Calmodulin

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[[Image:1prw.png|left|200px|thumb|Crystal structure of bovine brain Ca++ calmodulin in a compact form, [[1prw]]]]
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<StructureSection load='1cll' size='350' side='right' scene='39/398280/Cv/3' caption='Human calmodulin complex with ethanol and Ca+2 ions (green) (PDB code [[1cll]])'>
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{{STRUCTURE_1prw| PDB=1prw | SIZE=300| SCENE=Calmodulin/Cv/2 |right|CAPTION=Bovine calmodulin showing Ca+2 with trimethyl lysine, [[1prw]] }}
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__TOC__
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==Function==
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[[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]].
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[[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.
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The images at the left and at the right correspond to one representative calmodulin, ''i.e.'' crystal structure of bovine brain Ca++ calmodulin in a compact form ([[1prw]]).
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{{TOC limit|limit=2}}
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{{Clear}}
{{Clear}}
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== Calmodulin in Motion ==
== Calmodulin in Motion ==
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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).
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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]].
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<center><swf width="720" height="576">/flash/Apo_CaM_CaCaM.swf</swf></center>
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<jmol>
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<jmolButton>
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<script>
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script "/wiki/images/a/a2/Storymorph.spt";
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load files "=1prw" "=1cll";
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delete water;
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delete protein and not backbone;
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select all;cartoon only;cartoon off;
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select 4-147;cartoon on;
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model 1;
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center visible;color group;
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compare {2.1} {1.1} SUBSET{*.CA} ATOMS{4-138}{4-138} ROTATE TRANSLATE;
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</script>
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<text>Prepare Animation</text>
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</jmolButton>
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</jmol><jmol>
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<jmolButton>
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<script>
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model 2;
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display 4-147;
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backbone only;
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backbone 0.5
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structures = [{1.1}, {2.1}];
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my_recipe = [
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[{79-147},{79-147}, {(79-138) and alpha}],
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[{4-78}, {79}, {(8-78) and alpha}],
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];
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morph(20, structures, my_recipe);
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</script>
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<text>Open</text>
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</jmolButton>
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</jmol><jmol>
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<jmolButton>
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<script>
 +
model 1
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display 4-147;
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backbone only;
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backbone 0.5
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structures = [{2.1}, {1.1}];
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my_recipe = [
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[{79-147},{79-147}, {(79-138) and alpha}],
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[{4-78}, {79}, {(8-78) and alpha}],
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];
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morph(20, structures, my_recipe);
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</script>
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<text>Close</text>
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</jmolButton>
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</jmol>
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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.
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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.
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<jmol>
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<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}],
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[{4-78}, {79}, {(8-78) and alpha}],
 +
];
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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>
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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).
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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.
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<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>
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This movie was created by Andrei, Zini et al., of the
 
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[http://www.scivis.ifc.cnr.it Scientific Visualization Unit],
 
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Institute of Clinical Physiology - CNR of Itlay.
 
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[http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b097743-28520 Conformational change of Calmodulin]
 
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<applet load='1cll' size='350' color='white' frame='true' align='right' caption='Calmodulin showing Ca+2 ions' scene='Calmodulin/Inicio/1' />
 
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<scene name='Calmodulin/Inicio/1'>Unbound</scene>,
 
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<scene name='Calmodulin/Bound/4'>Bound</scene>
 
