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0  structures 1431  species 0  interactions 2387  sequences 49  architectures

Family: FAM210A-B_dom (PF06916)

Summary: FAM210A/B-like domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Domain of unknown function". More...

Domain of unknown function Edit Wikipedia article

A Domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF188 and DUF1000. There are now over 3,000 DUF families within the Pfam database representing over 20% of known families.

History

The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[1] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.

Structure

Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved.[2]

External Links

List of Pfam familes beginning with the letter D, including DUF families

References

  1. ^ Schultz J, Milpetz F, Bork P, Ponting CP (1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Proc. Natl. Acad. Sci. U.S.A. 95 (11): 5857–64. PMC 34487. PMID 9600884. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Jaroszewski L, Li Z, Krishna SS; et al. (2009). "Exploration of uncharted regions of the protein universe". PLoS Biol. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC 2744874. PMID 19787035. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

FAM210A/B-like domain Provide feedback

This domain is found in mitochondrial proteins, including FAM210A and B, which contains a transmembrane peptide [1,2,3]. Its function is not clear. FAM210A, a protein essential in maintaining skeletal muscle structure and strength [4] interacts with mitochondrial translation elongation factor EF-Tu and promotes mitochondrial protein expression. In FAM210A, this domain is responsible for binding EF-Tu [3]. FAM210B plays a role in erythroid differentiation and is involved in cell proliferation and tumour cell growth suppression [1,5].

Literature references

  1. Sun S, Liu J, Zhao M, Han Y, Chen P, Mo Q, Wang B, Chen G, Fang Y, Tian Y, Zhou J, Ma D, Gao Q, Wu P;, Cell Death Dis. 2017;8:e2870.: Loss of the novel mitochondrial protein FAM210B promotes metastasis via PDK4-dependent metabolic reprogramming. PUBMED:28594398 EPMC:28594398

  2. Boileau E, Doroudgar S, Riechert E, Jurgensen L, Ho TC, Katus HA, Volkers M, Dieterich C;, Front Genet. 2020;11:583124.: A Multi-Network Comparative Analysis of Transcriptome and Translatome Identifies Novel Hub Genes in Cardiac Remodeling. PUBMED:33304386 EPMC:33304386

  3. Wu J, Venkata Subbaiah KC, Jiang F, Hedaya O, Mohan A, Yang T, Welle K, Ghaemmaghami S, Tang WHW, Small E, Yan C, Yao P;, EMBO Mol Med. 2021;13:e12710.: MicroRNA-574 regulates FAM210A expression and influences pathological cardiac remodeling. PUBMED:33369227 EPMC:33369227

  4. Tanaka KI, Xue Y, Nguyen-Yamamoto L, Morris JA, Kanazawa I, Sugimoto T, Wing SS, Richards JB, Goltzman D;, Proc Natl Acad Sci U S A. 2018;115:E3759.: FAM210A is a novel determinant of bone and muscle structure and strength. PUBMED:29618611 EPMC:29618611

  5. Kondo A, Fujiwara T, Okitsu Y, Fukuhara N, Onishi Y, Nakamura Y, Sawada K, Harigae H;, Int J Hematol. 2016;103:387-395.: Identification of a novel putative mitochondrial protein FAM210B associated with erythroid differentiation. PUBMED:26968549 EPMC:26968549


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009688

This domain is found in mitochondrial proteins, including FAM210A (and its homologues) and B, which contains a transmembrane peptide [ PUBMED:28594398 , PUBMED:33304386 , PUBMED:33369227 ]. Its function is not clear. FAM210A, a protein essential in maintaining skeletal muscle structure and strength [ PUBMED:29618611 ], interacts with mitochondrial translation elongation factor EF‐Tu and promotes mitochondrial protein expression. In FAM210A, this domain is responsible for binding EF‐Tu [ PUBMED:33369227 ]. FAM210B plays a role in erythroid differentiation and is involved in cell proliferation and tumor cell growth suppression [ PUBMED:28594398 , PUBMED:26968549 ]. This domain is also present in the uncharacterised protein C106.07c from fission yeast and putative N-terminal acetyltransferase 2 from Baker's yeast.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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...

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
(25)
Full
(2387)
Representative proteomes UniProt
(4178)
RP15
(521)
RP35
(1163)
RP55
(1913)
RP75
(2485)
Jalview View  View  View  View  View  View  View 
HTML View  View           
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
(25)
Full
(2387)
Representative proteomes UniProt
(4178)
RP15
(521)
RP35
(1163)
RP55
(1913)
RP75
(2485)
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
(25)
Full
(2387)
Representative proteomes UniProt
(4178)
RP15
(521)
RP35
(1163)
RP55
(1913)
RP75
(2485)
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_7316 (release 10.0)
Previous IDs: DUF1279;
Type: Domain
Sequence Ontology: SO:0000417
Author: Vella Briffa B
Number in seed: 25
Number in full: 2387
Average length of the domain: 101.5 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 38.57 %

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 26.0 26.0
Trusted cut-off 26.0 26.0
Noise cut-off 25.9 25.9
Model length: 92
Family (HMM) version: 16
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

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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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
A0A044TJW6 View 3D Structure Click here
A0A077ZHR2 View 3D Structure Click here
A0A0D2E775 View 3D Structure Click here
A0A0H5SQX3 View 3D Structure Click here
A0A0K0EFD7 View 3D Structure Click here
A0A0N4U442 View 3D Structure Click here
A0A175WGQ2 View 3D Structure Click here
A0A1C1CT09 View 3D Structure Click here
A0A1D6EBF2 View 3D Structure Click here
A0A1D8PG06 View 3D Structure Click here
A1Z6G4 View 3D Structure Click here
A4I7K8 View 3D Structure Click here
A4IJ20 View 3D Structure Click here
B2RYM8 View 3D Structure Click here
C0H5E6 View 3D Structure Click here
C0HI43 View 3D Structure Click here
C0NIF3 View 3D Structure Click here
C1H9P2 View 3D Structure Click here
C6T2F9 View 3D Structure Click here
F1QMF2 View 3D Structure Click here
I1L652 View 3D Structure Click here
I1LKN2 View 3D Structure Click here
I1LRK0 View 3D Structure Click here
P37293 View 3D Structure Click here
Q05B67 View 3D Structure Click here
Q1MTD4 View 3D Structure Click here
Q388E4 View 3D Structure Click here
Q4V6K4 View 3D Structure Click here
Q54G09 View 3D Structure Click here
Q5CZQ0 View 3D Structure Click here
Q5RE99 View 3D Structure Click here
Q5XIJ4 View 3D Structure Click here
Q5ZML6 View 3D Structure Click here
Q7XTF4 View 3D Structure Click here
Q8BGY7 View 3D Structure Click here
Q96KR6 View 3D Structure Click here
Q96ND0 View 3D Structure Click here
Q9D8B6 View 3D Structure Click here
Q9SKR7 View 3D Structure Click here
Q9U237 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;