Summary: Intermediate filament head (DNA binding) region

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Intermediate filament Edit Wikipedia article

Structure of intermediate filament

Intermediate filament tail domain

structure of lamin a/c globular domain

Identifiers

Symbol

IF_tail

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Intermediate filament protein

human vimentin coil 2b fragment (cys2)

Identifiers

Symbol

Filament

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Intermediate filament head (DNA binding) region

Identifiers

Symbol

Filament_head

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Intermediate filaments (IFs) are cytoskeletal components found in metazoan cells. They are composed of a family of related proteins sharing common structural and sequence features. Intermediate filaments have an average diameter of 10 nanometers, which is between that of 7 nm actin (microfilaments), and that of 25 nm microtubules, although they were initially designated 'intermediate' because their average diameter is between those of narrower microfilaments (actin) and wider myosin filaments found in muscle cells.^[1]^[2] Most types of intermediate filaments are cytoplasmic, but one type, the lamins, are nuclear.

[edit] Structure

The structure of proteins that form IF was first predicted by computerized analysis of the amino acid sequence of a human epidermal keratin derived from cloned cDNAs.^[3] Analysis of a second keratin sequence revealed that the two types of keratins share only about 30% amino acid sequence homology but share similar patterns of secondary structure domains.^[4] As suggested by the first model, all IF proteins appear to have a central alpha-helical rod domain that is composed of four alpha-helical segments (named as 1A, 1B, 2A and 2B) separated by three linker regions. ^[4]^[5]

The N and C-termini of IF proteins are non-alpha-helical regions and show wide variation in their lengths and sequences across IF families. The basic building-block for IFs is a parallel and in-register dimer. The dimer is formed through the interaction of the rod domain to form a coiled coil.^[6] Cytoplasmic IF assemble into non-polar unit-length filaments (ULF), which then assemble into longer structures. Part of the assembly process includes a compaction step, in which ULF tighten and assume a smaller diameter. The reasons for this compaction are not well understood, and IF are routinely observed to have diameters ranging between 6 and 12 nm.

The N-terminal "head domain" binds DNA.^[7] Vimentin heads are able to alter nuclear architecture and chromatin distribution, and the liberation of heads by HIV-1 protease may play an important role in HIV-1 associated cytopathogenesis and carcinogenesis.^[8] Phosphorylation of the head region can affect filament stability.^[9] The head has been shown to interact with the rod domain of the same protein.^[10]

C-terminal "tail domain" shows extreme length variation between different IF proteins.^[11]

The anti-parallel orientation of tetramers means that, unlike microtubules and microfilaments, which have a plus end and a minus end, IFs lack polarity and cannot serve as basis for cell motility and intracellular transport.

Also, as opposed to actin or tubulin, intermediate filaments do not contain a binding site for a nucleoside triphosphate.

Cytoplasmic IF do not undergo treadmilling like microtubules and actin fibers, but they are dynamic. For a review see: [1].

[edit] Biomechanical properties

IFs are rather deformable proteins that can be stretched several times their initial length.^[12] The key to facilitate this large deformation is due to their hierarchical structure, which facilitates a cascaded activation of deformation mechanisms at different levels of strain.^[6]

[edit] Types

There are about 70 different genes coding for various intermediate filament proteins. However, different kinds of IFs share basic characteristics: In general, they are all polymers that measure between 9-11 nm in diameter when fully assembled.

IF are subcategorized into six types based on similarities in amino acid sequence and protein structure.

[edit] Types I and II - Acidic and Basic Keratins

keratin intermediate filaments (stained red)

For more details on this topic, see cytokeratin.

These proteins are the most diverse among IFs and constitute type I (acidic) and type II (basic) IF proteins. The many isoforms are divided in two groups:

epithelial keratins (about 20) in epithelial cells (image to right)
trichocytic keratins (about 13) (hair keratins), which make up hair, nails, horns and reptilian scales.

Regardless of the group, keratins are either acidic or basic. Acidic and basic keratins bind each other to form acidic-basic heterodimers and these heterodimers then associate to make a keratin filament.

[edit] Type III

There are four proteins classed as type III IF proteins, which may form homo- or heteropolymeric proteins.

