up5]] – cCaM – chicken<br />
 
-
**[[1clm]], [[1osa]], [[1exr]], [[5e1p]], [[5e1n]], [[5e1k]] – PtCaM - ''Paramecium tetraurelia''<br />
 
-
**[[3cln]] – rCaM - rat<br />
 
-
**[[1x02]], [[1dmo]] – XlCaM – NMR - ''Xenopus laevis''<br />
 
-
**[[2k61]], [[2k0e]] – hCaM – NMR - human<br />
 
-
**[[1y6w]], [[1cll]], [[4bw8]] - hCaM<br />
 
-
**[[4cln]] – DmCaM - ''Drosophila melanogaster''<br />
 
-
**[[1rfj]] – CaM – potato<br />
 
-
**[[1ooj]] – CaM – ''Caenorhabditis elegans''<br />
 
-
**[[4hex]] – mCaM – mouse<br />
 
-
**[[5a2h]] – AtCaM-7 – ''Arabidopsis thaliana''<br />
 
- 
-
* Mutant CaM
 
- 
-
**[[1ahr]], [[2m3s]] – cCaM (mutant)<br />
 
-
**[[2k0j]], [[1sw8]], [[5ggm]], [[5tp5]] – hCaM (mutant) – NMR<br />
 
- 
-
* apo CaM
 
- 
-
**[[1lkj]] – yapoCaM – NMR -yeast<br />
 
-
**[[1cfc]], [[1cfd]] - XlapoCaM – NMR<br />
 
-
**[[1qx5]] – rapoCaM – rat<br />
 
- 
-
* CaM N-terminal
 
- 
-
**[[2i08]], [[5dsu]] - hCaM N-terminal (mutant)<br />
 
-
**[[1j7o]], [[1j7p]] - hCaM N-terminal – NMR<br />
 
-
**[[1f70]] - XlCaM N-terminal – NMR <br />
 
-
**[[2ro8]], [[2roa]] - sCaM N-terminal+Ca – NMR - soybean<br />
 
-
**[[2ro9]], [[2rob]] - sCaM C-terminal+Ca – NMR<br />
 
-
**[[3ifk]], [[3b32]] – rCaM N-terminal <br />
 
-
**[[1f54]], [[1f55]] – yapoCaM N-terminal – NMR<br />
 
- 
-
* CaM C-terminal
 
- 
-
**[[1f71]] - XlCaM C-terminal – NMR<br />
 
-
**[[1cmg]] – bCaM C-terminal – NMR<br />
 
-
**[[1fw4]] - bCaM C-terminal<br />
 
-
**[[4rjd]] – rCaM<br />
 
-
**[[1cmf]] – bapoCaM C-terminal – NMR<br />
 
-
**[[2hf5]] - hCaM EF2 EF3 – NMR<br />
 
-
**[[2lqp]] - hCaM EF3 EF4 – NMR<br />
 
-
**[[2kxw]] – PtapoCaM + IQ motif of NAV1.2 – NMR<br />
 
-
**[[2m5e]] – PtCaM + Na channel protein<br />
 
-
**[[2kz2]], [[4bya]] – CaM (mutant) – chicken - NMR<br >
 
-
**[[2rrt]] – XlCaM (mutant) - NMR<br />
 
- 
-
* CaM+ cations (non calcium)
 