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{{Clear}}
 
== 3D Structures of Calmodulin ==
== 3D Structures of Calmodulin ==
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[[Calmodulin 3D structures]]
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''Update November 2011''
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</StructureSection>
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=== Native CaM ===
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[[1prw]], [[1deg]] – bCaM - bovine<br />
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[[1up5]] – cCaM – chicken<br />
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[[1clm]], [[1osa]], [[1exr]] – PtCaM - ''Paramecium tetraurelia''<br />
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[[3cln]] – rCaM - rat<br />
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[[1x02]], [[1dmo]] – XlCaM – NMR - ''Xenopus laevis''<br />
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[[2k61]], [[2k0e]] – hCaM – NMR - human<br />
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[[1y6w]], [[1cll]] - hCaM<br />
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[[4cln]] – DmCaM - ''Drosophila melanogaster''<br />
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[[1rfj]] – CaM – potato<br />
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[[1ooj]] – CaM – ''Caenorhabditis elegans''<br />
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=== Mutant CaM ===
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[[1ahr]] – cCaM (mutant)<br />
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[[2k0j]], [[1sw8]] – hCaM (mutant) – NMR<br />
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=== apo CaM ===
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[[1lkj]] – yapoCaM – NMR -yeast<br />
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[[1cfc]], [[1cfd]] - XlapoCaM – NMR<br />
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[[1qx5]] – rapoCaM – rat<br />
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=== CaM N-terminal ===
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[[2i08]] - hCaM N-terminal (mutant)<br />
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[[1j7o]], [[1j7p]] - hCaM N-terminal – NMR<br />
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[[1f70]] - XlCaM N-terminal – NMR <br />
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[[2ro8]], [[2roa]] - sCaM N-terminal+Ca – NMR - soybean<br />
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[[2ro9]], [[2rob]] - sCaM C-terminal+Ca – NMR<br />
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[[3ifk]], [[3b32]] – rCaM N-terminal <br />
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[[1f54]], [[1f55]] – yapoCaM N-terminal – NMR<br />
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=== CaM C-terminal ===
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[[1f71]] - XlCaM C-terminal – NMR<br />
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[[1cmg]] – bCaM C-terminal – NMR<br />
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[[1fw4]] - bCaM C-terminal<br />
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[[1cmf]] – bapoCaM C-terminal – NMR<br />
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[[2hf5]] - hCaM EF2 EF3 – NMR<br />
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[[2kxw]] – PtapoCaM + IQ motif of NAV1.2 – NMR<br />
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[[2kz2]] – CaM (mutant) – chicken<br >
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[[2rrt]] – XlCaM (mutant)
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=== CaM+ cations (not calcium) ===
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[[2ksz]] – sCaM N-terminal+Mg – NMR <br />
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[[1ak8]] - bCaM N-terminal+Ce – NMR<br />
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[[2eqc]] – XlCaM C-terminal+Mg– NMR<br />
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[[2pq3]] – rCaM+Zn<br />
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[[2v01]] – hCaM+Pb<br />
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[[2v02]] – hCaM+Ba<br />
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[[1n0y]] – PtCaM+Pb <br />
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=== CaM small molecule complexes ===
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[[3if7]] – bCaM+sphingosylphosphorylcholine<br />
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[[1qiv]], [[1qiw]] – bCaM+DPDv<br />
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[[1a29]], [[1lin]] – bCaM+trifluoperazine<br />
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[[1ctr]] - hCaM+trifluoperazine <br />
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[[2kug]], [[2kuh]] - hCaM N-terminal EF1 EF2+halothane – NMR<br />
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[[2kdu]] – XlCaM+MUNC13-1 – NMR<br />
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[[1mux]] – XlCaM+W-7 – NMR<br />
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=== CaM complexed with protein CBD domains ===
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[[3gp2]] – cCaM+CaM kinase II δ chain<br />
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[[2dfs]] – cCaM+myosin 5A<br />
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[[2o5g]] – cCaM+ myosin light chain kinase peptide<br />
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[[2bcx]] – cCaM+ryanodine receptor 1 peptide<br />
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[[3gof]], [[2o60]] – cCaM+nitric oxide synthase CBD<br />
