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2  structures 326  species 0  interactions 1986  sequences 31  architectures

Family: RINGv (PF12906)

Summary: RING-variant domain

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RING-variant domain Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011016

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 RING finger is a well characterised zinc finger which coordinates two zinc atoms in a cross-braced manner (see PROSITEDOC). According to the pattern of cysteines and histidines three different subfamilies of RING finger can be defined. The classical RING finger (RING-HC) has a histidine at the fourth coordinating position and a cysteine at the fifth. In the RING-H2 variant, both the fourth and fifth positions are occupied by histidines. The RING-CH, which is very similar to the classical RING finger, differs from both of these variants in that it has a cys residue in the fourth position and a His in the fifth. Another difference between the RING-CH and the common RING variants is a somewhat longer peptide segment between the fourth and fifth zinc-coordinating residues. The RING-CH zinc finger has thus the same arrangement of cysteine and histidine (C4HC3) as the PHD zinc finger (see PROSITEDOC) but it contains features (spacing between the cysteines and the histidine) characteristic of the genuine RING-finger (C3HC4) [PUBMED:11641273, PUBMED:12695663]. The RING-CH-type is an E3 ligase mainly found in proteins associated to membranes [PUBMED:16873052, PUBMED:17051211].

The solution structure of the RING-CH-type zinc finger of the herpesvirus Mir1 protein has shown that it is an outlying relative of the cellular RING finger domain family, with its polypeptide backbone much more closely resembling that of RING domains than PHD domains [PUBMED:15465811]. The only real difference between the classic and variant RING domains, other than the alteration of zinc ligands, is the loss of the small beta-sheet found in RING domains and the replacement of one strand of this sheet with a single turn of helix. Some proteins that contains a RING-CH-type zinc finger are listed below:

  • Yeast Doa10/SSM4 (SWISSPROT). An E3 ligase essential for the endoplasmic reticulum associated degradation (ERAD), an ubiquitin-proteasome system responsible for the degradation of membrane and lumenal proteins of the endoplasmic reticulum.
  • Mammalian membrane-associated RING-CH 1 to 9 (MARCH1 to 9) proteins.
  • Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus) modulator of immune recognition 1 (SWISSPROT). An E3 ubiquitin-protein ligase which promotes ubiquitination and subsequent degradation of host MHC-I and CD1D molecules, presumably to prevent lysis of infected cells by cytotoxic T-lymphocytes.

More information about these proteins can be found at Protein of the Month: Zinc Fingers [PUBMED:].

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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Pfam Clan

This family is a member of clan RING (CL0229), which has the following description:

This clan includes the Ring zinc finger domains as well as the U-box domain that appears to have lost the zinc coordinating cysteine residues [1].

The clan contains the following 24 members:

Baculo_RING FANCL_C Prok-RING_1 Prok-RING_2 Prok-RING_4 RINGv Rtf2 U-box zf-Apc11 zf-C3HC4 zf-C3HC4_2 zf-C3HC4_3 zf-C3HC4_4 zf-MIZ zf-Nse zf-rbx1 zf-RING-like zf-RING_2 zf-RING_4 zf-RING_5 zf-RING_6 zf-RING_UBOX zf-UBP zf-UDP

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(26)
Full
(1986)
Representative proteomes NCBI
(1950)
Meta
(106)
RP15
(402)
RP35
(693)
RP55
(1007)
RP75
(1289)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(26)
Full
(1986)
Representative proteomes NCBI
(1950)
Meta
(106)
RP15
(402)
RP35
(693)
RP55
(1007)
RP75
(1289)
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
(26)
Full
(1986)
Representative proteomes NCBI
(1950)
Meta
(106)
RP15
(402)
RP35
(693)
RP55
(1007)
RP75
(1289)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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
Author: Bateman A
Number in seed: 26
Number in full: 1986
Average length of the domain: 50.00 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 10.43 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 21.6 21.6
Noise cut-off 21.5 21.5
Model length: 47
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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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 RINGv 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 seqence.

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