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.
12  structures 1448  species 0  interactions 20288  sequences 823  architectures

Family: zf-RING_UBOX (PF13445)

Summary: RING-type 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-type zinc-finger Provide feedback

This zinc-finger is a typical RING-type of plant ubiquitin ligases [1].

Literature references

  1. Stone SL, Hauksdottir H, Troy A, Herschleb J, Kraft E, Callis J;, Plant Physiol. 2005;137:13-30.: Functional analysis of the RING-type ubiquitin ligase family of Arabidopsis. PUBMED:15644464 EPMC:15644464


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR027370

This zinc-finger is the dimerisation motif for LisH proteins [ PUBMED:16445939 ]. This domain can also be found in the typical RING-type of plant ubiquitin ligases [ PUBMED:15644464 ].

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

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 43 members:

Baculo_IE-1 Baculo_RING DUF1644 FANCL_C IBR Prok-RING_1 Prok-RING_2 Prok-RING_4 RINGv Rtf2 T3SS_NleG U-box UPF1_Zn_bind VATC zf-ANAPC11 zf-C3H2C3 zf-C3HC4 zf-C3HC4_2 zf-C3HC4_3 zf-C3HC4_4 zf-C3HC4_5 zf-MIZ zf-NOSIP zf-Nse zf-P11 zf-rbx1 zf-RING-like zf-RING_10 zf-RING_11 zf-RING_12 zf-RING_13 zf-RING_14 zf-RING_2 zf-RING_4 zf-RING_5 zf-RING_6 zf-RING_9 zf-RING_UBOX zf-UBP zf-UBP_var zf-UDP zinc_ribbon_16 Zn_ribbon_17

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
(515)
Full
(20288)
Representative proteomes UniProt
(34115)
RP15
(3938)
RP35
(8603)
RP55
(17781)
RP75
(23004)
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
(515)
Full
(20288)
Representative proteomes UniProt
(34115)
RP15
(3938)
RP35
(8603)
RP55
(17781)
RP75
(23004)
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
(515)
Full
(20288)
Representative proteomes UniProt
(34115)
RP15
(3938)
RP35
(8603)
RP55
(17781)
RP75
(23004)
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_49 (release 24.0)
Previous IDs: zf-RING_LisH;
Type: Domain
Sequence Ontology: SO:0000417
Author: Wood V , Coggill P
Number in seed: 515
Number in full: 20288
Average length of the domain: 44.10 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 7.99 %

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 25.2 18.0
Trusted cut-off 25.2 18.0
Noise cut-off 25.1 17.9
Model length: 40
Family (HMM) version: 8
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.

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-RING_UBOX domain has been found. There are 12 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.

Loading structure mapping...

