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98  structures 1159  species 0  interactions 6434  sequences 182  architectures

Family: Pre-SET (PF05033)

Summary: Pre-SET motif

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.

Pre-SET motif Provide feedback

This protein motif is a zinc binding motif [1]. It contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilising SET domains.

Literature references

  1. Min J, Zhang X, Cheng X, Grewal SI, Xu RM; , Nat Struct Biol 2002;0:0-0.: Structure of the SET domain histone lysine methyltransferase Clr4. PUBMED:12389037 EPMC:12389037


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007728

This region is found in a number of histone lysine methyltransferases (HMTase), N-terminal to the SET domain; it is generally described as the pre-SET domain.

Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [ PUBMED:12123582 ], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [ PUBMED:11691919 , PUBMED:11893494 ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities [ PUBMED:12540855 ].

The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils and stabilising the SET domain.

The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site [ PUBMED:12389037 ] when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site [ PUBMED:12887903 ]. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [ PUBMED:12372305 ].

Gene Ontology

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

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
(302)
Full
(6434)
Representative proteomes UniProt
(10147)
RP15
(792)
RP35
(2783)
RP55
(5309)
RP75
(7166)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(302)
Full
(6434)
Representative proteomes UniProt
(10147)
RP15
(792)
RP35
(2783)
RP55
(5309)
RP75
(7166)
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
(302)
Full
(6434)
Representative proteomes UniProt
(10147)
RP15
(792)
RP35
(2783)
RP55
(5309)
RP75
(7166)
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: Bateman A
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 302
Number in full: 6434
Average length of the domain: 111.20 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 14.07 %

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 29.1 29.1
Trusted cut-off 29.1 29.1
Noise cut-off 29.0 29.0
Model length: 110
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 Pre-SET domain has been found. There are 98 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
A0A0G2K5A7 View 3D Structure Click here
A0A0G2K889 View 3D Structure Click here
A0A0P0V8S0 View 3D Structure Click here
A0A0P0XYC1 View 3D Structure Click here
A0A0P0Y6F9 View 3D Structure Click here
A0A0R0ELD1 View 3D Structure Click here
A0A0R0F1F1 View 3D Structure Click here
A0A0R0FUI7 View 3D Structure Click here
A0A0R0GZF1 View 3D Structure Click here
A0A0R0I2D0 View 3D Structure Click here
A0A0R0IGL3 View 3D Structure Click here
A0A1D6E5H7 View 3D Structure Click here
A0A1D6EMN1 View 3D Structure Click here
A0A1D6EPB3 View 3D Structure Click here
A0A1D6FSK8 View 3D Structure Click here
A0A1D6G529 View 3D Structure Click here
A0A1D6HW59 View 3D Structure Click here
A0A1D6HY77 View 3D Structure Click here
A0A1D6KLQ2 View 3D Structure Click here
A0A1D6KLS4 View 3D Structure Click here
A0A1D6KQ57 View 3D Structure Click here
A0A1D6M742 View 3D Structure Click here
A0A1D6MTR0 View 3D Structure Click here
A0A1D6N2J4 View 3D Structure Click here
A0A1D6N963 View 3D Structure Click here
A0A1D6PYI9 View 3D Structure Click here
A0A1D6Q562 View 3D Structure Click here
A0A2R8QCU6 View 3D Structure Click here
A0A368UH13 View 3D Structure Click here
B6TYP5 View 3D Structure Click here
B7ZVG0 View 3D Structure Click here
D3ZIH5 View 3D Structure Click here
F1QJX1 View 3D Structure Click here
F1QKB1 View 3D Structure Click here
G3V6S6 View 3D Structure Click here
I1JRR3 View 3D Structure Click here
I1JVX0 View 3D Structure Click here
I1KKL7 View 3D Structure Click here
I1M0I3 View 3D Structure Click here
I1MII9 View 3D Structure Click here
K7K3X0 View 3D Structure Click here
K7K4I0 View 3D Structure Click here
K7K4X0 View 3D Structure Click here
K7K6P9 View 3D Structure Click here
K7KEJ7 View 3D Structure Click here
K7KFI8 View 3D Structure Click here
K7LHC7 View 3D Structure Click here
K7LMX3 View 3D Structure Click here
K7LNB1 View 3D Structure Click here
K7LZD4 View 3D Structure Click here
K7MHC3 View 3D Structure Click here
K7MYR2 View 3D Structure Click here
K7N0L2 View 3D Structure Click here
K7N1Z6 View 3D Structure Click here
K7N541 View 3D Structure Click here
M0RA29 View 3D Structure Click here
M9PGH7 View 3D Structure Click here
O17186 View 3D Structure Click here
O22781 View 3D Structure Click here
O43463 View 3D Structure Click here
O54864 View 3D Structure Click here
O60016 View 3D Structure Click here
O64827 View 3D Structure Click here
O82175 View 3D Structure Click here
O88974 View 3D Structure Click here
P34544 View 3D Structure Click here
P45975 View 3D Structure Click here
Q06ZW3 View 3D Structure Click here
Q08BR4 View 3D Structure Click here
Q0DY89 View 3D Structure Click here
Q10M77 View 3D Structure Click here
Q15047 View 3D Structure Click here
Q1L8U8 View 3D Structure Click here
Q2R1K5 View 3D Structure Click here
Q32KD2 View 3D Structure Click here
Q53H47 View 3D Structure Click here
Q55DR9 View 3D Structure Click here
Q5DW34 View 3D Structure Click here
Q5I0M0 View 3D Structure Click here
Q5JK06 View 3D Structure Click here
Q6DGD3 View 3D Structure Click here
Q6F322 View 3D Structure Click here
Q6K4E6 View 3D Structure Click here
Q6K9F7 View 3D Structure Click here
Q6MG72 View 3D Structure Click here
Q6Z2A2 View 3D Structure Click here
Q7XHM7 View 3D Structure Click here
Q7XN04 View 3D Structure Click here
Q80UJ9 View 3D Structure Click here
Q84Z97 View 3D Structure Click here
Q8C267 View 3D Structure Click here
Q8GZB6 View 3D Structure Click here
Q8RUS3 View 3D Structure Click here
Q8VZ17 View 3D Structure Click here
Q8W595 View 3D Structure Click here
Q946J2 View 3D Structure Click here
Q96KQ7 View 3D Structure Click here
Q96T68 View 3D Structure Click here
Q9C5P0 View 3D Structure Click here
Q9C5P1 View 3D Structure Click here
Q9C5P4 View 3D Structure Click here
Q9EQQ0 View 3D Structure Click here
Q9FF80 View 3D Structure Click here
Q9FNC7 View 3D Structure Click here
Q9H5I1 View 3D Structure Click here
Q9H9B1 View 3D Structure Click here
Q9T0G7 View 3D Structure Click here
Q9VGW0 View 3D Structure Click here
Q9Z148 View 3D Structure Click here