Desmin IFs are structural components of the sarcomeres in muscle cells.
GFAP (glial fibrillary acidic protein) is found in astrocytes and other glia.
Peripherin found in peripheral neurons.
Vimentin, the most widely distributed of all IF proteins, can be found in fibroblasts, leukocytes, and blood vessel endothelial cells. They support the cellular membranes, keep some organelles in a fixed place within the cytoplasm, and transmit membrane receptor signals to the nucleus.

[edit] Type IV

α-Internexin
Neurofilaments - the type IV family of intermediate filaments that is found in high concentrations along the axons of vertebrate neurons.
Synemin
Syncoilin

[edit] Type V - Nuclear Lamins

Lamins

Lamins are fibrous proteins having structural function in the cell nucleus.

In metazoan cells, there are A and B type lamins, which differ in their length and pI. Human cells have three differentially regulated genes. B-type lamins are present in every cell. B type lamins, B1 and B2, are expressed from the LMNB1 and LMNB2 genes on 5q23 and 19q13, respectively. A-type lamins are only expressed following gastrulation. Lamin A and C are the most common A-type lamins and are splice variants of the LMNA gene found at 1q21.

These proteins localize to two regions of the nuclear compartment, the nuclear lamina—a proteinaceous structure layer subjacent to the inner surface of the nuclear envelope and throughout the nucleoplasm in the nucleoplasmic "veil".

Comparison of the lamins to vertebrate cytoskeletal IFs shows that lamins have an extra 42 residues (six heptads) within coil 1b. The c-terminal tail domain contains a nuclear localization signal (NLS), an Ig-fold-like domain, and in most cases a carboxy-terminal CaaX box that is isoprenylated and carboxymethylated (lamin C does not have a CAAX box). Lamin A is further processed to remove the last 15 amino acids and its farnesylated cysteine.

During mitosis, lamins are phosphorylated by MPF, which drives the disassembly of the lamina and the nuclear envelope.

[edit] Type VI

Nestin^[13]

[edit] Unclassified

Beaded Filaments-- Filensin, Phakinin

[edit] Cell adhesion

At the plasma membrane, some keratins interact with desmosomes (cell-cell adhesion) and hemidesmosomes (cell-matrix adhesion) via adapter proteins.

[edit] Associated proteins

Filaggrin binds to keratin fibers in epidermal cells. Plectin links vimentin to other vimentin fibers, as well as to microfilaments, microtubules, and myosin II. Kinesin is being researched and is suggested to connect vimentin to tubulin via motor proteins.

Keratin filaments in epithelial cells link to desmosomes (desmosomes connect the cytoskeleton together) through plakoglobin, desmoplakin, desmogleins, and desmocollins; desmin filaments are connected in a similar way in heart muscle cells.

[edit] Diseases arising from mutations in IF genes

Epidermolysis bullosa simplex; K5 or K14 mutation
Laminopathies are a family of diseases caused by mutations in nuclear lamins and include Hutchinson Gilford Progeria Syndrome and various lipodystrophies and cardiomyopathies among others.
Human Intermediate Filament Database(HIFD), a comprehensive database of human intermediate filament proteins, their associated variations and diseases.

