Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 1162  species 0  interactions 3333  sequences 151  architectures

Family: zf-RING_11 (PF17123)

Summary: RING-like zinc finger

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.

RING-like zinc finger Provide feedback

No Pfam abstract.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001841

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 entry represents RING-type zinc finger domains. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [ PUBMED:8317827 , PUBMED:8804826 , PUBMED:8744354 ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which are clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain that has been implicated in a range of diverse biological processes. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain. E3 ubiquitin-protein ligases determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 [ PUBMED:12944364 ]. Various RING fingers also exhibit binding to E2 ubiquitin-conjugating enzymes (Ubc's) [ PUBMED:10662664 , PUBMED:10514377 , PUBMED:10577187 ].

Several 3D-structures for RING-fingers are known [ PUBMED:8804826 , PUBMED:8744354 ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C. Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second.

Note that in the older literature, some RING-fingers are denoted as LIM-domains. The LIM-domain Zn-finger is a fundamentally different family, albeit with similar Cys-spacing (see INTERPRO ).

Domain organisation

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

Loading domain graphics...

Pfam Clan

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
(114)
Full
(3333)
Representative proteomes UniProt
(5730)
RP15
(532)
RP35
(1689)
RP55
(2726)
RP75
(3526)
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, x not generated, not available.

Format an alignment

  Seed
(114)
Full
(3333)
Representative proteomes UniProt
(5730)
RP15
(532)
RP35
(1689)
RP55
(2726)
RP75
(3526)
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
(114)
Full
(3333)
Representative proteomes UniProt
(5730)
RP15
(532)
RP35
(1689)
RP55
(2726)
RP75
(3526)
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: Phmmer:Q10322
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Wood V , Coggill P
Number in seed: 114
Number in full: 3333
Average length of the domain: 29.30 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 5.99 %

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 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 29
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

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.

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
A0A096RB21 View 3D Structure Click here
A0A0N7KTK0 View 3D Structure Click here
A0A0P0W5W4 View 3D Structure Click here
A0A0P0XEQ8 View 3D Structure Click here
A0A0P0XV48 View 3D Structure Click here
A0A0P0XVD7 View 3D Structure Click here
A0A0P0Y6U3 View 3D Structure Click here
A0A0P0Y6U9 View 3D Structure Click here
A0A0P0Y743 View 3D Structure Click here
A0A0P0Y7Y6 View 3D Structure Click here
A0A0R0F7B1 View 3D Structure Click here
A0A0R0H2S3 View 3D Structure Click here
A0A0R0KHX3 View 3D Structure Click here
A0A1D6EG40 View 3D Structure Click here
A0A1D6GPU3 View 3D Structure Click here
A0A1D6HD96 View 3D Structure Click here
A0A1D6HNV0 View 3D Structure Click here
A0A1D6J2X3 View 3D Structure Click here
A0A1D6JNC8 View 3D Structure Click here
A0A1D6JNC9 View 3D Structure Click here
A0A1D6JNT2 View 3D Structure Click here
A0A1D6LVW3 View 3D Structure Click here
A0A1D6M347 View 3D Structure Click here
A0A1D6N1Y6 View 3D Structure Click here
A0A1D6N1Y8 View 3D Structure Click here
A0A1D6PF41 View 3D Structure Click here
A0A1D8PPB7 View 3D Structure Click here
A0A1P8BFJ4 View 3D Structure Click here
A0A2R8QPW9 View 3D Structure Click here
A0A368UHZ2 View 3D Structure Click here
B6SI61 View 3D Structure Click here
B9G9D0 View 3D Structure Click here
C0P695 View 3D Structure Click here
C7J9F4 View 3D Structure Click here
D3ZQ26 View 3D Structure Click here
F1R9R2 View 3D Structure Click here
F4JSV3 View 3D Structure Click here
I1J4W4 View 3D Structure Click here
I1J6W3 View 3D Structure Click here
I1JH43 View 3D Structure Click here
I1K7G8 View 3D Structure Click here
I1KYM9 View 3D Structure Click here
I1L4W2 View 3D Structure Click here
I1M9B4 View 3D Structure Click here
I1MC10 View 3D Structure Click here
I1MHZ7 View 3D Structure Click here
I1N083 View 3D Structure Click here
I1NBW9 View 3D Structure Click here
K7KU89 View 3D Structure Click here
K7LV20 View 3D Structure Click here
K7M7T1 View 3D Structure Click here
K7M7W3 View 3D Structure Click here
K7MD85 View 3D Structure Click here
K7TUS1 View 3D Structure Click here
K7U204 View 3D Structure Click here
K7UJM2 View 3D Structure Click here
K7VH86 View 3D Structure Click here
P38823 View 3D Structure Click here
P53924 View 3D Structure Click here
Q0IUP4 View 3D Structure Click here
Q0WQX9 View 3D Structure Click here
Q0WSW1 View 3D Structure Click here
Q10322 View 3D Structure Click here
Q10RY0 View 3D Structure Click here
Q5Z6V3 View 3D Structure Click here
Q6K8E9 View 3D Structure Click here
Q6K937 View 3D Structure Click here
Q7XM95 View 3D Structure Click here
Q8QGW4 View 3D Structure Click here
Q93ZD8 View 3D Structure Click here
Q9AV43 View 3D Structure Click here
Q9FF49 View 3D Structure Click here
Q9FFT1 View 3D Structure Click here
Q9LN03 View 3D Structure Click here
Q9LTA6 View 3D Structure Click here
Q9LTK5 View 3D Structure Click here
Q9LZV8 View 3D Structure Click here
Q9QZR0 View 3D Structure Click here
Q9SRM0 View 3D Structure Click here
Q9T0H0 View 3D Structure Click here
Q9ULT6 View 3D Structure Click here
Q9ZQ46 View 3D Structure Click here