- 
-
**[[2ksz]] – sCaM N-terminal+Mg – NMR <br />
 
-
**[[1ak8]] - bCaM N-terminal+Ce – NMR<br />
 
-
**[[2pq3]] – rCaM+Zn<br />
 
-
**[[2v01]] – hCaM+Pb<br />
 
-
**[[2v02]] – hCaM+Ba<br />
 
-
**[[4bw7]] – hCaM + Sr<br />
 
-
**[[3uct]] – hCaM + Mn + Zn<br />
 
-
**[[3ucw]] - hCaM N-terminal + Mg<br />
 
-
**[[3ucy]] - hCaM N-terminal + Mg + Zn<br />
 
-
**[[1n0y]] – PtCaM+Pb <br />
 
-
**[[2lhh]] – yCaM + Ca - NMR
 
- 
-
* CaM small molecule complexes
 
- 
-
**[[3if7]] – bCaM+sphingosylphosphorylcholine<br />
 
-
**[[1qiv]], [[1qiw]] – bCaM+DPDv<br />
 
-
**[[1a29]], [[1lin]] – bCaM+trifluoperazine<br />
 
-
**[[1ctr]] - hCaM+trifluoperazine <br />
 
-
**[[2kug]], [[2kuh]] - hCaM N-terminal EF1 EF2+halothane – NMR<br />
 
-
**[[2kdu]] – XlCaM+MUNC13-1 – NMR<br />
 
-
**[[1mux]] – XlCaM+W-7 – NMR<br />
 
-
**[[1xa5]] – bCaM+KAR-2<br />
 
- 
-
* CaM complexed with protein CBD domains
 
- 
-
**[[3gp2]] – cCaM+CaM kinase II δ chain<br />
 
-
**[[2dfs]] – cCaM+myosin 5A<br />
 
-
**[[2o5g]] – cCaM+ myosin light chain kinase peptide<br />
 
-
**[[2bcx]] – cCaM+ryanodine receptor 1 peptide<br />
 
-
**[[3gof]], [[2o60]] – cCaM+nitric oxide synthase CBD<br />
 
-
**[[1niw]] - rCaM+nitric oxide synthase CBD <br />
 
-
**[[2hqw]] - rCaM+glutamate receptor peptide<br />
 
-
**[[3bxk]], [[3bxl]], [[4ehq]], [[4j9y]], [[4j9z]] – rCaM+ calcium channel peptide<br />
 
-
**[[1g4y]], [[3sjq]], [[4g27]], [[4g28]], [[4qnh]] - rCaM+ potassium channel CBD<br />
 
-
**[[2ygg]] – rCaM + Na/H exchanger CBD<br />
 
-
**[[2mgu]] – rCaM + HIV-1 matrix protein CBD – NMR<br />
 
-
**[[1qx7]] – rapoCaM+potassium channel peptide<br />
 
-
**[[5hit]] – cCaM + potassium channel peptide<br />
 
-
**[[5dbr]] – hCaM + sodium channel peptide<br />
 
-
**[[4gow]], [[4umo]], [[4v0c]] – hCaM + potassium channel peptide<br />
 
-
**[[3hr4]], [[2ll6]], [[2ll7]], [[5tp6]] - hCaM+nitric oxide synthase CBD <br />
 
-
**[[1yr5]], [[1wrz]], [[2y4v]] – hCaM+death-associated protein kinase 1 (DAP)<br />
 
-
**[[2l7l]] - hCaM+ CaM-dependent protein kinase 1 CBD<br />
 
-
**[[2m0j]], [[2m0k]] - hCaM+olfactory channel peptide<br />
 
-
**[[2kne]] – hCaM+PMCA C-terminal CBD<br />
 
-
**[[4upu]] - hCaM+ IP3 3-K CBD<br />
 
-
**[[3ewt]], [[3ewv]] – hCaM+TNFR fragment<br />
 
-
**[[2w73]], [[2jzi]], [[2r28]] – hCaM+Ser/Thr phosphatase CBD<br />
 
-
**[[3bya]] – hCaM+glutamate receptor peptide<br />
 
-
**[[3g43]], [[2vay]], [[2f3y]], [[2f3z]], [[2be6]], [[2lqc]], [[3oxq]] – hCaM+calcium channel CAV1.2<br />
 
