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3  structures 225  species 0  interactions 4368  sequences 743  architectures

Family: zf-AD (PF07776)

Summary: Zinc-finger associated domain (zf-AD)

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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.

Zinc-finger associated domain (zf-AD) Provide feedback

The zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA [1].

Literature references

  1. Jauch R, Bourenkov GP, Chung HR, Urlaub H, Reidt U, Jackle H, Wahl MC;, Structure. 2003;11:1393-1402.: The zinc finger-associated domain of the Drosophila transcription factor grauzone is a novel zinc-coordinating protein-protein interaction module. PUBMED:14604529 EPMC:14604529


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012934

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [ PUBMED:10529348 , PUBMED:15963892 , PUBMED:15718139 , PUBMED:17210253 , PUBMED:12665246 ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [ PUBMED:11179890 ]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

The Znf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The Znf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA [ PUBMED:14604529 ].

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
(49)
Full
(4368)
Representative proteomes UniProt
(11367)
RP15
(986)
RP35
(2639)
RP55
(4127)
RP75
(6010)
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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
(49)
Full
(4368)
Representative proteomes UniProt
(11367)
RP15
(986)
RP35
(2639)
RP55
(4127)
RP75
(6010)
Alignment:
Format:
Order:
Sequence:
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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
(49)
Full
(4368)
Representative proteomes UniProt
(11367)
RP15
(986)
RP35
(2639)
RP55
(4127)
RP75
(6010)
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_14442 (release 14.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Guo JH , Finn RD , El-Gebali S
Number in seed: 49
Number in full: 4368
Average length of the domain: 75.70 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 12.99 %

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 28.0 28.0
Trusted cut-off 28.0 28.0
Noise cut-off 27.9 27.9
Model length: 77
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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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 zf-AD domain has been found. There are 3 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
A0A0B4K7S6 View 3D Structure Click here
A1ZBC5 View 3D Structure Click here
A8JNL9 View 3D Structure Click here
A8JQX6 View 3D Structure Click here
B6VQ99 View 3D Structure Click here
B7Z152 View 3D Structure Click here
E1JII8 View 3D Structure Click here
F1LN08 View 3D Structure Click here
M9PFA9 View 3D Structure Click here
M9PGR0 View 3D Structure Click here
O96395 View 3D Structure Click here
Q4V5A5 View 3D Structure Click here
Q4V6Y7 View 3D Structure Click here
Q59E05 View 3D Structure Click here
Q7JW60 View 3D Structure Click here
Q7K4G8 View 3D Structure Click here
Q7KSP9 View 3D Structure Click here
Q7YZ91 View 3D Structure Click here
Q8CE64 View 3D Structure Click here
Q8N554 View 3D Structure Click here
Q8SX40 View 3D Structure Click here
Q8SZ13 View 3D Structure Click here
Q8T051 View 3D Structure Click here
Q8T053 View 3D Structure Click here
Q8T092 View 3D Structure Click here
Q8T0D1 View 3D Structure Click here
Q95RQ8 View 3D Structure Click here
Q960Q9 View 3D Structure Click here
Q9I7J8 View 3D Structure Click here
Q9U405 View 3D Structure Click here
Q9V474 View 3D Structure Click here
Q9V9V8 View 3D Structure Click here
Q9VAT1 View 3D Structure Click here
Q9VBN9 View 3D Structure Click here
Q9VBR8 View 3D Structure Click here
Q9VBR9 View 3D Structure Click here
Q9VBY9 View 3D Structure Click here
Q9VDQ3 View 3D Structure Click here
Q9VDQ4 View 3D Structure Click here
Q9VDQ5 View 3D Structure Click here
Q9VDQ6 View 3D Structure Click here
Q9VEF0 View 3D Structure Click here
Q9VEF3 View 3D Structure Click here
Q9VEF4 View 3D Structure Click here
Q9VEW6 View 3D Structure Click here
Q9VFB9 View 3D Structure Click here
Q9VGG0 View 3D Structure Click here
Q9VGK1 View 3D Structure Click here
Q9VGL2 View 3D Structure Click here
Q9VGQ5 View 3D Structure Click here
Q9VGQ6 View 3D Structure Click here
Q9VGR8 View 3D Structure Click here
Q9VH18 View 3D Structure Click here
Q9VHA4 View 3D Structure Click here
Q9VHA9 View 3D Structure Click here
Q9VHJ3 View 3D Structure Click here
Q9VHM3 View 3D Structure Click here
Q9VHM4 View 3D Structure Click here
Q9VHM5 View 3D Structure Click here
Q9VHM6 View 3D Structure Click here
Q9VHR4 View 3D Structure Click here
Q9VI24 View 3D Structure Click here
Q9VIS9 View 3D Structure Click here
Q9VIY9 View 3D Structure Click here
Q9VJL7 View 3D Structure Click here
Q9VJN5 View 3D Structure Click here
Q9VKZ0 View 3D Structure Click here
Q9VLK8 View 3D Structure Click here
Q9VQY7 View 3D Structure Click here
Q9VR03 View 3D Structure Click here
Q9VR05 View 3D Structure Click here
Q9VRV4 View 3D Structure Click here
Q9VRV5 View 3D Structure Click here
Q9VRV6 View 3D Structure Click here
Q9VRX0 View 3D Structure Click here
Q9VUB3 View 3D Structure Click here
Q9VXG1 View 3D Structure Click here
Q9VXT1 View 3D Structure Click here
Q9VYG4 View 3D Structure Click here
Q9VYX0 View 3D Structure Click here
Q9VYX2 View 3D Structure Click here
Q9VZ63 View 3D Structure Click here
Q9W2U6 View 3D Structure Click here
Q9W3T3 View 3D Structure Click here
Q9W3X0 View 3D Structure Click here
Q9W409 View 3D Structure Click here
Q9W4V9 View 3D Structure Click here
R9PY35 View 3D Structure Click here