The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
The crystal structure of microtubule‐associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8
Abstract
Microtubule‐associated protein light chain 3 (LC3), a mammalian homologue of yeast Atg8, plays an essential role in autophagy, which is involved in the bulk degradation of cytoplasmic components by the lysosomal system. Here, we report the crystal structure of LC3 at 2.05 Å resolution with an R‐factor of 21.8% and a free R‐factor of 24.9%. The structure of LC3, which is similar to those of Golgi‐associated ATPase enhancer of 16 kDa (GATE‐16) and GABA A receptor‐associated protein (GABARAP), contains a ubiquitin core with two α helices, α1 and α2, attached at its N‐terminus. Some common and distinct features are observed among these proteins, including the conservation of residues required to form an interaction among α1, α2 and the ubiquitin core. However, the electrostatic potential surfaces of these helices differ, implicating particular roles to select specific binding partners. Hydrophobic patches on the ubiquitin core of LC3, GABARAP and GATE‐16 are well conserved and are similar to the E1 binding surface of ubiquitin and NEDD8. Therefore, we propose that the hydrophobic patch is a binding surface for mammalian Atg7 similar to a ubiquitin‐like conjugation system. We also propose the functional implications of the ubiquitin fold as a recognition module of target proteins.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The mammalian Atg8 homologs share from 29% to 94% sequence identity with the yeast protein and have all been demonstrated to be involved in autophagosome biogenesis.
“The mammalian Atg8 homologs share from 29% to 94% sequence identity with the yeast protein and have all been demonstrated to be involved in autophagosome biogenesis [200].”
From Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition) 1 (2021) · cites this paper as [200]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing.
Kabeya, Y., Mizushima, N., Ueno, T., Yamamoto, A., Kirisako, T., Noda, T., Kominami, E., Ohsumi, Y., & Yoshimori, T. (2000) · The EMBO Journal · doi:10.1093/emboj/19.21.5720 · Cited by 6,605
Self-citationMolecular dissection of autophagy: two ubiquitin-like systems
Ohsumi, Y. (2001) · Nature Reviews Molecular Cell Biology · doi:10.1038/35056522 · Cited by 1,240 · cited 1×
“Among them, four Atg proteins, namely Atg3, Atg4, Atg7 and Atg8, were shown to be involved in a novel ubiquitin-like conjugation system that mediates protein lipidation (Ohsumi 2001; Ichimura et al. 2000).”
BackgroundSelf-citation
Flagged first, then by citations
Research works printed but not linked: 36
- 10.1083/jcb.124.6.903 · DOI
- 10.1093/embo-reports/kvf026 · DOI
- 10.1107/S0907444998003254 · DOI
- Cambillau C., 1997, Turbo‐Frodo
- 10.1016/S0896-6273(01)00558-X · DOI
- 10.1074/jbc.M308762200 · DOI · Paper page
- 10.1126/science.273.5275.595 · DOI
- Ichimura Y., 2000, A ubiquitin‐like system mediates protein lipidation, Nature, 408, 489, 10.1038/35044114 · DOI
- 10.1242/jcs.01131 · DOI · Paper page
- 10.1083/jcb.151.2.263 · DOI
- 10.1146/annurev.cellbio.15.1.1 · DOI
- 10.1074/jbc.M109753200 · DOI
- 10.1107/S0021889891004399 · DOI
- 10.1074/jbc.273.5.3105 · DOI
- 10.1016/S0021-9258(19)78150-2 · DOI
- 10.1016/S0076-6879(97)77028-9 · DOI
- 10.1146/annurev.nu.07.070187.002543 · DOI
- 10.1038/375554a0 · DOI
- 10.1002/prot.340110407 · DOI
- 10.1016/S0076-6879(97)76066-X · DOI · Paper page
- 10.1074/jbc.C000307200 · DOI
- 10.1016/S0968-0004(01)02006-0 · DOI
- 10.1093/emboj/19.7.1494 · DOI
- 10.1074/jbc.M212108200 · DOI
- 10.1074/jbc.C200050200 · DOI
- 10.1107/S0907444903011314 · DOI
- 10.1016/S0006-291X(02)02907-8 · DOI
- 10.1074/jbc.M200385200 · DOI
- 10.1074/jbc.C000752200 · DOI
- 10.1093/emboj/20.15.3947 · DOI
- 10.1016/0014-5793(94)00672-5 · DOI
- 10.1016/0014-5793(93)80398-E · DOI
- Vijay‐Kumar S., 1987, Structure of ubiquitin refined at 1.8 Å resolution, J. Biol. Chem., 262, 6396
- 10.1016/S1097-2765(03)00452-0 · DOI
- Wang H., 1999, GABA (A)—receptor‐associated protein links GABA (A) receptors and the cytoskeleton, Nature, 397, 69, 10.1038/16264 · DOI
- 10.1093/emboj/cdg475 · DOI
Cited by
Sorted by citations
Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).