-
**[[3dve]], [[3dvj]], [[3dvk]], [[3dvm]] - hCaM+calcium channel CAV2.2<br />
 
-
**[[5jth]], [[5jqa]] – hCaM + myosin light chain kinase peptide<br />
 
-
**[[2k0f]], [[2lv6]] – hCaM+myosin light chain kinase peptide – NMR<br />
 
-
**[[1zuz]] – hCaM+DRP kinase peptide<br />
 
-
**[[1l7z]] – hCaM+CAP-23/NAP-22 CBD<br />
 
-
**[[1cdl]] - hCaM+CaM dependent kinase CBD<br />
 
-
**[[1iwq]] - hCaM+MARCKS CBD<br />
 
-
**[[3sui]] – hCaM + capsaicin receptor peptide<br />
 
-
**[[2m55]] – hCaM + α-synuclein peptide<br />
 
-
**[[5nin]] – hCaM + A-kinase anchor peptide<br />
 
-
**[[5j8h]] - hCaM + elongation factor 2 kinase CBD – NMR<br />
 
-
**[[5dow]] - hCaM + chloride anion exchanger CBD <br />
 
-
**[[2lgf]] – hCaM + selectin peptide<br />
 
-
**[[2kn2]] – sCaM C-terminal+NtMKP1 CBD – NMR<br />
 
-
**[[1cff]] - XlCaM+ calcium channel CBD - NMR<br />
 
-
**[[1sy9]] – XlCaM+olfactory channel peptide<br />
 
-
**[[1nwd]] – XlCaM+glutamate decarboxylase CBD<br />
 
-
**[[1iq5]] – XlCaM+CaM dependent kinase CBD<br />
 
-
**[[1ckk]] - XlCaM+CaM dependent kinase CBD - NMR<br />
 
-
**[[2llo]], [[2llq]] – XlCaM EF-hand domain + estrogen receptor CBD – NMR<br />
 
-
**[[5t0x]] - XlCaM + estrogen receptor CBD – NMR<br />
 
-
**[[2mes]], [[5j7j]] – XlCaM +PSD95 peptide - NMR<br />
 
-
**[[2mg5]] - XlCaM+nitric oxide synthase peptide - NMR<br />
 
-
**[[2bbm]], [[2bbn]] - DmCaM+myosin light chain kinase peptide<br />
 
-
**[[1mxe]] – DmCaM+rCaMKI CBD <br />
 
-
**[[2fot]] - bCaM+α-II spectrin CBD<br />
 
-
**[[2f2o]], [[2f2p]] – bCaM+calcium<br />
 
-
**[[1xa5]] – bCaM+KAR-2<br />
 
-
**[[1cm1]], [[1cm4]], [[1cdm]] - bCaM+CaM dependent kinase CBD<br />
 
-
**[[4e50]] – mCam/linker/neurogranin IQ motif <br />
 
-
**[[4e53]] – mCam/linker/neuromoduin IQ motif <br />
 
-
**[[4aqr]] – AtCaM-7 + calcium-transporting ATPase peptide <br />
 
-
**[[5k8q]] – faCaM + STRA6 peptide – fall armyworm<br />
 
-
**[[2l1w]] – CaM + vacuolar calcium ATPase peptide – soybean – NMR<br />
 
- 
-
*Calmodulin complex with myosin
 
- 
-
**[[2vas]], [[2vb6]], [[3gn4]], [[3l9i]], [[4dbp]], [[4dbq]], [[2x51]], [[4anj]] – DmCaM + pMyosin IV<br />
 
-
**[[4pjj]] - DmCaM + pMyosin VI<br />
 
-
**[[3ek4]], [[3ek7]], [[3ek8]], [[3ekh]], [[3ekj]], [[3evr]], [[3evu]], [[3evv]], [[3o77]], [[3o78]] – CaM/DFP/myosin light chain kinase<br />
 
