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84  structures 505  species 0  interactions 21973  sequences 176  architectures

Family: Filament (PF00038)

Summary: Intermediate filament 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 "Intermediate filament". More...

Intermediate filament Edit Wikipedia article

Intermediate filaments are assebled from several different proteins.

Details

10nm.

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.

Intermediate filament protein Provide feedback

No Pfam abstract.

Literature references

  1. Quinlan R, Hutchison C, Lane B; , Protein Profile 1995;2:801-951.: Intermediate filament proteins. PUBMED:8771189 EPMC:8771189


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR039008

Intermediate filaments (IF) [ PUBMED:2183847 , PUBMED:28101862 ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in six types:

  • Type I: Acidic cytokeratins.
  • Type II: Basic cytokeratins.
  • Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin.
  • Type IV: Neurofilaments L, H and M, alpha-internexin and nestin.
  • Type V: Nuclear lamins A, B1, B2 and C.
  • Type VI: 'Orphan' IF proteins, which are more distant in terms of their amino acid sequences.

All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled- coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins.

While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. The IF rod domain is approximately 310 residues long in all cytoplasmic IF proteins and close to 350 residues in the nuclear ones. The IF rod domain exhibits an interrupted alpha-helical conformation and reveals a pronounced seven-residue periodicity in the distribution of apolar residues. The heptad periodicity within the rod domain is interrupted in several places, which generates four consecutive alpha-helical segments: 1A and 1B, which together form the so-called coil 1, and 2A and 2B, which form coil 2. The four alpha-helical segments are interconnected by relatively short, variable linkers L1, L12 and L2 [ PUBMED:12596228 , PUBMED:22869704 ].

IF proteins have a very strong tendency to dimerize via the formation of an alpha-helical coiled coil (CC) by their rod domains [ PUBMED:22869704 ].

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
(26)
Full
(21973)
Representative proteomes UniProt
(39126)
RP15
(1921)
RP35
(6237)
RP55
(15872)
RP75
(22111)
Jalview View  View  View  View  View  View  View 
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
(26)
Full
(21973)
Representative proteomes UniProt
(39126)
RP15
(1921)
RP35
(6237)
RP55
(15872)
RP75
(22111)
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
(26)
Full
(21973)
Representative proteomes UniProt
(39126)
RP15
(1921)
RP35
(6237)
RP55
(15872)
RP75
(22111)
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: filament;
Type: Coiled-coil
Sequence Ontology: SO:0001080
Author: Sonnhammer ELL
Number in seed: 26
Number in full: 21973
Average length of the domain: 275.5 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 58 %

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 40.0 40.0
Trusted cut-off 40.0 40.0
Noise cut-off 39.9 39.9
Model length: 312
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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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 Filament domain has been found. There are 84 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
A0A044QV69 View 3D Structure Click here
A0A044UFF5 View 3D Structure Click here
A0A044V2F8 View 3D Structure Click here
A0A077Z6U0 View 3D Structure Click here
A0A077ZG58 View 3D Structure Click here
A0A077ZIY8 View 3D Structure Click here
A0A077ZJF5 View 3D Structure Click here
A0A0G2JU48 View 3D Structure Click here
A0A0G2JUG1 View 3D Structure Click here
A0A0G2JVA8 View 3D Structure Click here
A0A0G2JZM4 View 3D Structure Click here
A0A0G2K0I4 View 3D Structure Click here
A0A0G2K4H7 View 3D Structure Click here
A0A0J9XVJ6 View 3D Structure Click here
A0A0K0DTC5 View 3D Structure Click here
A0A0K0DTG1 View 3D Structure Click here
A0A0K0DVE4 View 3D Structure Click here
A0A0K0E9D4 View 3D Structure Click here
A0A0K0EN92 View 3D Structure Click here
A0A0K0ESM2 View 3D Structure Click here
A0A0N4U679 View 3D Structure Click here
A0A0N4UAR1 View 3D Structure Click here
A0A0N4UE53 View 3D Structure Click here
A0A0N4UFG3 View 3D Structure Click here
A0A0R4IIU9 View 3D Structure Click here
A0A140TA62 View 3D Structure Click here
A0A158Q674 View 3D Structure Click here
A0A183XIJ6 View 3D Structure Click here
A0A1I9G628 View 3D Structure Click here
A0A286Y951 View 3D Structure Click here
A0A286YA92 View 3D Structure Click here
A0A2K6VS99 View 3D Structure Click here
A0A2K6WLA7 View 3D Structure Click here
A0A2R8PXK4 View 3D Structure Click here
A0A2R8PYZ9 View 3D Structure Click here
A0A2R8Q483 View 3D Structure Click here
A0A2R8QD52 View 3D Structure Click here
A0A2R8QPG3 View 3D Structure Click here
A0A2R8RV77 View 3D Structure Click here
A0A2R8VHP3 View 3D Structure Click here