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59  structures 2516  species 1  interaction 4348  sequences 48  architectures

Family: zf-CDGSH (PF09360)

Summary: Iron-binding zinc finger CDGSH type

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Iron-binding zinc finger CDGSH type Provide feedback

The CDGSH-type zinc finger domain binds iron rather than zinc as a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family [1]. The domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, MitoNEET_N, PF10660 [2]. The domain forms a uniquely folded homo-dimer and spans the outer mitochondrial membrane, orienting the iron-binding residues towards the cytoplasm [3].

Literature references

  1. Wiley SE, Murphy AN, Ross SA, van der Geer P, Dixon JE; , Proc Natl Acad Sci U S A. 2007;104:5318-5323.: MitoNEET is an iron-containing outer mitochondrial membrane protein that regulates oxidative capacity. PUBMED:17376863 EPMC:17376863

  2. Wiley SE, Paddock ML, Abresch EC, Gross L, van der Geer P, Nechushtai R, Murphy AN, Jennings PA, Dixon JE; , J Biol Chem. 2007;282:23745-23749.: The outer mitochondrial membrane protein mitoNEET contains a novel redox-active 2Fe-2S cluster. PUBMED:17584744 EPMC:17584744

  3. Paddock ML, Wiley SE, Axelrod HL, Cohen AE, Roy M, Abresch EC, Capraro D, Murphy AN, Nechushtai R, Dixon JE, Jennings PA; , Proc Natl Acad Sci U S A. 2007;104:14342-14347.: MitoNEET is a uniquely folded 2Fe 2S outer mitochondrial membrane protein stabilized by pioglitazone. PUBMED:17766440 EPMC:17766440


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018967

This entry represents iron-sulphur domain containing proteins that have a CDGSH sequence motif (although the Ser residue can also be an Ala or Thr), and is found in proteins from a wide range of organisms with the exception of fungi. The CDGSH-type domain binds a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family [PUBMED:17376863].

CDGSH-type domains are found in mitoNEET, an iron-containing integral protein of the outer mitochondrian membrane (OMM). MitoNEET forms a dimeric structure with a NEET fold, and contains two domains: a beta-cap region and a cluster-binding domain that coordinated two acid-labile 2Fe-2S clusters (one bound to each protomer) [PUBMED:17766440]. The CDGSH iron-sulphur domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, (INTERPRO) [PUBMED:17584744, PUBMED:17766440]. The whole protein regulates oxidative capacity and may function in electron transfer, for instance in redox reactions with metabolic intermediates, cofactors and/or proteins localized at the OMM.

Gene Ontology

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Domain organisation

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Alignments

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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
(209)
Full
(4348)
Representative proteomes UniProt
(9714)
NCBI
(12279)
Meta
(932)
RP15
(1219)
RP35
(2855)
RP55
(4306)
RP75
(5502)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(209)
Full
(4348)
Representative proteomes UniProt
(9714)
NCBI
(12279)
Meta
(932)
RP15
(1219)
RP35
(2855)
RP55
(4306)
RP75
(5502)
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
(209)
Full
(4348)
Representative proteomes UniProt
(9714)
NCBI
(12279)
Meta
(932)
RP15
(1219)
RP35
(2855)
RP55
(4306)
RP75
(5502)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: PSI2 target BIG_227
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 209
Number in full: 4348
Average length of the domain: 43.80 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 41.86 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.1 27.1
Trusted cut-off 27.1 27.1
Noise cut-off 27.0 27.0
Model length: 48
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

zf-CDGSH

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-CDGSH domain has been found. There are 59 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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