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11  structures 1246  species 0  interactions 7547  sequences 260  architectures

Family: zf-GRF (PF06839)

Summary: GRF zinc finger

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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.

GRF zinc finger Provide feedback

This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to PF01396.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010666

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.

This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to INTERPRO .

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
(12)
Full
(7547)
Representative proteomes UniProt
(12562)
RP15
(1055)
RP35
(3835)
RP55
(6403)
RP75
(8404)
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
(12)
Full
(7547)
Representative proteomes UniProt
(12562)
RP15
(1055)
RP35
(3835)
RP55
(6403)
RP75
(8404)
Alignment:
Format:
Order:
Sequence:
Gaps:
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
(12)
Full
(7547)
Representative proteomes UniProt
(12562)
RP15
(1055)
RP35
(3835)
RP55
(6403)
RP75
(8404)
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: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 12
Number in full: 7547
Average length of the domain: 45.20 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 10.84 %

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 25.9 25.9
Trusted cut-off 25.9 25.9
Noise cut-off 25.8 25.8
Model length: 45
Family (HMM) version: 14
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 zf-GRF domain has been found. There are 11 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
A0A0G2K8A6 View 3D Structure Click here
A0A0N7KL24 View 3D Structure Click here
A0A0P0VJD8 View 3D Structure Click here
A0A0P0WHK9 View 3D Structure Click here
A0A0P0Y2S5 View 3D Structure Click here
A0A0P0Y8V6 View 3D Structure Click here
A0A0R0FQ15 View 3D Structure Click here
A0A0R0KAU5 View 3D Structure Click here
A0A0R4IFG3 View 3D Structure Click here
A0A0R4IVN4 View 3D Structure Click here
A0A1D6IA11 View 3D Structure Click here
A0A1D6JPQ3 View 3D Structure Click here
A0A1D6L6V1 View 3D Structure Click here
A0A1D6L6V1 View 3D Structure Click here
A0A1D6MQY5 View 3D Structure Click here
A0A1I9LRT2 View 3D Structure Click here
A0A1P8ANJ8 View 3D Structure Click here
A0A1P8AUP0 View 3D Structure Click here
A0A1P8AUP0 View 3D Structure Click here
A0A1P8B2E9 View 3D Structure Click here
A0A1P8BEI2 View 3D Structure Click here
A0A2R8RKD0 View 3D Structure Click here
A0A2R8RKD0 View 3D Structure Click here
A3A6S7 View 3D Structure Click here
A3ARN5 View 3D Structure Click here
A4IDA8 View 3D Structure Click here
A8K979 View 3D Structure Click here
B9FJU1 View 3D Structure Click here
C7J0A2 View 3D Structure Click here
D3ZKJ8 View 3D Structure Click here
D3ZKJ8 View 3D Structure Click here
D3ZPZ3 View 3D Structure Click here
D3ZV31 View 3D Structure Click here
D4A625 View 3D Structure Click here
D4A6J4 View 3D Structure Click here
D4A6J4 View 3D Structure Click here
F1M404 View 3D Structure Click here
F1Q865 View 3D Structure Click here
F4JNY0 View 3D Structure Click here
I1JCH3 View 3D Structure Click here
I1N832 View 3D Structure Click here
K7KV90 View 3D Structure Click here
O61660 View 3D Structure Click here
O70157 View 3D Structure Click here
O70157 View 3D Structure Click here
P38207 View 3D Structure Click here
Q0VGT4 View 3D Structure Click here
Q10RC4 View 3D Structure Click here
Q13472 View 3D Structure Click here
Q13472 View 3D Structure Click here
Q2QWQ9 View 3D Structure Click here
Q2R399 View 3D Structure Click here
Q4DJB7 View 3D Structure Click here
Q4DNR5 View 3D Structure Click here
Q502M8 View 3D Structure Click here
Q53L34 View 3D Structure Click here
Q5BKS4 View 3D Structure Click here
Q5NC05 View 3D Structure Click here
Q68G58 View 3D Structure Click here
Q69JZ1 View 3D Structure Click here
Q6F3B9 View 3D Structure Click here
Q6F3B9 View 3D Structure Click here
Q75H59 View 3D Structure Click here
Q7XDU8 View 3D Structure Click here
Q86YA3 View 3D Structure Click here
Q8BKW4 View 3D Structure Click here
Q8K203 View 3D Structure Click here
Q8K203 View 3D Structure Click here
Q8TAT5 View 3D Structure Click here
Q8TAT5 View 3D Structure Click here
Q9H5U6 View 3D Structure Click here
Q9LVP1 View 3D Structure Click here
Q9M1L9 View 3D Structure Click here
Q9M1L9 View 3D Structure Click here
Q9NG98 View 3D Structure Click here
Q9NG98 View 3D Structure Click here
Q9UBZ4 View 3D Structure Click here
Q9UNY4 View 3D Structure Click here
X1WCF3 View 3D Structure Click here
X1WCF3 View 3D Structure Click here