PDBsum entry 1ugm

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protein links
Structural protein PDB id
Protein chain
113 a.a. *
Waters ×65
* Residue conservation analysis
PDB id:
Name: Structural protein
Title: Crystal structure of lc3
Structure: Microtubule-associated proteins 1a/1b light chain 3. Chain: a. Fragment: residues -4-120. Synonym: lc3-i. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
2.05Å     R-factor:   0.215     R-free:   0.249
Authors: K.Sugawara,N.N.Suzuki,Y.Fujioka,N.Mizushima,Y.Ohsumi, F.Inagaki
Key ref: K.Sugawara et al. (2004). The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8. Genes Cells, 9, 611-618. PubMed id: 15265004
16-Jun-03     Release date:   06-Jul-04    
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Protein chain
Pfam   ArchSchema ?
Q62625  (MLP3B_RAT) -  Microtubule-associated proteins 1A/1B light chain 3B
142 a.a.
113 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


Genes Cells 9:611-618 (2004)
PubMed id: 15265004  
The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8.
K.Sugawara, N.N.Suzuki, Y.Fujioka, N.Mizushima, Y.Ohsumi, F.Inagaki.
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 A 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 GABAA receptor-associated protein (GABARAP), contains a ubiquitin core with two alpha helices, alpha1 and alpha2, 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 alpha1, alpha2 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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21126205 A.M.Gusdon, and C.T.Chu (2011).
To eat or not to eat: neuronal metabolism, mitophagy, and Parkinson's disease.
  Antioxid Redox Signal, 14, 1979-1987.  
20398630 H.Jiang, D.Cheng, W.Liu, J.Peng, and J.Feng (2010).
Protein kinase C inhibits autophagy and phosphorylates LC3.
  Biochem Biophys Res Commun, 395, 471-476.  
20352102 K.R.Drake, M.Kang, and A.K.Kenworthy (2010).
Nucleocytoplasmic distribution and dynamics of the autophagosome marker EGFP-LC3.
  PLoS One, 5, e9806.  
20723759 L.Radoshevich, L.Murrow, N.Chen, E.Fernandez, S.Roy, C.Fung, and J.Debnath (2010).
ATG12 conjugation to ATG3 regulates mitochondrial homeostasis and cell death.
  Cell, 142, 590-600.  
20713600 S.J.Cherra, S.M.Kulich, G.Uechi, M.Balasubramani, J.Mountzouris, B.W.Day, and C.T.Chu (2010).
Regulation of the autophagy protein LC3 by phosphorylation.
  J Cell Biol, 190, 533-539.  
20100911 S.Pankiv, E.A.Alemu, A.Brech, J.A.Bruun, T.Lamark, A.Overvatn, G.Bjørkøy, and T.Johansen (2010).
FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport.
  J Cell Biol, 188, 253-269.  
  21113398 T.P.Yao (2010).
The role of ubiquitin in autophagy-dependent protein aggregate processing.
  Genes Cancer, 1, 779-786.  
20665069 V.Pacheco, P.Ma, Y.Thielmann, R.Hartmann, O.H.Weiergräber, J.Mohrlüder, and D.Willbold (2010).
Assessment of GABARAP self-association by its diffusion properties.
  J Biomol NMR, 48, 49-58.  
20811353 Z.Yang, and D.J.Klionsky (2010).
Eaten alive: a history of macroautophagy.
  Nat Cell Biol, 12, 814-822.  
19322194 K.Satoo, N.N.Noda, H.Kumeta, Y.Fujioka, N.Mizushima, Y.Ohsumi, and F.Inagaki (2009).
The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy.
  EMBO J, 28, 1341-1350.
PDB codes: 2z0d 2z0e 2zzp
19941614 M.H.Stipanuk (2009).
Macroautophagy and its role in nutrient homeostasis.
  Nutr Rev, 67, 677-689.  
19450525 V.Kirkin, D.G.McEwan, I.Novak, and I.Dikic (2009).
A role for ubiquitin in selective autophagy.
