7brq: Difference between revisions

Latest revision as of 15:28, 29 November 2023

Crystal structure of human FAM134B LIR fused to human GABARAP

Structural highlights

7brq is a 1 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 1.404Å
Ligands:	GOL
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

RETR1_HUMAN Hereditary sensory and autonomic neuropathy type 2. The disease is caused by mutations affecting the gene represented in this entry.

Function

GBRAP_HUMAN May play a role in intracellular transport of GABA(A) receptors and its interaction with the cytoskeleton. Involved in apoptosis. Involved in autophagy (By similarity).^[1] RETR1_HUMAN Endoplasmic reticulum-anchored autophagy receptor that mediates ER delivery into lysosomes through sequestration into autophagosomes (PubMed:26040720). Promotes membrane remodeling and ER scission via its membrane bending capacity and targets the fragments into autophagosomes via interaction with ATG8 family proteins (PubMed:26040720). Required for long-term survival of nociceptive and autonomic ganglion neurons (PubMed:19838196, PubMed:26040720).^[2] ^[3]

Publication Abstract from PubMed

The endoplasmic reticulum (ER) is selectively degraded by autophagy (ER-phagy) through proteins called ER-phagy receptors. In Saccharomyces cerevisiae, Atg40 acts as an ER-phagy receptor to sequester ER fragments into autophagosomes by binding Atg8 on forming autophagosomal membranes. During ER-phagy, parts of the ER are morphologically rearranged, fragmented, and loaded into autophagosomes, but the mechanism remains poorly understood. Here we find that Atg40 molecules assemble in the ER membrane concurrently with autophagosome formation via multivalent interaction with Atg8. Atg8-mediated super-assembly of Atg40 generates highly-curved ER regions, depending on its reticulon-like domain, and supports packing of these regions into autophagosomes. Moreover, tight binding of Atg40 to Atg8 is achieved by a short helix C-terminal to the Atg8-family interacting motif, and this feature is also observed for mammalian ER-phagy receptors. Thus, this study significantly advances our understanding of the mechanisms of ER-phagy and also provides insights into organelle fragmentation in selective autophagy of other organelles.

Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes.,Mochida K, Yamasaki A, Matoba K, Kirisako H, Noda NN, Nakatogawa H Nat Commun. 2020 Jul 3;11(1):3306. doi: 10.1038/s41467-020-17163-y. PMID:32620754^[4]

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

References

↑ Lee JH, Rho SB, Chun T. GABAA receptor-associated protein (GABARAP) induces apoptosis by interacting with DEAD (Asp-Glu-Ala-Asp/His) box polypeptide 47 (DDX 47). Biotechnol Lett. 2005 May;27(9):623-8. PMID:15977068 doi:https://dx.doi.org/10.1007/s10529-005-3628-2
↑ Kurth I, Pamminger T, Hennings JC, Soehendra D, Huebner AK, Rotthier A, Baets J, Senderek J, Topaloglu H, Farrell SA, Nurnberg G, Nurnberg P, De Jonghe P, Gal A, Kaether C, Timmerman V, Hubner CA. Mutations in FAM134B, encoding a newly identified Golgi protein, cause severe sensory and autonomic neuropathy. Nat Genet. 2009 Nov;41(11):1179-81. doi: 10.1038/ng.464. Epub 2009 Oct 18. PMID:19838196 doi:https://dx.doi.org/10.1038/ng.464
↑ Khaminets A, Heinrich T, Mari M, Grumati P, Huebner AK, Akutsu M, Liebmann L, Stolz A, Nietzsche S, Koch N, Mauthe M, Katona I, Qualmann B, Weis J, Reggiori F, Kurth I, Hubner CA, Dikic I. Regulation of endoplasmic reticulum turnover by selective autophagy. Nature. 2015 Jun 3. doi: 10.1038/nature14498. PMID:26040720 doi:https://dx.doi.org/10.1038/nature14498
↑ Mochida K, Yamasaki A, Matoba K, Kirisako H, Noda NN, Nakatogawa H. Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes. Nat Commun. 2020 Jul 3;11(1):3306. doi: 10.1038/s41467-020-17163-y. PMID:32620754 doi:https://dx.doi.org/10.1038/s41467-020-17163-y

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OCA

[1] Lee JH, Rho SB, Chun T. GABAA receptor-associated protein (GABARAP) induces apoptosis by interacting with DEAD (Asp-Glu-Ala-Asp/His) box polypeptide 47 (DDX 47). Biotechnol Lett. 2005 May;27(9):623-8. PMID:15977068 doi:https://dx.doi.org/10.1007/s10529-005-3628-2