[edit] References

^ Ishikawa H, Bischoff R, Holtzer H (September 1968). "Mitosis and intermediate-sized filaments in developing skeletal muscle". J. Cell Biol. 38 (3): 538–55. doi:10.1083/jcb.38.3.538. PMC 2108373. PMID 5664223.
^ Herrmann H, Bär H, Kreplak L, Strelkov SV, Aebi U (July 2007). "Intermediate filaments: from cell architecture to nanomechanics". Nat. Rev. Mol. Cell Biol. 8 (7): 562–73. doi:10.1038/nrm2197. PMID 17551517.
^ Hanukoglu I, Fuchs E (November 1982). "The cDNA sequence of a human epidermal keratin: divergence of sequence but conservation of structure among intermediate filament proteins". Cell 31 (1): 243–52. doi:10.1016/0092-8674(82)90424-X. PMID 6186381.
^ ^a ^b Hanukoglu I, Fuchs E (July 1983). "The cDNA sequence of a Type II cytoskeletal keratin reveals constant and variable structural domains among keratins". Cell 33 (3): 915–24. doi:10.1016/0092-8674(83)90034-X. PMID 6191871.
^ Lee CH, Kim MS, Chung BM, Leahy DJ, Coulombe PA (July 2012). "Structural basis for heteromeric assembly and perinuclear organization of keratin filaments". Nat. Struct. Mol. Biol. 19 (7): 707–15. doi:10.1038/nsmb.2330. PMID 22705788.
^ ^a ^b Qin Z, Kreplak L, Buehler MJ (2009). "Hierarchical structure controls nanomechanical properties of vimentin intermediate filaments". PLoS ONE 4 (10): e7294. doi:10.1371/journal.pone.0007294. PMC 2752800. PMID 19806221.
^ Wang Q, Tolstonog GV, Shoeman R, Traub P (August 2001). "Sites of nucleic acid binding in type I-IV intermediate filament subunit proteins". Biochemistry 40 (34): 10342–9. doi:10.1021/bi0108305. PMID 11513613.
^ Shoeman RL, Huttermann C, Hartig R, Traub P (January 2001). "Amino-terminal polypeptides of vimentin are responsible for the changes in nuclear architecture associated with human immunodeficiency virus type 1 protease activity in tissue culture cells". Mol. Biol. Cell 12 (1): 143–54. PMC 30574. PMID 11160829.
^ Takemura M, Gomi H, Colucci-Guyon E, Itohara S (August 2002). "Protective role of phosphorylation in turnover of glial fibrillary acidic protein in mice". J. Neurosci. 22 (16): 6972–9. PMID 12177195.
^ Parry DA, Marekov LN, Steinert PM, Smith TA (2002). "A role for the 1A and L1 rod domain segments in head domain organization and function of intermediate filaments: structural analysis of trichocyte keratin". J. Struct. Biol. 137 (1-2): 97–108. doi:10.1006/jsbi.2002.4437. PMID 12064937.
^ Quinlan R, Hutchison C, Lane B (1995). "Intermediate filament proteins". Protein Profile 2 (8): 795–952. PMID 8771189.
^ Herrmann H, Bär H, Kreplak L, Strelkov SV, Aebi U (July 2007). "Intermediate filaments: from cell architecture to nanomechanics". Nat. Rev. Mol. Cell Biol. 8 (7): 562–73. doi:10.1038/nrm2197. PMID 17551517. Qin Z, Kreplak L, Buehler MJ (2009). "Hierarchical structure controls nanomechanical properties of vimentin intermediate filaments". PLoS ONE 4 (10): e7294. doi:10.1371/journal.pone.0007294. PMC 2752800. PMID 19806221. Kreplak L, Fudge D (January 2007). "Biomechanical properties of intermediate filaments: from tissues to single filaments and back". Bioessays 29 (1): 26–35. doi:10.1002/bies.20514. PMID 17187357. Qin Z, Buehler MJ, Kreplak L (January 2010). "A multi-scale approach to understand the mechanobiology of intermediate filaments". J Biomech 43 (1): 15–22. doi:10.1016/j.jbiomech.2009.09.004. PMID 19811783. Qin Z, Kreplak L, Buehler MJ (October 2009). "Nanomechanical properties of vimentin intermediate filament dimers". Nanotechnology 20 (42): 425101. doi:10.1088/0957-4484/20/42/425101. PMID 19779230.
^ Steinert PM, Chou YH, Prahlad V, Parry DA, Marekov LN, Wu KC, Jang SI, Goldman RD (April 1999). "A high molecular weight intermediate filament-associated protein in BHK-21 cells is nestin, a type VI intermediate filament protein. Limited co-assembly in vitro to form heteropolymers with type III vimentin and type IV alpha-internexin". J. Biol. Chem. 274 (14): 9881–90. doi:10.1074/jbc.274.14.9881. PMID 10092680.

[edit] Further reading

Herrmann H, Harris JR, ed. (1998). Intermediate filaments. Springer. ISBN 978-0-306-45854-5.
Omary MB, Coulombe PA, ed. (2004). Intermediate filament cytoskeleton. Gulf Professional Publishing. ISBN 978-0-12-564173-9.
Paramio JM, ed. (2006). Intermediate filaments. Springer. ISBN 978-0-387-33780-7.