Klionsky, D. J., Abdelmohsen, K., Abe, A., Abedin, M. J., Abeliovich, H., Acevedo Arozena, A., Adachi, H., Adams, C. M., Adams, P. D., Adeli, K., et al. (2016) · Autophagy · doi:10.1080/15548627.2015.1100356 · Cited by 5,894
Self-citationPankiv, S., Clausen, T. H., Lamark, T., Brech, A., Bruun, J.-A., Outzen, H., Øvervatn, A., Bjørkøy, G., & Johansen, T. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m702824200 · Cited by 4,578
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition) 1
Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., Abeliovich, H., Abildgaard, M. H., Abudu, Y. P., Acevedo-Arozena, A., et al. (2021) · Autophagy · doi:10.1080/15548627.2020.1797280 · Cited by 2,897
Self-citationThe machinery of macroautophagy
Feng, Y., He, D., Yao, Z., & Klionsky, D. J. (2014) · Cell Research · doi:10.1038/cr.2013.168 · Cited by 2,083
Chu, C. T., Ji, J., Dagda, R. K., Jiang, J. F., Tyurina, Y. Y., Kapralov, A. A., Tyurin, V. A., Yanamala, N., Shrivastava, I. H., Mohammadyani, D., et al. (2013) · Nature Cell Biology · doi:10.1038/ncb2837 · Cited by 1,083
Autophagy-Independent Functions of the Autophagy Machinery
Galluzzi, L., & Green, D. R. (2019) · Cell · doi:10.1016/j.cell.2019.05.026 · Cited by 863
“Indeed, considerable attention has been given so far to the structural characterization of single proteins and protein complexes linked to degradative autophagy, including ATG3 (Yamada et al., 2007), ATG4B (Sugawara et al., 2005), BECN1 (Li et al., 2012b), VPS34 (Miller et al., 2010; Rostislavleva et al., 2015), the A…”
Structural Basis for Sorting Mechanism of p62 in Selective Autophagy
Ichimura, Y., Kumanomidou, T., Sou, Y.-S., Mizushima, T., Ezaki, J., Ueno, T., Kominami, E., Yamane, T., Tanaka, K., & Komatsu, M. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m802182200 · Cited by 803
Atg8: an autophagy-related ubiquitin-like protein family.
Shpilka, T., Weidberg, H., Pietrokovski, S., & Elazar, Z. (2011) · Genome biology · doi:10.1186/gb-2011-12-7-226 · Cited by 543
“Subsequent studies confirmed that these features are a unique characteristic of all Atg8 proteins [8-15] (Figure 2).”
BackgroundMechanisms of selective autophagy and mitophagy: Implications for neurodegenerative diseases
Chu, C. T. (2019) · Neurobiology of Disease · doi:10.1016/j.nbd.2018.07.015 · Cited by 218
Characterization of macroautophagic flux in vivo using a leupeptin-based assay
Haspel, J., Shaik, R. S., Ifedigbo, E., Nakahira, K., Dolinay, T., Englert, J. A., & Choi, A. M. K. (2011) · Autophagy · doi:10.4161/auto.7.6.15100 · Cited by 152
Metadata
- Authors
- Sugawara, K., Suzuki, N. N., Fujioka, Y., Mizushima, N., Ohsumi, Y., & Inagaki, F.
- Venue
- Genes to Cells
- Publisher
- Wiley
- Published
- 2004-07
- Volume
- 9
- Issue
- 7
- Pages
- 611-618
- ISSN
- 1356-9597
- 1365-2443
- Cited by
- 158
- References
- 2
- Language
- en
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