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
A0A0G2JWJ3 View 3D Structure Click here
A0A0G2JXY7 View 3D Structure Click here
A0A0G2K313 View 3D Structure Click here
A0A0G2K6C7 View 3D Structure Click here
A0A0G2K884 View 3D Structure Click here
A0A0H2UKH6 View 3D Structure Click here
A0A0N4SU11 View 3D Structure Click here
A0A0P0XGM3 View 3D Structure Click here
A0A0R0I510 View 3D Structure Click here
A0A0R0L450 View 3D Structure Click here
A0A0R4IB88 View 3D Structure Click here
A0A0R4IBN3 View 3D Structure Click here
A0A0R4IBP6 View 3D Structure Click here
A0A0R4IBT4 View 3D Structure Click here
A0A0R4ICD1 View 3D Structure Click here
A0A0R4IEH8 View 3D Structure Click here
A0A0R4IFW2 View 3D Structure Click here
A0A0R4IIJ3 View 3D Structure Click here
A0A0R4IIL0 View 3D Structure Click here
A0A0R4IL07 View 3D Structure Click here
A0A0R4IL45 View 3D Structure Click here
A0A0R4IPB1 View 3D Structure Click here
A0A0R4IPI6 View 3D Structure Click here
A0A0R4IQ29 View 3D Structure Click here
A0A0R4ISE2 View 3D Structure Click here
A0A0R4IUT0 View 3D Structure Click here
A0A0R4IVY0 View 3D Structure Click here
A0A0R4IZN1 View 3D Structure Click here
A0A140LGW2 View 3D Structure Click here
A0A1D5NS95 View 3D Structure Click here
A0A1D5NSF2 View 3D Structure Click here
A0A1D6ENS7 View 3D Structure Click here
A0A1D6FGF6 View 3D Structure Click here
A0A1D6FWL4 View 3D Structure Click here
A0A1D6HX03 View 3D Structure Click here
A0A1D6IJX7 View 3D Structure Click here
A0A1D6KES8 View 3D Structure Click here
A0A1D6KZD4 View 3D Structure Click here
A0A1D6LIP4 View 3D Structure Click here
A0A1D6M7Z6 View 3D Structure Click here
A0A1P8ANT6 View 3D Structure Click here
A0A286YB14 View 3D Structure Click here
A0A286YBY1 View 3D Structure Click here
A0A2R8PXH8 View 3D Structure Click here
A0A2R8Q0H5 View 3D Structure Click here
A0A2R8Q5N3 View 3D Structure Click here
A0A2R8Q883 View 3D Structure Click here
A0A2R8QJ74 View 3D Structure Click here
A0A2R8QKK6 View 3D Structure Click here
A0A2R8QN57 View 3D Structure Click here
A0A2R9YJN1 View 3D Structure Click here
A2BFT4 View 3D Structure Click here
A2RT81 View 3D Structure Click here
A3KQE0 View 3D Structure Click here
A4F321 View 3D Structure Click here
A4I290 View 3D Structure Click here
A4I3F1 View 3D Structure Click here
A4IG09 View 3D Structure Click here
A5D8S5 View 3D Structure Click here
A5PMH4 View 3D Structure Click here
A6NCQ9 View 3D Structure Click here
A6NIN4 View 3D Structure Click here
A8DZI0 View 3D Structure Click here
A8E7M3 View 3D Structure Click here
A8WG17 View 3D Structure Click here
A9JSZ8 View 3D Structure Click here
B0G105 View 3D Structure Click here
B1WBW7 View 3D Structure Click here
B4FJS4 View 3D Structure Click here
B5DF13 View 3D Structure Click here
B6U8G9 View 3D Structure Click here
B8JI86 View 3D Structure Click here
B8JLS7 View 3D Structure Click here
C4IZE2 View 3D Structure Click here
C4JAV5 View 3D Structure Click here
C6T8R2 View 3D Structure Click here
C6TC62 View 3D Structure Click here
C6TEZ7 View 3D Structure Click here
C6TIH4 View 3D Structure Click here
D3YVI9 View 3D Structure Click here
D3YY23 View 3D Structure Click here
D3ZA22 View 3D Structure Click here
D3ZBM2 View 3D Structure Click here
D3ZL60 View 3D Structure Click here
D3ZQG6 View 3D Structure Click here
D3ZTZ3 View 3D Structure Click here
D3ZUK4 View 3D Structure Click here
D3ZWU9 View 3D Structure Click here
D3ZY16 View 3D Structure Click here
D4A3L4 View 3D Structure Click here
D4A7S9 View 3D Structure Click here
D4A9N5 View 3D Structure Click here
D4ACF2 View 3D Structure Click here
E7F136 View 3D Structure Click here
E7F1U3 View 3D Structure Click here
E7F6W7 View 3D Structure Click here
E7F6W7 View 3D Structure Click here
E7F8P0 View 3D Structure Click here
E7FAU0 View 3D Structure Click here
