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0  structures 2  species 0  interactions 2  sequences 1  architecture

Family: CM2 (PF03021)

Summary: Influenza C virus M2 protein

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 "M2 proton channel". More...

M2 proton channel Edit Wikipedia article

The M2 protein is a proton-selective ion channel protein, integral in the cell membrane of the influenza A virus. The channel itself is a homotetramer (consists of four identical units), where the units are helixes stabilized by two disulfide bonds. It is activated by low pH.


The M2 protein unit consists of three protein domains: the 24 aminoacids on the N-terminal region, exposed to the outside environment, the 19 hydrophobic aminoacids on the transmembrane region, and the 54 aminoacids on the C-terminal, oriented towards the inside of the viral particle.


The M2 protein has an important role in the life cycle of the influenza A virus. It is located in the viral envelope. Its role lies in letting the protons enter the viral particle, thus lowering pH of the inside of the virus, which causes dissociation of the viral matrix protein M1 from the ribonucleoprotein RNP. This is a crucial step in uncoating of the virus and exposing its content to the cytoplasm of the host cell.


The function of the M2 channel can be inhibited by antiviral drugs amantadine and rimantadine, which then blocks the virus from taking over the host cell.


However, the M2 gene is susceptible to mutations. When one of five aminoacids in the transmembrane region gets suitably subtituted, the virus gains resistance to the existing M2 inhibitors. As the mutations are relatively frequent, presence of the selection factors (eg. using amantadine for treatment of sick poultry) can lead to emergence of a resistent strain.

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.

Influenza C virus M2 protein Provide feedback

Influenza C virus M1 protein is encoded by a spliced mRNA. The unspliced mRNA is also found in small quantities and can encode the protein represented by this family.

Literature references

  1. Hongo S, Sugawara K, Nishimura H, Muraki Y, Kitame F, Nakamura K; , J Gen Virol 1994;75:3503-3510.: Identification of a second protein encoded by influenza C virus RNA segment 6. PUBMED:7996141 EPMC:7996141

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004267

This family represents the matrix protein, M2, of Influenza C virus. The M1 protein is the product of a spliced mRNA (see INTERPRO ). Small quantities of the unspliced mRNA are found in the cell additionally encoding the M2 protein.

Domain organisation

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

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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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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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...


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_1092 (release 6.4)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Griffiths-Jones SR
Number in seed: 1
Number in full: 2
Average length of the domain: 144.5 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 37.98 %

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 27.0 27.0
Trusted cut-off 36.2 52.0
Noise cut-off 26.6 18.9
Model length: 139
Family (HMM) version: 17
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


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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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The tree shows the occurrence of this domain across different species. More...


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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;