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[[1niw]] - rCaM+nitric oxide synthase CBD <br />
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[[2hqw]] - rCaM+glutamate receptor peptide<br />
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[[3bxk]], [[3bxl]] – rCaM+ calcium channel peptide<br />
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[[1g4y]] - rCaM+ potassium channel CBD<br />
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[[2ygg]] – rCaM + Na/H exchanger CBD<br />
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[[1qx7]] – rapoCaM+potassium channel peptide<br />
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[[3hr4]] - hCaM+nitric oxide synthase CBD <br />
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[[2x0g]], [[1yr5]], [[1wrz]] – hCaM+death-associated protein kinase 1 (DAP)<br />
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[[2kne]] – hCaM+PMCA C-terminal CBD<br />
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[[3ewt]], [[3ewv]] – hCaM+TNFR fragment<br />
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[[2w73]], [[2jzi]], [[2r28]] – hCaM+Ser/Thr phosphatase CBD<br />
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[[3bya]] – hCaM+glutamate receptor peptide<br />
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[[3g43]], [[2vay]], [[2f3y]], [[2f3z]], [[2be6]] – hCaM+calcium channel CAV1.2<br />
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[[3dve]], [[3dvj]], [[3dvk]], [[3dvm]] - hCaM+calcium channel CAV2.2<br />
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[[2k0f]] – hCaM+myosin light chain kinase peptide – NMR<br />
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[[1zuz]] – hCaM+DRP kinase peptide<br />
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[[1l7z]] – hCaM+CAP-23/NAP-22 CBD<br />
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[[1cdl]] - hCaM+CaM dependent kinase CBD<br />
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[[1iwq]] - hCaM+MARCKS CBD<br />
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[[2kn2]] – sCaM C-terminal+NtMKP1 CBD – NMR<br />
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[[2x51]] – DmCaM+pMyosin IV<br />
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[[2k3s]] – CaM+smoothelin-like protein 1 – NMR<br />
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[[1cff]] - XlCaM+ calcium channel CBD - NMR<br />
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[[1sy9]] – XlCaM+olfactory channel peptide<br />
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[[1nwd]] – XlCaM+glutamate decarboxylase CBD<br />
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[[1iq5]] – XlCaM+CaM dependent kinase CBD<br />
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[[1ckk]] - XlCaM+CaM dependent kinase CBD - NMR<br />
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[[2ix7]] – apoCaM+myosin-5A<br />
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[[2bbm]], [[2bbn]] - DmCaM+myosin light chain kinase <br />
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[[1mxe]] – DmCaM+rCaMKI CBD <br />
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[[2vas]], [[2vb6]], [[3gn4]], [[3l9i]] – DmCaM+myosin VI<br />
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[[2bki]], [[2bkh]] – CaM+myosin VI – pig<br />
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[[2fot]] - bCaM+α-II spectrin CBD<br />
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[[2f2o]], [[2f2p]] – bCaM+calcineurin CBD<br />
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[[1xa5]] – bCaM+KAR-2<br />
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[[1cm1]], [[1cm4]], [[1cdm]] - bCaM+CaM dependent kinase CBD<br />
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[[2col]], [[1yrt]], [[1yru]] – BpCaM+adenyl cyclase – ''Bordetella pertussis''<br />
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[[1zot]] – BpCaM C-terminal+adenyl cyclase<br />
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[[1xfu]], [[1xfv]], [[1xfw]], [[1xfx]], [[1xfy]], [[1xfz]], [[1y0v]], [[1sk6]], [[1pk0]], [[1lvc]], [[1k90]], [[1k93]] - CaM+adenyl cyclase – ''Bacillus anthracis''<br />
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[[2l1w]] – CaM+vacuolar calcium ATPase peptide – soybean – NMR<br />
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[[3oxq]] – hCaM + calcium channel Cav1.2<br />
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[[1qs7]], [[1qtx]] – CaM+RS20 – ''Escherichia coli''<br />
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[[1vrk]] – CaM (mutant)+RS20<br />
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[[3ek4]], [[3ek7]], [[3ek8]], [[3ekh]], [[3ekj]], [[3evr]], [[3evu]], [[3evv]], [[3o77]], [[3o78]] – CaM/DFP/myosin light chain kinase
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==See Also==
==See Also==
Line 177: Line 177:
* [http://en.wikipedia.org/wiki/Calmodulin Calmodulin at Wikipedia]
* [http://en.wikipedia.org/wiki/Calmodulin Calmodulin at Wikipedia]
* [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb44_1.html Molecule of the Month (08/2003) at RCSB PDB]
* [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb44_1.html Molecule of the Month (08/2003) at RCSB PDB]
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*{{Proteopedia|2fot}} page for Calmodulin crystal complex between calmodulin and alpha11-[[spectrin]]
 
== Bibliography ==
== Bibliography ==

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.
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