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261  structures 7257  species 0  interactions 31425  sequences 1023  architectures

Family: Fer4 (PF00037)

Summary: 4Fe-4S binding domain

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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.

4Fe-4S binding domain Provide feedback

Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR017896

Ferredoxins are a group of iron-sulphur proteins which mediate electron transfer in a wide variety of metabolic reactions. Ferredoxins can be divided into several subgroups depending upon the physiological nature of the iron-sulphur cluster(s). One of these subgroups are the 4Fe-4S ferredoxins, which are found in bacteria and which are thus often referred as 'bacterial-type' ferredoxins. The structure of these proteins [ PUBMED:3129571 ] consists of the duplication of a domain of twenty six amino acid residues; each of these domains contains four cysteine residues that bind to a 4Fe-4S centre.

Several structures of the 4Fe-4S ferredoxin domain have been determined [ PUBMED:7966291 ]. The clusters consist of two interleaved 4Fe- and 4S-tetrahedra forming a cubane-like structure, in such a way that the four iron occupy the eight corners of a distorted cube. Each 4Fe-4S is attached to the polypeptide chain by four covalent Fe-S bonds involving cysteine residues.

A number of proteins have been found [ PUBMED:2185975 ] that include one or more 4Fe-4S binding domains similar to those of bacterial-type ferredoxins.

The pattern of cysteine residues in the iron-sulphur region is sufficient to detect this class of 4Fe-4S binding proteins. This entry represents the whole domain.

Note:In some bacterial ferredoxins, one of the two duplicated domains has lost one or more of the four conserved cysteines. The consequence of such variations is that these domains have either lost their iron-sulphur binding property or bind to a 3Fe-3S centre instead of a 4Fe-4S centre.

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 4Fe-4S (CL0344), which has the following description:

Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.

The clan contains the following 29 members:

ETF_QO Fer4 Fer4_10 Fer4_11 Fer4_12 Fer4_13 Fer4_14 Fer4_15 Fer4_16 Fer4_17 Fer4_18 Fer4_19 Fer4_2 Fer4_20 Fer4_21 Fer4_22 Fer4_23 Fer4_24 Fer4_3 Fer4_4 Fer4_5 Fer4_6 Fer4_7 Fer4_8 Fer4_9 FeS Molybdop_Fe4S4 Nitr_red_alph_N RLI

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
(528)
Full
(31425)
Representative proteomes UniProt
(152506)
RP15
(6012)
RP35
(17591)
RP55
(30736)
RP75
(48694)
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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
(528)
Full
(31425)
Representative proteomes UniProt
(152506)
RP15
(6012)
RP35
(17591)
RP55
(30736)
RP75
(48694)
Alignment:
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Sequence:
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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
(528)
Full
(31425)
Representative proteomes UniProt
(152506)
RP15
(6012)
RP35
(17591)
RP55
(30736)
RP75
(48694)
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: Prosite
Previous IDs: fer4;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Eddy SR
Number in seed: 528
Number in full: 31425
Average length of the domain: 23.40 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 8.04 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 24
Family (HMM) version: 30
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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

Selections

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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...

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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 Fer4 domain has been found. There are 261 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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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
A0A0P0Y344 View 3D Structure Click here
A0A1D6K1X2 View 3D Structure Click here
A0A1D6PB11 View 3D Structure Click here
A4HZ70 View 3D Structure Click here
D3ZD23 View 3D Structure Click here
I1LIG5 View 3D Structure Click here
I1N1X8 View 3D Structure Click here
K7LWZ9 View 3D Structure Click here
K7MSH8 View 3D Structure Click here
O50433 View 3D Structure Click here
O60102 View 3D Structure Click here
P0AAJ1 View 3D Structure Click here
P0AAJ3 View 3D Structure Click here
P0AAJ8 View 3D Structure Click here
P0AAK1 View 3D Structure Click here
P0AAK4 View 3D Structure Click here
P0AAK7 View 3D Structure Click here
P0AAL0 View 3D Structure Click here
P0AAL3 View 3D Structure Click here
P0AAL6 View 3D Structure Click here
P0AFD6 View 3D Structure Click here
P16432 View 3D Structure Click here
P23481 View 3D Structure Click here
P37127 View 3D Structure Click here
P39409 View 3D Structure Click here
P46722 View 3D Structure Click here
P52102 View 3D Structure Click here
P52647 View 3D Structure Click here
P56256 View 3D Structure Click here
P61221 View 3D Structure Click here
P61222 View 3D Structure Click here
P77223 View 3D Structure Click here
P77423 View 3D Structure Click here
P81292 View 3D Structure Click here
P81293 View 3D Structure Click here
P9WJG9 View 3D Structure Click here
P9WJI1 View 3D Structure Click here
P9WN89 View 3D Structure Click here
P9WNE7 View 3D Structure Click here
Q03195 View 3D Structure Click here