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40  structures 268  species 0  interactions 1065  sequences 18  architectures

Family: Zn-C2H2_12 (PF18112)

Summary: Autophagy receptor zinc finger-C2H2 domain

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Autophagy receptor zinc finger-C2H2 domain Provide feedback

This domain is found in calcium-binding and coiled-coil domain 2/NDP25 (CALCOCO2/NDP25) found in Homo sapiens. CALCOCO2/NDP25 is an ubiquitin-binding autophagy receptor involved in the selective autophagic degradation of invading pathogens. This domain is a typical C2H2-type zinc finger which specifically recognizes mono-ubiquitin or poly-ubiquitin chain. The overall ubiquitin-binding mode utilizes the C-terminal alpha-helix to interact with the solvent-exposed surface of the central beta-sheet of ubiquitin, similar to that observed in the RABGEF1/Rabex-5 or POLN/Pol-eta zinc finger [1].

Literature references

  1. Xie X, Li F, Wang Y, Wang Y, Lin Z, Cheng X, Liu J, Chen C, Pan L;, Autophagy. 2015;11:1775-1789.: Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2. PUBMED:26506893 EPMC:26506893


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR041641

This entry represents the UBZ1 type zinc finger domain found in calcium-binding and coiled-coil domain 1/2 (CALCOCO1/2), tax-binding protein 1 and protein spindle-F.

This domain is a typical C2H2-type zinc finger which specifically recognizes mono-ubiquitin or poly-ubiquitin chain. The overall ubiquitin-binding mode utilizes the C-terminal alpha-helix to interact with the solvent-exposed surface of the central beta-sheet of ubiquitin, similar to that observed in the RABGEF1/Rabex-5 or POLN/Pol-eta zinc finger [ PUBMED:26506893 ].

CALCOCO2 (also known as NDP25) is an ubiquitin-binding autophagy receptor involved in the selective autophagic degradation of invading pathogens [ PUBMED:26506893 ]. Tax binding protein 1 is a ubiquitin binding protein [ PUBMED:28314591 ] and protein spindle-F plays a role in oocyte axis determination and microtubule organization during oogenesis in Drosophila [ PUBMED:18796167 , PUBMED:16540510 ].

The ubiquitin-binding zinc finger (UBZ) is a type of zinc-coordinating beta- beta-alpha fold domain found mainly in proteins involved in DNA repair and transcriptional regulation. UBZ domains coordinate a zinc ion with cysteine or histidine residues; depending on their amino acid sequence, UBZ domains are classified into several families [ PUBMED:19213613 , PUBMED:27062441 ]. Type 1 UBZs are CCHH-type zinc fingers found in tandem UBZ domains of TAX1-binding protein 1 (TAX1BP1) [ PUBMED:24239949 , PUBMED:26506893 , PUBMED:27370208 ], type 2 UBZs are CCHC-type zinc fingers found in FAAP20 which is a subunit of the Fanconi anemia (FA) core complex [ PUBMED:25414354 , PUBMED:25799058 ], type 3 UBZs are CCHH-type zinc fingers found only in the Y-family translesion polymerase eta [ PUBMED:17304240 , PUBMED:17550419 , PUBMED:20837403 ], and type 4 UBZs are CCHC-type zinc fingers found in Y-family translesion polymerase kappa, Werner helicase-interacting protein 1 (WRNIP1), and Rad18 [ PUBMED:20385554 , PUBMED:25162118 , PUBMED:24794496 ].

The UBZ domain consists of two short antiparallel beta-strands followed by one alpha-helix. The alpha-helix packs against the beta-strands with a zinc ion sandwiched between the alpha-helix and the beta-strands. The zinc ion is coordinated by two cysteines located on the fingertip formed by the beta- strands and two histidines [ PUBMED:19213613 , PUBMED:17304240 ] or one hisidine and one cysteine [ PUBMED:25414354 ] on the alpha-helix [ PUBMED:27062441 ].

Domain organisation

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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...

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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
(7)
Full
(1065)
Representative proteomes UniProt
(1870)
RP15
(90)
RP35
(268)
RP55
(854)
RP75
(1237)
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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
(7)
Full
(1065)
Representative proteomes UniProt
(1870)
RP15
(90)
RP35
(268)
RP55
(854)
RP75
(1237)
Alignment:
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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
(7)
Full
(1065)
Representative proteomes UniProt
(1870)
RP15
(90)
RP35
(268)
RP55
(854)
RP75
(1237)
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.

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Curation and family details

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Curation View help on the curation process

Seed source: ECOD:EUF06881
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: El-Gebali S , Smart A
Number in seed: 7
Number in full: 1065
Average length of the domain: 26.80 aa
Average identity of full alignment: 56 %
Average coverage of the sequence by the domain: 6.09 %

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 23.2 23.2
Trusted cut-off 23.2 23.2
Noise cut-off 23.1 23.1
Model length: 27
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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

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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 Zn-C2H2_12 domain has been found. There are 40 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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