E9PVL6 View 3D Structure Click here
E9QIP2 View 3D Structure Click here
F1LY63 View 3D Structure Click here
F1Q4Q5 View 3D Structure Click here
F1Q674 View 3D Structure Click here
F1QB52 View 3D Structure Click here
F1QFW2 View 3D Structure Click here
F1QJQ0 View 3D Structure Click here
F1QLY9 View 3D Structure Click here
F1QMZ7 View 3D Structure Click here
F1QN09 View 3D Structure Click here
F1QQG3 View 3D Structure Click here
F1QQV8 View 3D Structure Click here
F1QSW1 View 3D Structure Click here
F1QUB4 View 3D Structure Click here
F1QWI8 View 3D Structure Click here
F1QZB6 View 3D Structure Click here
F1QZQ5 View 3D Structure Click here
F1R3Q1 View 3D Structure Click here
F2Z4W9 View 3D Structure Click here
F6P534 View 3D Structure Click here
F7ENQ2 View 3D Structure Click here
G3X8Y1 View 3D Structure Click here
G5ED20 View 3D Structure Click here
I1J5X8 View 3D Structure Click here
I1J6W1 View 3D Structure Click here
I1JEB9 View 3D Structure Click here
I1JW34 View 3D Structure Click here
I1K915 View 3D Structure Click here
I1KAD9 View 3D Structure Click here
I1KWB9 View 3D Structure Click here
I1KX38 View 3D Structure Click here
I1LKZ6 View 3D Structure Click here
I1LLG6 View 3D Structure Click here
I1LNN5 View 3D Structure Click here
I1M2J4 View 3D Structure Click here
I1M3T6 View 3D Structure Click here
I1M660 View 3D Structure Click here
I1ME36 View 3D Structure Click here
I1N2A0 View 3D Structure Click here
J3QNR8 View 3D Structure Click here
K7LGD3 View 3D Structure Click here
K7MUW9 View 3D Structure Click here
K7MW63 View 3D Structure Click here
K7MZD8 View 3D Structure Click here
O01482 View 3D Structure Click here
O15344 View 3D Structure Click here
O16616 View 3D Structure Click here
O16683 View 3D Structure Click here
O59668 View 3D Structure Click here
O60858 View 3D Structure Click here
O70277 View 3D Structure Click here
O70583 View 3D Structure Click here
O75382 View 3D Structure Click here
O76354 View 3D Structure Click here
P0C090 View 3D Structure Click here
P0DH78 View 3D Structure Click here
P36406 View 3D Structure Click here
P36407 View 3D Structure Click here
P82458 View 3D Structure Click here
P91131 View 3D Structure Click here
P91482 View 3D Structure Click here
P93030 View 3D Structure Click here
Q06436 View 3D Structure Click here
Q08C26 View 3D Structure Click here
Q09654 View 3D Structure Click here
Q10Q37 View 3D Structure Click here
Q11072 View 3D Structure Click here
Q13049 View 3D Structure Click here
Q17RB8 View 3D Structure Click here
Q19214 View 3D Structure Click here
Q19600 View 3D Structure Click here
Q19818 View 3D Structure Click here
Q1L5Z9 View 3D Structure Click here
Q1L8G6 View 3D Structure Click here
Q1MT11 View 3D Structure Click here
Q1RLP5 View 3D Structure Click here
Q20369 View 3D Structure Click here
Q20397 View 3D Structure Click here
Q20798 View 3D Structure Click here
Q22302 View 3D Structure Click here
Q22441 View 3D Structure Click here
Q29RB6 View 3D Structure Click here
Q38HM4 View 3D Structure Click here
Q3UIW8 View 3D Structure Click here
Q3UV31 View 3D Structure Click here
Q496Y0 View 3D Structure Click here
Q4D662 View 3D Structure Click here
Q4DKZ7 View 3D Structure Click here
Q4DR65 View 3D Structure Click here
Q4DZ28 View 3D Structure Click here
Q4E5S0 View 3D Structure Click here
Q4VGL6 View 3D Structure Click here
Q503E5 View 3D Structure Click here
Q503I2 View 3D Structure Click here
Q54DE4 View 3D Structure Click here
Q54L05 View 3D Structure Click here
Q555R9 View 3D Structure Click here
Q557I6 View 3D Structure Click here
Q59UP4 View 3D Structure Click here
Q5A2I3 View 3D Structure Click here
Q5A7M8 View 3D Structure Click here
Q5M7V1 View 3D Structure Click here
Q5PQN5 View 3D Structure Click here
Q5RH21 View 3D Structure Click here
Q5RHH1 View 3D Structure Click here