-
**[[2dfs]] – cCaM + myosin 5A<br />
 
-
**[[6bnv]] – cCaM + myosin 6 + actin<br />
 
-
**[[4l79]], [[4byf]], [[5v7x]] – hCaM + myosin 1B<br />
 
-
**[[6c1h]], [[6c1g]] – hCaM + myosin 1B + actin<br />
 
-
**[[6c1d]] – hCaM + myosin 1B + actin + phalloidin<br />
 
-
**[[5wsv]], [[5wsu]] – hCaM + myosin VII-A<br />
 
-
**[[5i0i]] – hCaM + myosin X<br />
 
-
**[[4zlk]] – mCaM + myosin VA<br />
 
-
**[[4r8g]] – rCaM + myosin 1B<br />
 
-
**[[2ix7]] – mCaM + myosin-5A<br />
 
-
**[[2bki]], [[2bkh]] – pCaM + myosin VI – pig<br />
 
- 
-
*Calmodulin complex with ion channels
 
- 
-
**[[4djc]], [[2l53]], [[4ovn]] - hCaM + sodium channel protein type V α subunit<br />
 
-
**[[4dck]], [[4jpz]] - hCaM + sodium channel protein type V α subunit + fibroblast growth factor 13<br />
 
-
**[[4jq0]] - hCaM + sodium channel protein type V α subunit + fibroblast growth factor 12<br />
 
-
**[[5k7l]] - hCaM + potassium channel EAG1 – Cryo EM <br />
 
-
**[[5j03]], [[6feh]], [[6feg]], [[6b8q]], [[6b8p]], [[6b8n]], [[6b8m]], [[6b8l]], [[5vms]] - hCaM + potassium channel subfamily KQT <br />
 
-
**[[5wc5]], [[5wbx]], [[5v03]], [[5v02]] – hCaM + potassium channel KCAT2.2 <br />
 
- 
-
*Calmodulin complex with other proteins
 
-
**[[2col]], [[1yrt]], [[1yru]] – BpCaM +a denyl cyclase – ''Bordetella pertussis''<br />
 
-
**[[1zot]] – BpCaM C-terminal+ adenyl cyclase<br />
 
-
**[[1xfu]], [[1xfv]], [[1xfw]], [[1xfx]], [[1xfy]], [[1xfz]], [[1y0v]], [[1sk6]], [[1pk0]], [[1lvc]], [[1k90]], [[1k93]] - CaM + adenyl cyclase – ''Bacillus anthracis''<br />
 
-
**[[3j41]] – hCaM + lens fiber major intrinsic protein – Cryo EM<br />
 
-
**[[1qs7]], [[1qtx]] – EcCaM + RS20 – ''Escherichia coli''<br />
 
-
**[[1vrk]] – EcCaM (mutant) + RS20<br />
 
-
**[[4ds7]] – CaM + spindle pole body component 10 – ''Kluyveromyces lactis''<br />
 
-
**[[2x0g]] – hCaM + death-associated protein kinase 1 (DAP)<br />
 
-
**[[2k3s]] – XlCaM + smoothelin-like protein 1 – NMR<br />
 
-
**[[4lzx]], [[4m1l]] - hCaM + IQ domain-containing protein G<br />
 
-
**[[4q57]] – hCaM N-terminal + plectin<br />
 
-
**[[4q5u]] – hCaM + calcineurin<br />
 
-
**[[5sy1]] – faCaM + STRA6 <br />
 
-
}}
 
==See Also==
==See Also==

Current revision

Human calmodulin complex with ethanol and Ca+2 ions (green) (PDB code 1cll)

Drag the structure with the mouse to rotate

See Also

Bibliography

  1. ↑ Chattopadhyaya R, Meador WE, Means AR, Quiocho FA. Calmodulin structure refined at 1.7 A resolution. J Mol Biol. 1992 Dec 20;228(4):1177-92. PMID:1474585
  2. ↑ Bertini I, Giachetti A, Luchinat C, Parigi G, Petoukhov MV, Pierattelli R, Ravera E, Svergun DI. Conformational Space of Flexible Biological Macromolecules from Average Data. J Am Chem Soc. 2010 Sep 7. PMID:20822180 doi:10.1021/ja1063923
  3. ↑ The Storymorph Jmol scripts creates the interpolated coordinates of the morph on the fly.
Retrieved from "http://52.214.119.220/wiki/index.php/Calmodulin"
Personal tools