[edit] External links

Wikimedia Commons has media related to: Intermediate filament protein, coiled coil region

Intermediate Filament Proteins at the US National Library of Medicine Medical Subject Headings (MeSH)
http://www.interfil.org/browse_interfil.php

Proteins of the cytoskeleton

Human

Microfilaments
(ABPs)

Myofilament

Actins	A1 A2 B C1 G1 G2

Myosins	I MYO1A MYO1B MYO1C MYO1D MYO1E MYO1F MYO1G MYO1H) II MYH1 MYH2 MYH3 MYH4 MYH6 MYH7 MYH7B MYH8 MYH9 MYH10 MYH11 MYH13 MYH14 MYH15 MYH16 III MYO3A MYO3B V MYO5A MYO5B MYO5C VI MYO6 VII MYO7A MYO7B IX MYO9A MYO9B X MYO10 XV MYO15A XVIII MYO18A MYO18B LC MYL1 MYL2 MYL3 MYL4 MYL5 MYL6 MYL6B MYL7 MYL9 MYLIP MYLK MYLK2 MYLL1

Other	Tropomodulin 1 2 3 4 Troponin T 1 2 3 C 1 2 I 1 2 3 Tropomyosin 1 2 3 4 Actinin 1 2 3 4 Arp2/3 complex actin depolymerizing factors Cofilin 1 2 Destrin Gelsolin Profilin 1 2 Titin

Other

IFs

Type 1/2
(Keratin,
Cytokeratin)

Epithelial keratins (soft alpha-keratins)	type I/chromosome 17 10 12 13 14 15 16 17 19 20 chromosome 12 18 none 21 type II/chromosome 12 1 2A 3 4 5 6A 6B 7 8 9

Hair keratins (hard alpha-keratins)	type I/chromosome 17 31 32 33A 33B 34 35 36 37 38 type II/chromosome 12 81 82 83 84 85 86

Ungrouped alpha	chromosome 17 23 24 25 26 27 28 39 40 chromosome 12 71 72 73 74 75 76 77 78 79 80

Not alpha	Beta-keratin

Type 3

Type 4

Type 5

Lamin A
B

Microtubules/
MAPs

Kinesins	KIF1A KIF1B KIF2A KIF2C KIF3B KIF3C KIF4A KIF4B KIF5A KIF5B KIF5C KIF6 KIF7 KIF9 KIF11 KIF12 KIF13A KIF13B KIF14 KIF15 KIF16B KIF17 KIF18A KIF18B KIF19 KIF20A KIF20B KIF21A KIF21B KIF22 KIF23 KIF24 KIF25 KIF26A KIF26B KIF27 KIFC1 KIFC2 KIFC3

Dyneins	axonemal: DNAH1 DNAH2 DNAH3 DNAH5 DNAH6 DNAH7 DNAH8 DNAH9 DNAH10 DNAH11 DNAH12 DNAH13 DNAH14 DNAH17 DNAI1 DNAI2 DNALI1 DNAL1 DNAL4 cytoplasmic: DYNC1H1 DYNC2H1 DYNC1I1 DYNC1I2 DYNC1LI1 DYNC1LI2 DYNC2LI1 DYNLL1 DYNLL2 DYNLRB1 DYNLRB2 DYNLT1 DYNLT3

Other	Tau protein Dynactin DCTN1 Tubulins TUBA1A TUBA1B TUBA1C TUBA3C TUBA3D TUBA3E TUBA4A TUBA8 Stathmin Tektin TEKT1 TEKT2 TEKT3 TEKT4 TEKT5 Dynamin DNM1 DNM2 DNM3

Catenins

Membrane

Dystrophin
- Dystroglycan
Utrophin
Ankyrin
- ANK1
- ANK2
- ANK3
Spectrin
- SPTA1
- SPTAN1
- SPTB
- SPTBN1
- SPTBN2
- SPTBN4
- SPTBN5

Other

Nonhuman

See also: cytoskeletal defects B strc: edmb (perx), skel (ctrs), epit, cili, mito, nucl (chro)

This article incorporates text from the public domain Pfam and InterPro IPR001322

This article incorporates text from the public domain Pfam and InterPro IPR006821

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 head (DNA binding) region Provide feedback

This family represents the N-terminal head region of intermediate filaments. Intermediate filament heads bind DNA [1]. Vimentin heads are able to alter nuclear architecture and chromatin distribution, and the liberation of heads by HIV-1 protease liberates may play an important role in HIV-1 associated cytopathogenesis and carcinogenesis [2]. Phosphorylation of the head region can affect filament stability [3]. The head has been shown to interaction with the rod domain of the same protein [4].