  Mol Cell, 34, 259-269.  
19001416 Y.Chen, C.Chen, E.Kotsikorou, D.L.Lynch, P.H.Reggio, and L.Y.Liu-Chen (2009).
GEC1-kappa opioid receptor binding involves hydrophobic interactions: GEC1 has chaperone-like effect.
  J Biol Chem, 284, 1673-1685.  
19462014 Y.Thielmann, O.H.Weiergräber, J.Mohrlüder, and D.Willbold (2009).
Structural characterization of GABARAP-ligand interactions.
  Mol Biosyst, 5, 575-579.  
18704115 J.Geng, and D.J.Klionsky (2008).
The Atg8 and Atg12 ubiquitin-like conjugation systems in macroautophagy. 'Protein modifications: beyond the usual suspects' review series.
  EMBO Rep, 9, 859-864.  
19021777 N.N.Noda, H.Kumeta, H.Nakatogawa, K.Satoo, W.Adachi, J.Ishii, Y.Fujioka, Y.Ohsumi, and F.Inagaki (2008).
Structural basis of target recognition by Atg8/LC3 during selective autophagy.
  Genes Cells, 13, 1211-1218.
PDB codes: 2k6q 2zpn
18388399 S.Kimura, T.Noda, and T.Yoshimori (2008).
Dynein-dependent movement of autophagosomes mediates efficient encounters with lysosomes.
  Cell Struct Funct, 33, 109-122.  
18500386 Y.B.Zhang, S.X.Li, X.P.Chen, L.Yang, Y.G.Zhang, R.Liu, and L.Y.Tao (2008).
Autophagy is activated and might protect neurons from degeneration after traumatic brain injury.
  Neurosci Bull, 24, 143-149.  
18567048 Y.Thielmann, J.Mohrlüder, B.W.Koenig, T.Stangler, R.Hartmann, K.Becker, H.D.Höltje, and D.Willbold (2008).
An indole-binding site is a major determinant of the ligand specificity of the GABA type A receptor-associated protein GABARAP.
  Chembiochem, 9, 1767-1775.  
17712358 D.J.Klionsky (2007).
Autophagy: from phenomenology to molecular understanding in less than a decade.
  Nat Rev Mol Cell Biol, 8, 931-937.  
17632063 H.Nakatogawa, Y.Ichimura, and Y.Ohsumi (2007).
Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusion.
  Cell, 130, 165-178.  
  17277449 K.Satoo, N.N.Suzuki, Y.Fujioka, N.Mizushima, Y.Ohsumi, and F.Inagaki (2007).
Crystallization and preliminary crystallographic analysis of human Atg4B-LC3 complex.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 99.  
17311494 N.Mizushima, and D.J.Klionsky (2007).
Protein turnover via autophagy: implications for metabolism.
  Annu Rev Nutr, 27, 19-40.  
17083446 Z.W.Chen, and R.W.Olsen (2007).
GABAA receptor associated proteins: a key factor regulating GABAA receptor function.
  J Neurochem, 100, 279-294.  
16942488 G.Jia, G.Cheng, D.M.Gangahar, and D.K.Agrawal (2006).
Insulin-like growth factor-1 and TNF-alpha regulate autophagy through c-jun N-terminal kinase and Akt pathways in human atherosclerotic vascular smooth cells.
  Immunol Cell Biol, 84, 448-454.  
16680092 N.Amar, G.Lustig, Y.Ichimura, Y.Ohsumi, and Z.Elazar (2006).
Two newly identified sites in the ubiquitin-like protein Atg8 are essential for autophagy.
  EMBO Rep, 7, 635-642.  
  17012800 Y.Yamada, N.N.Suzuki, Y.Fujioka, Y.Ichimura, Y.Ohsumi, and F.Inagaki (2006).
Crystallization and preliminary X-ray analysis of Atg3.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1016-1017.  
15615779 D.J.Klionsky (2005).
The molecular machinery of autophagy: unanswered questions.
  J Cell Sci, 118, 7.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.