2dyo: Difference between revisions

Latest revision as of 13:48, 13 March 2024

The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-57) complex

Structural highlights

2dyo is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.97Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ATG5_YEAST Involved in cytoplasm to vacuole transport (Cvt) and autophagy vesicles formation. Required for ATG8 association to the vesicle membranes.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Kametaka S, Matsuura A, Wada Y, Ohsumi Y. Structural and functional analyses of APG5, a gene involved in autophagy in yeast. Gene. 1996 Oct 31;178(1-2):139-43. PMID:8921905
↑ Tsukada M, Ohsumi Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett. 1993 Oct 25;333(1-2):169-74. PMID:8224160
↑ Mizushima N, Noda T, Yoshimori T, Tanaka Y, Ishii T, George MD, Klionsky DJ, Ohsumi M, Ohsumi Y. A protein conjugation system essential for autophagy. Nature. 1998 Sep 24;395(6700):395-8. PMID:9759731 doi:10.1038/26506
↑ Mizushima N, Noda T, Ohsumi Y. Apg16p is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway. EMBO J. 1999 Jul 15;18(14):3888-96. PMID:10406794 doi:10.1093/emboj/18.14.3888
↑ George MD, Baba M, Scott SV, Mizushima N, Garrison BS, Ohsumi Y, Klionsky DJ. Apg5p functions in the sequestration step in the cytoplasm-to-vacuole targeting and macroautophagy pathways. Mol Biol Cell. 2000 Mar;11(3):969-82. PMID:10712513
↑ Kim J, Huang WP, Klionsky DJ. Membrane recruitment of Aut7p in the autophagy and cytoplasm to vacuole targeting pathways requires Aut1p, Aut2p, and the autophagy conjugation complex. J Cell Biol. 2001 Jan 8;152(1):51-64. PMID:11149920

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kametaka S, Matsuura A, Wada Y, Ohsumi Y. Structural and functional analyses of APG5, a gene involved in autophagy in yeast. Gene. 1996 Oct 31;178(1-2):139-43. PMID:8921905

[2] Tsukada M, Ohsumi Y. Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett. 1993 Oct 25;333(1-2):169-74. PMID:8224160

[3] Mizushima N, Noda T, Yoshimori T, Tanaka Y, Ishii T, George MD, Klionsky DJ, Ohsumi M, Ohsumi Y. A protein conjugation system essential for autophagy. Nature. 1998 Sep 24;395(6700):395-8. PMID:9759731 doi:10.1038/26506

[4] Mizushima N, Noda T, Ohsumi Y. Apg16p is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway. EMBO J. 1999 Jul 15;18(14):3888-96. PMID:10406794 doi:10.1093/emboj/18.14.3888

[5] George MD, Baba M, Scott SV, Mizushima N, Garrison BS, Ohsumi Y, Klionsky DJ. Apg5p functions in the sequestration step in the cytoplasm-to-vacuole targeting and macroautophagy pathways. Mol Biol Cell. 2000 Mar;11(3):969-82. PMID:10712513

[6] Kim J, Huang WP, Klionsky DJ. Membrane recruitment of Aut7p in the autophagy and cytoplasm to vacuole targeting pathways requires Aut1p, Aut2p, and the autophagy conjugation complex. J Cell Biol. 2001 Jan 8;152(1):51-64. PMID:11149920

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@@ Line 1: / Line 1: @@
-[[Image:2dyo.png|left|200px]]
-<!--
+==The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-57) complex==
-The line below this paragraph, containing "STRUCTURE_2dyo", creates the "Structure Box" on the page.
+<StructureSection load='2dyo' size='340' side='right'caption='[[2dyo]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2dyo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DYO FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.97&#8491;</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=2dyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dyo OCA], [https://pdbe.org/2dyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dyo RCSB], [https://www.ebi.ac.uk/pdbsum/2dyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dyo ProSAT]</span></td></tr>
-{{STRUCTURE_2dyo|  PDB=2dyo  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ATG5_YEAST ATG5_YEAST] Involved in cytoplasm to vacuole transport (Cvt) and autophagy vesicles formation. Required for ATG8 association to the vesicle membranes.<ref>PMID:8921905</ref> <ref>PMID:8224160</ref> <ref>PMID:9759731</ref> <ref>PMID:10406794</ref> <ref>PMID:10712513</ref> <ref>PMID:11149920</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dy/2dyo_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dyo ConSurf].
+<div style="clear:both"></div>
-===The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-57) complex===
+==See Also==
+*[[Autophagy-related protein 3D structures|Autophagy-related protein 3D structures]]
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_17192262}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 17192262 is the PubMed ID number.
+</StructureSection>
--->
+[[Category: Large Structures]]
-{{ABSTRACT_PUBMED_17192262}}
-==About this Structure==
-[[2dyo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYO OCA].
-==Reference==
-<ref group="xtra">PMID:17192262</ref><ref group="xtra">PMID:17012802</ref><references group="xtra"/>
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Inagaki, F.]]
+[[Category: Inagaki F]]
-[[Category: Matsushita, M.]]
+[[Category: Matsushita M]]
-[[Category: Suzuki, N N.]]
+[[Category: Suzuki NN]]
-[[Category: Herix-bundle]]
-[[Category: Protein turnover/protein turnover complex]]
-[[Category: Ubiquitin-fold]]

2dyo: Difference between revisions

Latest revision as of 13:48, 13 March 2024

The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-57) complex

Structural highlights

Function

Evolutionary Conservation

See Also

References

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Proteopedia Page Contributors and Editors (what is this?)

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