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48  structures 2852  species 3  interactions 4302  sequences 16  architectures

Family: Pilin (PF00114)

Summary: Pilin (bacterial filament)

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This is the Wikipedia entry entitled "Pilin". More...

Pilin Edit Wikipedia article

Pilin (bacterial filament)
Pilin protein from Neisseria gonorrhoeae, a parasitic bacterium that requires functional pili for pathogenesis.
Symbol Pilin
Pfam PF00114
InterPro IPR001082
SCOP 1paj
OPM superfamily 74
OPM protein 2hil

Pilin refers to a class of fibrous proteins that are found in pilus structures in bacteria. Bacterial pili are used in the exchange of genetic material during bacterial conjugation, while a shorter type of appendages also made up of pilin, called fimbriae, are used as a cell adhesion mechanism. Although not all bacteria have pili or fimbriae, bacterial pathogens often use their fimbriae to attach to host cells. In gram-negative bacteria, where pili are more common, individual pilin molecules are linked by noncovalent protein-protein interactions, while gram-positive bacteria often have polymerized pilin.[1]

Pilin proteins themselves are α+β proteins characterized by a very long N-terminal alpha helix. Many pilins are post-translationally modified by glycosylation or phosphorylation. The assembly of a complete pilus relies on interactions between the N-terminal helices of the individual monomers. The pilus structure sequesters the helices in the center of the fiber lining a central pore, while antiparallel beta sheets occupy the exterior of the fiber.[2] The exact mechanism of pilus assembly from monomers is not known, although chaperone proteins have been identified for some types of pilin.[3] and specific amino acids required for proper pilus formation have been isolated.[4]

Development of molecular tools

Pili in Gram-positive bacteria contain spontaneously formed isopeptide bonds. These bonds provide enhanced stability to the protein. Recently, the pilin protein from Streptococcus pyogenes has been split into two fragments to develop a new molecular tool called the isopeptag. [5] The isopeptag is a short peptide that can be attached to a protein of interest and can bind its binding partner through a spontaneously formed isopeptide bond. This new peptide tag can allow scientists to target and isolate their proteins of interest through a permanent covalent bond.


  1. ^ Telford JL, Barocchi MA, Margarit I, Rappuoli R, Grandi G. (2006). Pili in gram-positive pathogens. Nat Rev Microbiol 4(7):509-19.
  2. ^ Forest KT, Tainer JA. (1997). Type-4 pilus-structure: outside to inside and top to bottom—a minireview. Gene 192(1):165-9.
  3. ^ Jones CH, Pinkner JS, Nicholes AV, Slonim LN, Abraham SN, Hultgren SJ. (1993). FimC is a periplasmic PapD-like chaperone that directs assembly of type 1 pili in bacteria. Proc Natl Acad Sci USA 90(18):8397-401.
  4. ^ Mu XQ, Jiang ZG, Bullitt E. (2005). Localization of a critical interface for helical rod formation of bacterial adhesion P-pili. J Mol Biol 346(1):13-20.
  5. [6] Zakeri,B. and Howarth,M. (2010). Spontaneous intermolecular amide bond formation between side chains for irreversible peptide targeting. J. Am. Chem. Soc. 132, 4526-4527.

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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.

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Proteins with only the short N-terminal methylation site are not separated from the noise. The Prosite pattern detects those better.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001082

Pilin is a subunit of the pilus, a polar flexible filament, which consists of a single polypeptide chain arranged in a helical configuration of five subunits per turn. Gram-negative bacteria produce pilin which is characterised by the presence of a very short leader peptide of 6 to 7 residues, followed by a methylated N-terminal phenylalanine residue and by a highly conserved sequence of about 24 hydrophobic residues, of the NMePhe type pilin [PUBMED:2898203, PUBMED:3118043].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 Pilus (CL0327), which has the following description:

This is a clan contains bacterial pilus subunits and proteins involved in secretion. Pili proteins enable the transfer of plasmid between bacteria. The families in this clan adopt an alpha helical structure which is packed against a beta sheet [2-3].

The clan contains the following 11 members:

Bundlin ComP_DUS N_methyl N_methyl_2 N_methyl_3 Pilin PilS T2SSG T2SSI TcpA YadA_anchor


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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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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.

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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: pilin;
Type: Domain
Author: Sonnhammer ELL
Number in seed: 145
Number in full: 4302
Average length of the domain: 106.90 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 72.31 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.8 21.8
Trusted cut-off 21.8 21.8
Noise cut-off 21.7 21.7
Model length: 108
Family (HMM) version: 15
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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There are 3 interactions for this family. More...

N_methyl_2 Pilin N_methyl_2


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 Pilin domain has been found. There are 48 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 seqence.

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