Summary: YEATS family

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Wikipedia: YEATS domain
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This is the Wikipedia entry entitled "YEATS domain". More...

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YEATS domain Edit Wikipedia article

YEATS domain

Identifiers

Symbol

YEATS

Available protein structures:
Pfam Â	structures / ECOD Â
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary
PDB	4tmpâ€‹, 3fk3â€‹, 3rlsâ€‹, 2l7eâ€‹, 3qrlâ€‹

YEATS domain

In molecular biology, the YEATS domain is a protein domain found in a variety of proteins from eukaryotic organisms.^[1] YEATS domain proteins are found in a variety of chromatin modification molecular complexes. Structurally the domain has an immunoglobulin like fold.^[2] The YEATS domain has shown to bind to acetyllysine protein modifications. For example, the YEATS domain of yeast Af9 protein.^[3] The YEATS domain has shown to be a reader domain for the protein modification of lysine crotonylation.^[4]

References

^ Schulze JM, Wang AY, Kobor MS (2009). "YEATS domain proteins: a diverse family with many links to chromatin modification and transcription". Biochem. Cell Biol. 87 (1): 65â€“75. doi:10.1139/O08-111. PMIDÂ 19234524.
^ Wang AY, Schulze JM, Skordalakes E, Gin JW, Berger JM, Rine J, Kobor MS (2009). "Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation". Proc. Natl. Acad. Sci. U.S.A. 106 (51): 21573â€“8. doi:10.1073/pnas.0906539106. PMCÂ 2799888. PMIDÂ 19966225.
^ Li Y, Wen H, Xi Y, Tanaka K, Wang H, Peng D, Ren Y, Jin Q, Dent SY, Li W, Li H, Shi X (2014). "AF9 YEATS domain links histone acetylation to DOT1L-mediated H3K79 methylation". Cell. 159 (3): 558â€“71. doi:10.1016/j.cell.2014.09.049. PMCÂ 4344132. PMIDÂ 25417107.
^ Andrews FH, Shinsky SA, Shanle EK, Bridgers JB, Gest A, Tsun IK, Krajewski K, Shi X, Strahl BD, Kutateladze TG (2016). "The Taf14 YEATS domain is a reader of histone crotonylation". Nat. Chem. Biol. 12 (6): 396â€“8. doi:10.1038/nchembio.2065. PMIDÂ 27089029.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

YEATS family Provide feedback

We have named this family the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit'. This family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activity

Literature references

Harborth J, Weber K, Osborn M; , J Biol Chem 2000;275:31979-31985.: GAS41, a highly conserved protein in eukaryotic nuclei, binds to NuMA. PUBMED:10913114 EPMC:10913114
Schreiner S, Birke M, Garcia-Cuellar MP, Zilles O, Greil J, Slany RK; , Cancer Res 2001;61:6480-6486.: MLL-ENL causes a reversible and myc-dependent block of myelomonocytic cell differentiation. PUBMED:11522644 EPMC:11522644
Hemenway CS, de Erkenez AC, Gould GC; , Oncogene 2001;20:3798-3805.: The polycomb protein MPc3 interacts with AF9, an MLL fusion partner in t(9;11)(p22;q23) acute leukemias. PUBMED:11439343 EPMC:11439343

Internal database links

SCOOP:	pYEATS
Similarity to PfamA using HHSearch:	pYEATS

This tab holds annotation information from the InterPro database.

InterPro entry IPR005033

This family is named after YEATS (Yaf9, ENL, AF9, Taf14, and Sas5), an evolutionarily conserved module present in 4 proteins (ENL, AF9, GAS41, and YEATS2) in humans and 3 proteins (Sas5, Taf14, and Yaf9) in yeast. These proteins are found in major chromatin-remodeling and histone acetyl-transferase (HAT) complexes and implicated in regulation of chromatin structure, histone acetylation and deposition, gene transcription and DNA damage response. The YEATS domain, which as previously shown is found in a number of chromatin-associated proteins, has recently been shown to have the capacity to bind histone lysine acetylation [ PUBMED:27545619 ]. The ability of the YEATS domains of human AF9 and yeast Taf14 to recognise the histone mark H3K9ac, have shown that these proteins are members of the family of acetyllysine readers [ PUBMED:26341557 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Biological process

regulation of transcription, DNA-templated (GO:0006355)

Domain organisation

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

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Pfam Clan

This family is a member of clan C2 (CL0154), which has the following description:

This superfamily includes C2 domains and C2-like domains.

