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197  structures 1412  species 0  interactions 4642  sequences 81  architectures

Family: ATG8 (PF02991)

Summary: Autophagy protein Atg8 ubiquitin like

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Autophagy protein Atg8 ubiquitin like Provide feedback

Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N-terminus and the C-terminus of Atg19.

Literature references

  1. Mann SS, Hammarback JA; , J Biol Chem 1994;269:11492-11497.: Molecular characterization of light chain 3. A microtubule binding subunit of MAP1A and MAP1B. PUBMED:7908909 EPMC:7908909

  2. Yoshimoto K, Hanaoka H, Sato S, Kato T, Tabata S, Noda T, Ohsumi Y;, Plant Cell. 2004;16:2967-2983.: Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy. PUBMED:15494556 EPMC:15494556

  3. Chang CY, Huang WP;, Mol Biol Cell. 2007;18:919-929.: Atg19 mediates a dual interaction cargo sorting mechanism in selective autophagy. PUBMED:17192412 EPMC:17192412


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004241

A number of autophagy-related proteins have been identified in yeast, including the key autophagic protein Atg8, which is a ubiquitin-like protein with a structure consisting of two amino-terminal alpha-helices and a ubiquitin-like core [ PUBMED:18508918 , PUBMED:15265004 ]. Many other eukaryotes contain multiple Atg8 orthologues. Atg8 genes of multicellular animals can be divided into three subfamilies: microtubule-associated protein 1 light chain 3 (MAP1LC3 or LC3) [ PUBMED:7908909 ], gamma-aminobutyric acid receptor-associated protein (GABARAP) and Golgi-associated ATPase enhancer of 16kDa (GATE-16) [ PUBMED:21867568 , PUBMED:20562859 ]. Family members are involved in diverse intracellular trafficking and autophagy processes.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(9)
Full
(4642)
Representative proteomes UniProt
(8115)
RP15
(774)
RP35
(2051)
RP55
(3777)
RP75
(4993)
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HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(9)
Full
(4642)
Representative proteomes UniProt
(8115)
RP15
(774)
RP35
(2051)
RP55
(3777)
RP75
(4993)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(9)
Full
(4642)
Representative proteomes UniProt
(8115)
RP15
(774)
RP35
(2051)
RP55
(3777)
RP75
(4993)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1384 (release 6.4)
Previous IDs: MAP1_LC3; Atg8;
Type: Domain
Sequence Ontology: SO:0000417
Author: Griffiths-Jones SR
Number in seed: 9
Number in full: 4642
Average length of the domain: 98.80 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 67.17 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.8
Model length: 104
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the ATG8 domain has been found. There are 197 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2JU55 View 3D Structure Click here
A0A0G2K9Q7 View 3D Structure Click here
A0A0R0F6W3 View 3D Structure Click here
A0A0R0G9G6 View 3D Structure Click here
A0A140LGA1 View 3D Structure Click here
A0A1D6EWW6 View 3D Structure Click here
A0A1D6HQC9 View 3D Structure Click here
A0A1D6IYD0 View 3D Structure Click here
A0A381MAT2 View 3D Structure Click here
A0A381MBG2 View 3D Structure Click here
A0A381MCF0 View 3D Structure Click here
A0A381MFR9 View 3D Structure Click here
A4HTT6 View 3D Structure Click here
A4HYA4 View 3D Structure Click here
A4HYA5 View 3D Structure Click here
A4HYJ2 View 3D Structure Click here
A6NCE7 View 3D Structure Click here
B6SH45 View 3D Structure Click here
B6SUL0 View 3D Structure Click here
B9A7M1 View 3D Structure Click here
B9A7M2 View 3D Structure Click here
C6T0R7 View 3D Structure Click here
C6T418 View 3D Structure Click here
C6T5Q4 View 3D Structure Click here
E9AGS4 View 3D Structure Click here
E9AH00 View 3D Structure Click here
F1M1J6 View 3D Structure Click here
F1M1J6 View 3D Structure Click here
F1QY33 View 3D Structure Click here
I1J9W7 View 3D Structure Click here
I1K0N9 View 3D Structure Click here
I1KND4 View 3D Structure Click here
I1LGN7 View 3D Structure Click here
I1MUZ8 View 3D Structure Click here
O94272 View 3D Structure Click here
O95166 View 3D Structure Click here
P0C075 View 3D Structure Click here
P38182 View 3D Structure Click here
P60517 View 3D Structure Click here
P60520 View 3D Structure Click here
P60521 View 3D Structure Click here
P60522 View 3D Structure Click here
Q09490 View 3D Structure Click here
Q0VGK0 View 3D Structure Click here
Q23536 View 3D Structure Click here
Q2RBS4 View 3D Structure Click here
Q4DQT1 View 3D Structure Click here
Q4DV83 View 3D Structure Click here
Q4DWZ7 View 3D Structure Click here
Q54G11 View 3D Structure Click here
Q62625 View 3D Structure Click here
Q69RC4 View 3D Structure Click here
Q6DH82 View 3D Structure Click here
Q6H6P0 View 3D Structure Click here
Q6NX90 View 3D Structure Click here
Q6PSS4 View 3D Structure Click here
Q6TH05 View 3D Structure Click here
Q6XVN8 View 3D Structure Click here
Q6Z1D5 View 3D Structure Click here
Q7XPR1 View 3D Structure Click here
Q7ZUD8 View 3D Structure Click here
Q7ZWC0 View 3D Structure Click here
Q86CR8 View 3D Structure Click here
Q8IJK2 View 3D Structure Click here
Q8LEM4 View 3D Structure Click here
Q8R3R8 View 3D Structure Click here
Q8S925 View 3D Structure Click here
Q8S926 View 3D Structure Click here
Q8S927 View 3D Structure Click here
Q8VYK7 View 3D Structure Click here
Q91VR7 View 3D Structure Click here
Q9BXW4 View 3D Structure Click here
Q9BY60 View 3D Structure Click here
Q9CQV6 View 3D Structure Click here
Q9DCD6 View 3D Structure Click here
Q9GZQ8 View 3D Structure Click here
Q9H0R8 View 3D Structure Click here
Q9H492 View 3D Structure Click here
Q9LRP7 View 3D Structure Click here
Q9LZZ9 View 3D Structure Click here
Q9SL04 View 3D Structure Click here
Q9VEG5 View 3D Structure Click here
Q9W2S2 View 3D Structure Click here
Q9XEB5 View 3D Structure Click here