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2  structures 671  species 0  interactions 6753  sequences 329  architectures

Family: zf-BED (PF02892)

Summary: BED zinc finger

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This is the Wikipedia entry entitled "BED zinc finger". More...

BED zinc finger Edit Wikipedia article

zf-BED
PDB 2ct5 EBI.jpg
Solution structure of the zinc finger bed domain of the zinc finger BED domain containing protein 1
Identifiers
Symbolzf-BED
PfamPF02892
Pfam clanCL0361
InterProIPR003656

In molecular biology the BED-type zinc finger domain is a protein domain which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain.[1] Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. Most genes in this family are believed to have evolved from the hAT family of DNA transposons.[2]

See also

References

  1. ^ Aravind L (September 2000). "The BED finger, a novel DNA-binding domain in chromatin-boundary-element-binding proteins and transposases". Trends in Biochemical Sciences. 25 (9): 421–3. doi:10.1016/s0968-0004(00)01620-0. PMID 10973053.
  2. ^ Hayward, Alexander; Ghazal, Awaisa; Andersson, Göran; Andersson, Leif; Jern, Patric; Robinson-Rechavi, Marc (22 March 2013). "ZBED Evolution: Repeated Utilization of DNA Transposons as Regulators of Diverse Host Functions". PLoS ONE. 8 (3): e59940. doi:10.1371/journal.pone.0059940. PMC 3606216.
This article incorporates text from the public domain Pfam and InterPro: IPR003656

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.

BED zinc finger Provide feedback

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Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003656

The BED finger, which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain [ PUBMED:10973053 ].

Some proteins known to contain a BED domain are listed below:

  • Animal, fungal and plant AC1 and Hobo-like transposases.
  • Caenorhabditis elegans protein dpy-20, a predicted cuticular-gene transcriptional regulator.
  • Drosophila BEAF (boundary element-associated factor), which is thought to be involved in chromatin insulation.
  • Drosophila DREF, a transcriptional regulator for S-phase genes.
  • Tobacco 3AF1 and tomato E4/E8-BP1, which are light- and ethylene-regulated DNA binding proteins that contain two BED fingers [ PUBMED:2152132 , PUBMED:9225464 ].

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...

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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
(17)
Full
(6753)
Representative proteomes UniProt
(11682)
RP15
(1381)
RP35
(3576)
RP55
(6202)
RP75
(7815)
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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
(17)
Full
(6753)
Representative proteomes UniProt
(11682)
RP15
(1381)
RP35
(3576)
RP55
(6202)
RP75
(7815)
Alignment:
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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
(17)
Full
(6753)
Representative proteomes UniProt
(11682)
RP15
(1381)
RP35
(3576)
RP55
(6202)
RP75
(7815)
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: [1]
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 17
Number in full: 6753
Average length of the domain: 46.50 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 10.19 %

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 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 44
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Selections

