6k67

From Proteopedia

(Difference between revisions)

Current revision

Application of anti-helix antibodies in protein structure determination (9011-3LRH)

Structural highlights

6k67 is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

CALM3_HUMAN Catecholaminergic polymorphic ventricular tachycardia;Romano-Ward syndrome. The disease may be caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry.

Function

CALM3_HUMAN Calmodulin acts as part of a calcium signal transduction pathway by mediating the control of a large number of enzymes, ion channels, aquaporins and other proteins through calcium-binding (PubMed:16760425, PubMed:31454269). Calcium-binding is required for the activation of calmodulin (PubMed:35568036, PubMed:16760425, PubMed:31454269). Among the enzymes to be stimulated by the calmodulin-calcium complex are a number of protein kinases, such as myosin light-chain kinases and calmodulin-dependent protein kinase type II (CaMK2), and phosphatases (PubMed:16760425, PubMed:35568036). Together with CCP110 and centrin, is involved in a genetic pathway that regulates the centrosome cycle and progression through cytokinesis (PubMed:16760425).^[1] ^[2] ^[3] (Microbial infection) Required for C.violaceum CopC arginine ADP-riboxanase activity.^[4] ^[5]

Publication Abstract from PubMed

Antibodies are indispensable tools in protein engineering and structural biology. Antibodies suitable for structural studies should recognize the 3-dimensional (3D) conformations of target proteins. Generating such antibodies and characterizing their complexes with antigens take a significant amount of time and effort. Here, we show that we can expand the application of well-characterized antibodies by "transplanting" the epitopes that they recognize to proteins with completely different structures and sequences. Previously, several antibodies have been shown to recognize the alpha-helical conformation of antigenic peptides. We demonstrate that these antibodies can be made to bind to a variety of unrelated "off-target" proteins by modifying amino acids in the preexisting alpha helices of such proteins. Using X-ray crystallography, we determined the structures of the engineered protein-antibody complexes. All of the antibodies bound to the epitope-transplanted proteins, forming accurately predictable structures. Furthermore, we showed that binding of these antihelix antibodies to the engineered target proteins can modulate their catalytic activities by trapping them in selected functional states. Our method is simple and efficient, and it will have applications in protein X-ray crystallography, electron microscopy, and nanotechnology.

Application of antihelix antibodies in protein structure determination.,Kim JW, Kim S, Lee H, Cho G, Kim SC, Lee H, Jin MS, Lee JO Proc Natl Acad Sci U S A. 2019 Aug 1. pii: 1910080116. doi:, 10.1073/pnas.1910080116. PMID:31371498^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Tsang WY, Spektor A, Luciano DJ, Indjeian VB, Chen Z, Salisbury JL, Sanchez I, Dynlacht BD. CP110 cooperates with two calcium-binding proteins to regulate cytokinesis and genome stability. Mol Biol Cell. 2006 Aug;17(8):3423-34. Epub 2006 Jun 7. PMID:16760425 doi:10.1091/mbc.E06-04-0371
↑ Wren LM, Jimenez-Jaimez J, Al-Ghamdi S, Al-Aama JY, Bdeir A, Al-Hassnan ZN, Kuan JL, Foo RY, Potet F, Johnson CN, Aziz MC, Carvill GL, Kaski JP, Crotti L, Perin F, Monserrat L, Burridge PW, Schwartz PJ, Chazin WJ, Bhuiyan ZA, George AL Jr. Genetic Mosaicism in Calmodulinopathy. Circ Genom Precis Med. 2019 Sep;12(9):375-385. doi: 10.1161/CIRCGEN.119.002581. , Epub 2019 Aug 27. PMID:31454269 doi:http://dx.doi.org/10.1161/CIRCGEN.119.002581
↑ Alphonse N, Wanford JJ, Voak AA, Gay J, Venkhaya S, Burroughs O, Mathew S, Lee T, Evans SL, Zhao W, Frowde K, Alrehaili A, Dickenson RE, Munk M, Panina S, Mahmood IF, Llorian M, Stanifer ML, Boulant S, Berchtold MW, Bergeron JRC, Wack A, Lesser CF, Odendall C. A family of conserved bacterial virulence factors dampens interferon responses by blocking calcium signaling. Cell. 2022 Jun 23;185(13):2354-2369.e17. doi: 10.1016/j.cell.2022.04.028. Epub , 2022 May 13. PMID:35568036 doi:http://dx.doi.org/10.1016/j.cell.2022.04.028
↑ Peng T, Tao X, Xia Z, Hu S, Xue J, Zhu Q, Pan X, Zhang Q, Li S. Pathogen hijacks programmed cell death signaling by arginine ADPR-deacylization of caspases. Mol Cell. 2022 May 19;82(10):1806-1820.e8. doi: 10.1016/j.molcel.2022.03.010. , Epub 2022 Mar 25. PMID:35338844 doi:http://dx.doi.org/10.1016/j.molcel.2022.03.010
↑ Liu Y, Zeng H, Hou Y, Li Z, Li L, Song X, Ding J, Shao F, Xu Y. Calmodulin Binding Activates Chromobacterium CopC Effector to ADP-Riboxanate Host Apoptotic Caspases. mBio. 2022 Jun 28;13(3):e0069022. doi: 10.1128/mbio.00690-22. Epub 2022 Apr 21. PMID:35446120 doi:http://dx.doi.org/10.1128/mbio.00690-22
↑ Kim JW, Kim S, Lee H, Cho G, Kim SC, Lee H, Jin MS, Lee JO. Application of antihelix antibodies in protein structure determination. Proc Natl Acad Sci U S A. 2019 Aug 1. pii: 1910080116. doi:, 10.1073/pnas.1910080116. PMID:31371498 doi:http://dx.doi.org/10.1073/pnas.1910080116