Q5RKG6 View 3D Structure Click here
Q5TC82 View 3D Structure Click here
Q5TZ71 View 3D Structure Click here
Q5XIH6 View 3D Structure Click here
Q61510 View 3D Structure Click here
Q62921 View 3D Structure Click here
Q66H79 View 3D Structure Click here
Q680I0 View 3D Structure Click here
Q69K99 View 3D Structure Click here
Q6DHS0 View 3D Structure Click here
Q6IQH8 View 3D Structure Click here
Q6J0N1 View 3D Structure Click here
Q6J2U6 View 3D Structure Click here
Q6K9N9 View 3D Structure Click here
Q6L4Y0 View 3D Structure Click here
Q6NZ21 View 3D Structure Click here
Q6P9F5 View 3D Structure Click here
Q6PBS0 View 3D Structure Click here
Q6PFY8 View 3D Structure Click here
Q6Q0C0 View 3D Structure Click here
Q6Z8T9 View 3D Structure Click here
Q75I59 View 3D Structure Click here
Q7TPM3 View 3D Structure Click here
Q7XZZ3 View 3D Structure Click here
Q80VI1 View 3D Structure Click here
Q80WG7 View 3D Structure Click here
Q80YQ8 View 3D Structure Click here
Q810I1 View 3D Structure Click here
Q810I2 View 3D Structure Click here
Q84JZ7 View 3D Structure Click here
Q86AD8 View 3D Structure Click here
Q86UV6 View 3D Structure Click here
Q86UV7 View 3D Structure Click here
Q86XT4 View 3D Structure Click here
Q8BGE7 View 3D Structure Click here
Q8BGX0 View 3D Structure Click here
Q8C006 View 3D Structure Click here
Q8C0E3 View 3D Structure Click here
Q8C7M3 View 3D Structure Click here
Q8CEF8 View 3D Structure Click here
Q8CH72 View 3D Structure Click here
Q8IBH2 View 3D Structure Click here
Q8IID0 View 3D Structure Click here
Q8IS11 View 3D Structure Click here
Q8IWR1 View 3D Structure Click here
Q8IYM9 View 3D Structure Click here
Q8LBL5 View 3D Structure Click here
Q8TEC5 View 3D Structure Click here
Q8VYZ0 View 3D Structure Click here
Q91Z63 View 3D Structure Click here
Q91ZY8 View 3D Structure Click here
Q920M2 View 3D Structure Click here
Q922B6 View 3D Structure Click here
Q922Y2 View 3D Structure Click here
Q93343 View 3D Structure Click here
Q969Q1 View 3D Structure Click here
Q96LD4 View 3D Structure Click here
Q99PP6 View 3D Structure Click here
Q99PP7 View 3D Structure Click here
Q9BRZ2 View 3D Structure Click here
Q9BYM8 View 3D Structure Click here
Q9BYV2 View 3D Structure Click here
Q9BYV6 View 3D Structure Click here
Q9C019 View 3D Structure Click here
Q9C030 View 3D Structure Click here
Q9C035 View 3D Structure Click here
Q9C040 View 3D Structure Click here
Q9C546 View 3D Structure Click here
Q9C8E1 View 3D Structure Click here
Q9CA76 View 3D Structure Click here
Q9CYB0 View 3D Structure Click here
Q9D241 View 3D Structure Click here
Q9D4H7 View 3D Structure Click here
Q9ERP3 View 3D Structure Click here
Q9ESN6 View 3D Structure Click here
Q9ET26 View 3D Structure Click here
Q9FKA7 View 3D Structure Click here
Q9FVS2 View 3D Structure Click here
Q9FW25 View 3D Structure Click here
Q9FY48 View 3D Structure Click here
Q9H0A6 View 3D Structure Click here
Q9H871 View 3D Structure Click here
Q9H8W5 View 3D Structure Click here
Q9HBD1 View 3D Structure Click here
Q9JIT1 View 3D Structure Click here
Q9N3T6 View 3D Structure Click here
Q9NQ86 View 3D Structure Click here
Q9QUS6 View 3D Structure Click here
Q9R1R2 View 3D Structure Click here
Q9T075 View 3D Structure Click here
Q9U1S9 View 3D Structure Click here
Q9U5C2 View 3D Structure Click here
Q9UDY6 View 3D Structure Click here
Q9UJV3 View 3D Structure Click here
Q9UPN9 View 3D Structure Click here
Q9VJB0 View 3D Structure Click here
Q9VLR7 View 3D Structure Click here
Q9WUB0 View 3D Structure Click here
Q9WV59 View 3D Structure Click here
Q9Y508 View 3D Structure Click here
Q9Y577 View 3D Structure Click here
Q9Y7K6 View 3D Structure Click here
Q9ZQ45 View 3D Structure Click here
X1WBJ0 View 3D Structure Click here
X1WBW4 View 3D Structure Click here
X1WCD1 View 3D Structure Click here