The clan contains the following 18 members:

Aida_C2 Anillin B9-C2 C2 C2-C2_1 CC2D2AN-C2 CEP76-C2 DOCK-C2 IcmF_C MNNL NT-C2 PI3K_C2 PTEN_C2 pYEATS RPGR1_C SPATA6 Spond_N YEATS

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...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

Selex
Stockholm
FASTA
MSF

You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

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 (218)	Full (4285)	Representative proteomes				UniProt (6740)
	Seed (218)	Full (4285)	RP15 (772)	RP35 (1802)	RP55 (3246)	RP75 (4434)	UniProt (6740)
Jalview	View	View	View	View	View	View	View
HTML	View	View
PP/heatmap	₁	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (218)	Full (4285)	Representative proteomes				UniProt (6740)
	Seed (218)	Full (4285)	RP15 (772)	RP35 (1802)	RP55 (3246)	RP75 (4434)	UniProt (6740)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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 (218)	Full (4285)	Representative proteomes				UniProt (6740)
	Seed (218)	Full (4285)	RP15 (772)	RP35 (1802)	RP55 (3246)	RP75 (4434)	UniProt (6740)
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

Seed source:

Pfam-B_2273 (release 6.6)

Previous IDs:

none

Type:

Domain

Sequence Ontology:

SO:0000417

Author:

Mifsud W

Number in seed:

218

Number in full:

4285

Average length of the domain:

81 aa

Average identity of full alignment:

36 %

Average coverage of the sequence by the domain:

16.74 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	22.0	22.0
Trusted cut-off	22.2	22.2
Noise cut-off	21.8	21.5

Model length:

82

Family (HMM) version:

19

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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Colour assignments

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Selections

Generate a FASTA-format file

Clear selection

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...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

Loading sunburst data...

Tree controls

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The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 YEATS domain has been found. There are 95 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.

Loading structure mapping...

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
A0A044RGV4	View 3D Structure	Click here
A0A044SA38	View 3D Structure	Click here
A0A077ZG49	View 3D Structure	Click here
A0A0A2V6P4	View 3D Structure	Click here
A0A0D2DJX4	View 3D Structure	Click here
A0A0D2FH50	View 3D Structure	Click here
A0A0D2GST5	View 3D Structure	Click here
A0A0K0E0C0	View 3D Structure	Click here
A0A0K0EF18	View 3D Structure	Click here
A0A0N4UDL8	View 3D Structure	Click here
A0A0N4UG67	View 3D Structure	Click here
A0A0R0IBU1	View 3D Structure	Click here
A0A175VZ03	View 3D Structure	Click here
A0A175W7C7	View 3D Structure	Click here
A0A1C1C8T6	View 3D Structure	Click here
A0A1C1CP64	View 3D Structure	Click here
A0A1C1CZP4	View 3D Structure	Click here
A0A1D8PH31	View 3D Structure	Click here
A0A2R8QDF9	View 3D Structure	Click here
A0A3P7DGN1	View 3D Structure	Click here
A0A3Q0KQ97	View 3D Structure	Click here
A0A5S6PCG3	View 3D Structure	Click here
A0A5S6PCS5	View 3D Structure	Click here
A2AM29	View 3D Structure	Click here
A4HSW4	View 3D Structure	Click here
A4I8X3	View 3D Structure	Click here
B0S8H1	View 3D Structure	Click here
B2RYE9	View 3D Structure	Click here
B4FY75	View 3D Structure	Click here
C0H4S5	View 3D Structure	Click here
C0NFN4	View 3D Structure	Click here
C0NY59	View 3D Structure	Click here
C1HBY7	View 3D Structure	Click here
D3ZBV9	View 3D Structure	Click here
F1QAS4	View 3D Structure	Click here
F1QAV3	View 3D Structure	Click here
F4IPK2	View 3D Structure	Click here
G4VEL9	View 3D Structure	Click here
I1LI12	View 3D Structure	Click here
I1LPV8	View 3D Structure	Click here

Showing 40 matches

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Family: YEATS (PF03366)

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Summary: YEATS family

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YEATS domain Edit Wikipedia article

YEATS domain

See also

References

YEATS family Provide feedback

Literature references

Internal database links

InterPro entry IPR005033

Gene Ontology

Domain organisation

Pfam Clan

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Structures

AlphaFold Structure Predictions

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