[2] Kurth I, Pamminger T, Hennings JC, Soehendra D, Huebner AK, Rotthier A, Baets J, Senderek J, Topaloglu H, Farrell SA, Nurnberg G, Nurnberg P, De Jonghe P, Gal A, Kaether C, Timmerman V, Hubner CA. Mutations in FAM134B, encoding a newly identified Golgi protein, cause severe sensory and autonomic neuropathy. Nat Genet. 2009 Nov;41(11):1179-81. doi: 10.1038/ng.464. Epub 2009 Oct 18. PMID:19838196 doi:https://dx.doi.org/10.1038/ng.464

[3] Khaminets A, Heinrich T, Mari M, Grumati P, Huebner AK, Akutsu M, Liebmann L, Stolz A, Nietzsche S, Koch N, Mauthe M, Katona I, Qualmann B, Weis J, Reggiori F, Kurth I, Hubner CA, Dikic I. Regulation of endoplasmic reticulum turnover by selective autophagy. Nature. 2015 Jun 3. doi: 10.1038/nature14498. PMID:26040720 doi:https://dx.doi.org/10.1038/nature14498

[4] Mochida K, Yamasaki A, Matoba K, Kirisako H, Noda NN, Nakatogawa H. Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes. Nat Commun. 2020 Jul 3;11(1):3306. doi: 10.1038/s41467-020-17163-y. PMID:32620754 doi:https://dx.doi.org/10.1038/s41467-020-17163-y

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[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='7brq' size='340' side='right'caption='[[7brq]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7brq]] is a 1 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=7BRQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BRQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7brq]] is a 1 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=7BRQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BRQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.404&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[7brn|7brn]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GABARAP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=7brq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7brq OCA], [https://pdbe.org/7brq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7brq RCSB], [https://www.ebi.ac.uk/pdbsum/7brq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7brq ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7brq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7brq OCA], [http://pdbe.org/7brq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7brq RCSB], [http://www.ebi.ac.uk/pdbsum/7brq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7brq ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/RETR1_HUMAN RETR1_HUMAN]] Hereditary sensory and autonomic neuropathy type 2. The disease is caused by mutations affecting the gene represented in this entry.
+[https://www.uniprot.org/uniprot/RETR1_HUMAN RETR1_HUMAN] Hereditary sensory and autonomic neuropathy type 2. The disease is caused by mutations affecting the gene represented in this entry.
 == Function ==
-[[http://www.uniprot.org/uniprot/RETR1_HUMAN RETR1_HUMAN]] Endoplasmic reticulum-anchored autophagy receptor that mediates ER delivery into lysosomes through sequestration into autophagosomes (PubMed:26040720). Promotes membrane remodeling and ER scission via its membrane bending capacity and targets the fragments into autophagosomes via interaction with ATG8 family proteins (PubMed:26040720). Required for long-term survival of nociceptive and autonomic ganglion neurons (PubMed:19838196, PubMed:26040720).<ref>PMID:19838196</ref> <ref>PMID:26040720</ref>
+[https://www.uniprot.org/uniprot/GBRAP_HUMAN GBRAP_HUMAN] May play a role in intracellular transport of GABA(A) receptors and its interaction with the cytoskeleton. Involved in apoptosis. Involved in autophagy (By similarity).<ref>PMID:15977068</ref> [https://www.uniprot.org/uniprot/RETR1_HUMAN RETR1_HUMAN] Endoplasmic reticulum-anchored autophagy receptor that mediates ER delivery into lysosomes through sequestration into autophagosomes (PubMed:26040720). Promotes membrane remodeling and ER scission via its membrane bending capacity and targets the fragments into autophagosomes via interaction with ATG8 family proteins (PubMed:26040720). Required for long-term survival of nociceptive and autonomic ganglion neurons (PubMed:19838196, PubMed:26040720).<ref>PMID:19838196</ref> <ref>PMID:26040720</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 </div>
 <div class="pdbe-citations 7brq" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[GABA receptor-associated protein 3D structures|GABA receptor-associated protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Noda, N N]]
+[[Category: Noda NN]]
-[[Category: Yamasaki, A]]
+[[Category: Yamasaki A]]
-[[Category: Autophagy]]
-[[Category: Endoplasmic reticulum]]
-[[Category: Membrane protein]]

7brq: Difference between revisions

Latest revision as of 15:28, 29 November 2023

Crystal structure of human FAM134B LIR fused to human GABARAP

Structural highlights

Disease

Function

Publication Abstract from PubMed

See Also

References

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