1 Structural highlights
2 Disease
3 Function
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6k67"

@@ Line 3: / Line 3: @@
 <StructureSection load='6k67' size='340' side='right'caption='[[6k67]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6k67]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K67 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K67 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6k67]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K67 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K67 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6k67 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k67 OCA], [http://pdbe.org/6k67 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k67 RCSB], [http://www.ebi.ac.uk/pdbsum/6k67 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k67 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6k67 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k67 OCA], [https://pdbe.org/6k67 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k67 RCSB], [https://www.ebi.ac.uk/pdbsum/6k67 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k67 ProSAT]</span></td></tr>
 </table>
+== Disease ==
+[https://www.uniprot.org/uniprot/CALM3_HUMAN CALM3_HUMAN] Catecholaminergic polymorphic ventricular tachycardia;Romano-Ward syndrome. The disease may be caused by variants affecting the gene represented in this entry.  The disease is caused by variants affecting the gene represented in this entry.
+== Function ==
+[https://www.uniprot.org/uniprot/CALM3_HUMAN CALM3_HUMAN] Calmodulin acts as part of a calcium signal transduction pathway by mediating the control of a large number of enzymes, ion channels, aquaporins and other proteins through calcium-binding (PubMed:16760425, PubMed:31454269). Calcium-binding is required for the activation of calmodulin (PubMed:35568036, PubMed:16760425, PubMed:31454269). Among the enzymes to be stimulated by the calmodulin-calcium complex are a number of protein kinases, such as myosin light-chain kinases and calmodulin-dependent protein kinase type II (CaMK2), and phosphatases (PubMed:16760425, PubMed:35568036). Together with CCP110 and centrin, is involved in a genetic pathway that regulates the centrosome cycle and progression through cytokinesis (PubMed:16760425).<ref>PMID:16760425</ref> <ref>PMID:31454269</ref> <ref>PMID:35568036</ref>   (Microbial infection) Required for C.violaceum CopC arginine ADP-riboxanase activity.<ref>PMID:35338844</ref> <ref>PMID:35446120</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 16: / Line 21: @@
 </div>
 <div class="pdbe-citations 6k67" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Antibody 3D structures|Antibody 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Cho, G Y]]
+[[Category: Cho GY]]
-[[Category: Jin, M S]]
+[[Category: Jin MS]]
-[[Category: Kim, J W]]
+[[Category: Kim JW]]
-[[Category: Kim, S]]
+[[Category: Kim S]]
-[[Category: Lee, H]]
+[[Category: Lee H]]
-[[Category: Lee, J O]]
+[[Category: Lee JO]]
-[[Category: Antibody]]
-[[Category: Protein design]]
-[[Category: Structural protein]]

6k67

From Proteopedia

Current revision

Application of anti-helix antibodies in protein structure determination (9011-3LRH)

Structural highlights

Disease

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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