Literature references

Wang Q, Tolstonog GV, Shoeman R, Traub P; , Biochemistry 2001;40:10342-10349.: Sites of nucleic acid binding in type I-IV intermediate filament subunit proteins. PUBMED:11513613 EPMC:11513613
Shoeman RL, Huttermann C, Hartig R, Traub P; , Mol Biol Cell 2001;12:143-154.: Amino-terminal polypeptides of vimentin are responsible for the changes in nuclear architecture associated with human immunodeficiency virus type 1 protease activity in tissue culture cells. PUBMED:11160829 EPMC:11160829
Takemura M, Gomi H, Colucci-Guyon E, Itohara S; , J Neurosci 2002;22:6972-6979.: Protective role of phosphorylation in turnover of glial fibrillary acidic protein in mice. PUBMED:12177195 EPMC:12177195
Parry DA, Marekov LN, Steinert PM, Smith TA; , J Struct Biol 2002;137:97-108.: A Role for the 1A and L1 Rod Domain Segments in Head Domain Organization and Function of Intermediate Filaments: Structural Analysis of Trichocyte Keratin. PUBMED:12064937 EPMC:12064937

External database links

PANDIT:	PF04732
Pseudofam:	PF04732
SCOP:	1gk7
SYSTERS:	Filament_head

This tab holds annotation information from the InterPro database.

InterPro entry IPR006821

This entry represents the N-terminal head domain of intermediate filaments. Intermediate filament heads bind DNA [PUBMED:11513613]. Vimentin heads are able to alter nuclear architecture and chromatin distribution, and the liberation of heads by HIV-1 protease liberates may play an important role in HIV-1 associated cytopathogenesis and carcinogenesis [PUBMED:11160829]. Phosphorylation of the head region can affect filament stability [PUBMED:12177195]. The head has been shown to interaction with the rod domain of the same protein [PUBMED:12064937].

Gene Ontology

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

Cellular component

intermediate filament (GO:0005882)

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 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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RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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	Seed (45)	Full (462)	Representative proteomes				NCBI (404)	Meta (0)
	Seed (45)	Full (462)	RP15 (6)	RP35 (27)	RP55 (78)	RP75 (185)	NCBI (404)	Meta (0)
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¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (45)	Full (462)	Representative proteomes				NCBI (404)	Meta (0)
	Seed (45)	Full (462)	RP15 (6)	RP35 (27)	RP55 (78)	RP75 (185)	NCBI (404)	Meta (0)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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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.

	Seed (45)	Full (462)	Representative proteomes				NCBI (404)	Meta (0)
	Seed (45)	Full (462)	RP15 (6)	RP35 (27)	RP55 (78)	RP75 (185)	NCBI (404)	Meta (0)
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.

External links

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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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.

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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

Seed source:

DOMO:DM04896;

Previous IDs:

filament_head;

Type:

Family

Author:

Kerrison ND

Number in seed:

45

Number in full:

462

Average length of the domain:

84.80 aa

Average identity of full alignment:

31 %

Average coverage of the sequence by the domain:

16.72 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	21.8	21.8
Trusted cut-off	22.1	21.9
Noise cut-off	21.0	21.7

Model length:

89

Family (HMM) version:

9

Download:

download the raw HMM for this family

Species distribution

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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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order
family
genus
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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Filament_head (PF04732)

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Summary: Intermediate filament head (DNA binding) region

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Intermediate filament Edit Wikipedia article

Contents

[edit] Structure

[edit] Biomechanical properties

[edit] Types

[edit] Types I and II - Acidic and Basic Keratins

[edit] Type III

[edit] Type IV

[edit] Type V - Nuclear Lamins

[edit] Type VI

[edit] Unclassified

[edit] Cell adhesion

[edit] Associated proteins

[edit] Diseases arising from mutations in IF genes

[edit] References

[edit] Further reading

[edit] External links

Intermediate filament head (DNA binding) region Provide feedback

Literature references

External database links

InterPro entry IPR006821

Gene Ontology

Domain organisation

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How the sunburst is generated

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Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

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Interactive tree