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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 zf-BED domain has been found. There are 2 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
A0A0G2KHS7 View 3D Structure Click here
A0A0G2KUY4 View 3D Structure Click here
A0A0P0V3S3 View 3D Structure Click here
A0A0P0VH42 View 3D Structure Click here
A0A0P0WKW1 View 3D Structure Click here
A0A0P0XD22 View 3D Structure Click here
A0A0P0XL75 View 3D Structure Click here
A0A0P0XLN1 View 3D Structure Click here
A0A0P0YCI3 View 3D Structure Click here
A0A0R0EKH4 View 3D Structure Click here
A0A0R0ES97 View 3D Structure Click here
A0A0R0EYZ3 View 3D Structure Click here
A0A0R0EZ27 View 3D Structure Click here
A0A0R0EZ86 View 3D Structure Click here
A0A0R0F023 View 3D Structure Click here
A0A0R0F0J5 View 3D Structure Click here
A0A0R0F9Y4 View 3D Structure Click here
A0A0R0FAF2 View 3D Structure Click here
A0A0R0FHE0 View 3D Structure Click here
A0A0R0FP77 View 3D Structure Click here
A0A0R0FPF7 View 3D Structure Click here
A0A0R0FQL7 View 3D Structure Click here
A0A0R0FZH2 View 3D Structure Click here
A0A0R0G3D4 View 3D Structure Click here
A0A0R0GF66 View 3D Structure Click here
A0A0R0GLD0 View 3D Structure Click here
A0A0R0H3S6 View 3D Structure Click here
A0A0R0H5G3 View 3D Structure Click here
A0A0R0HR48 View 3D Structure Click here
A0A0R0HZ72 View 3D Structure Click here
A0A0R0I156 View 3D Structure Click here
A0A0R0I4P9 View 3D Structure Click here
A0A0R0I7Y2 View 3D Structure Click here
A0A0R0IQD1 View 3D Structure Click here
A0A0R0IU97 View 3D Structure Click here
A0A0R0IWR4 View 3D Structure Click here
A0A0R0J8P6 View 3D Structure Click here
A0A0R0J9E4 View 3D Structure Click here
A0A0R0JP60 View 3D Structure Click here
A0A0R0JWV4 View 3D Structure Click here
A0A0R0JYP2 View 3D Structure Click here
A0A0R0K6W7 View 3D Structure Click here
A0A0R0K8D4 View 3D Structure Click here
A0A0R0KD83 View 3D Structure Click here
A0A0R0KG63 View 3D Structure Click here
A0A0R0KGL7 View 3D Structure Click here
A0A0R0KQJ8 View 3D Structure Click here
A0A0R0L4R7 View 3D Structure Click here
A0A0R0L6C6 View 3D Structure Click here
A0A0R0L8W9 View 3D Structure Click here
A0A0R4IPS8 View 3D Structure Click here
A0A0R4IWH1 View 3D Structure Click here
A0A0R4IWH1 View 3D Structure Click here
A0A1D6E6X7 View 3D Structure Click here
A0A1D6E7B9 View 3D Structure Click here
A0A1D6EEP3 View 3D Structure Click here
A0A1D6EZN0 View 3D Structure Click here
A0A1D6FXH3 View 3D Structure Click here
A0A1D6H9B7 View 3D Structure Click here
A0A1D6INV7 View 3D Structure Click here
A0A1D6IV44 View 3D Structure Click here
A0A1D6J5J1 View 3D Structure Click here
A0A1D6J6I0 View 3D Structure Click here
A0A1D6K174 View 3D Structure Click here
A0A1D6L370 View 3D Structure Click here
A0A1D6MFC8 View 3D Structure Click here
A0A1D6NAV6 View 3D Structure Click here
A0A1D6PEU7 View 3D Structure Click here
A0A1X7YIR5 View 3D Structure Click here
A3A558 View 3D Structure Click here
A3BQI0 View 3D Structure Click here
B0UXM5 View 3D Structure Click here
C7IYE5 View 3D Structure Click here
C7J6M2 View 3D Structure Click here
D2EAC2 View 3D Structure Click here
D2EAC2 View 3D Structure Click here
D3ZUV0 View 3D Structure Click here
D3ZUV0 View 3D Structure Click here
D3ZUV0 View 3D Structure Click here
D3ZUV0 View 3D Structure Click here
E9QBU6 View 3D Structure Click here
F1QLZ5 View 3D Structure Click here
F1QLZ5 View 3D Structure Click here
F1QP08 View 3D Structure Click here
F1RBD5 View 3D Structure Click here
F4HQA2 View 3D Structure Click here
F4I1K8 View 3D Structure Click here
F4ICA1 View 3D Structure Click here
G4SI18 View 3D Structure Click here
K7K3E4 View 3D Structure Click here
K7K3S3 View 3D Structure Click here
K7K8N7 View 3D Structure Click here
K7KJY6 View 3D Structure Click here
K7KP98 View 3D Structure Click here
K7L0T3 View 3D Structure Click here
K7L8X1 View 3D Structure Click here
K7LA07 View 3D Structure Click here
K7LCF8 View 3D Structure Click here
K7LCF8 View 3D Structure Click here
K7LCW2 View 3D Structure Click here
K7LD09 View 3D Structure Click here
K7LE93 View 3D Structure Click here
K7LIV3 View 3D Structure Click here
K7M0M3 View 3D Structure Click here
K7MBE5 View 3D Structure Click here
K7MCB9 View 3D Structure Click here
K7MCB9 View 3D Structure Click here
K7MCQ2 View 3D Structure Click here
K7MDE2 View 3D Structure Click here
K7MFX4 View 3D Structure Click here
K7MLB0 View 3D Structure Click here
K7MR51 View 3D Structure Click here
K7MXR9 View 3D Structure Click here
K7N231 View 3D Structure Click here
K7N248 View 3D Structure Click here
O75132 View 3D Structure Click here
O75132 View 3D Structure Click here
O75132 View 3D Structure Click here
O75132 View 3D Structure Click here
O96006 View 3D Structure Click here
P34807 View 3D Structure Click here
P34807 View 3D Structure Click here
P53246 View 3D Structure Click here
P86452 View 3D Structure Click here
P86452 View 3D Structure Click here
Q0DQY3 View 3D Structure Click here
Q0E8Q6 View 3D Structure Click here
Q0J0T2 View 3D Structure Click here
Q0J9W3 View 3D Structure Click here
Q0JK40 View 3D Structure Click here
Q0JMB2 View 3D Structure Click here
Q0JPH5 View 3D Structure Click here
Q0JRB0 View 3D Structure Click here
Q0WQA4 View 3D Structure Click here
Q0WQA4 View 3D Structure Click here
Q19787 View 3D Structure Click here
Q21374 View 3D Structure Click here
Q2QN49 View 3D Structure Click here
Q56VX2 View 3D Structure Click here
Q5RFV1 View 3D Structure Click here
Q5RFV1 View 3D Structure Click here
Q5RFV1 View 3D Structure Click here
Q5RFV1 View 3D Structure Click here
Q75HY5 View 3D Structure Click here
Q80WQ9 View 3D Structure Click here
Q80WQ9 View 3D Structure Click here
Q80WQ9 View 3D Structure Click here
Q80WQ9 View 3D Structure Click here
Q86S30 View 3D Structure Click here
Q8T419 View 3D Structure Click here
Q94883 View 3D Structure Click here
Q96IU2 View 3D Structure Click here
Q9BTP6 View 3D Structure Click here
Q9M305 View 3D Structure Click here
Q9VAF2 View 3D Structure Click here
Q9VAF2 View 3D Structure Click here
Q9VEP0 View 3D Structure Click here
Q9VM61 View 3D Structure Click here
X1WFE2 View 3D Structure Click here