Summary: Talin, middle domain

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Wikipedia: Talin protein
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Talin protein Edit Wikipedia article

Talin, middle domain

Identifiers

Symbol

Talin_middle

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

talin 1
Identifiers
Symbol	TLN1
Alt. symbols	TLN
Entrez	7094
HUGO	11845
OMIM	186745
RefSeq	NM_006289
UniProt	Q9Y490
Other data
Locus	Chr. 9 p23-p21

talin 2
Identifiers
Symbol	TLN2
Entrez	83660
HUGO	15447
OMIM	607349
RefSeq	NM_015059
UniProt	Q9Y4G6
Other data
Locus	Chr. 15 q15-q21

Talin is a high-molecular-weight cytoskeletal protein concentrated at regions of cell–substratum contact^[1] and, in lymphocytes, at cell–cell contacts.^[2]^[3] Discovered in 1983 by Keith Burridge and colleagues,^[1] talin is a ubiquitous cytosolic protein that is found in high concentrations in focal adhesions. It is capable of linking integrins to the actin cytoskeleton either directly or indirectly by interacting with vinculin and alpha-actinin.^[4]

Integrin receptors are involved in the attachment of adherent cells to the extracellular matrix^[5]^[6] and of lymphocytes to other cells. In these situations, talin codistributes with concentrations of integrins in the plasma membrane.^[7]^[8] Furthermore, in vitro binding studies suggest that integrins bind to talin, although with low affinity.^[9] Talin also binds with high affinity to vinculin,^[10] another cytoskeletal protein concentrated at points of cell adhesion.^[11] Finally, talin is a substrate for the calcium-ion activated protease, calpain II,^[12] which is also concentrated at points of cell–substratum contact.^[13]

[edit] Protein domains

Talin consists of a large C-terminal rod domain that contains bundles of alpha helices and an N-terminal FERM (band 4.1, ezrin, radixin, and moesin) domain with three subdomains: F1, F2, and F3.^[14]^[15]^[16]^[17] The F3 subdomain of the FERM domain contains the highest affinity integrin-binding site for integrin β tails and is sufficient to activate integrins.^[18]

[edit] Middle domain

[edit] Structure

Talin also has a middle domain, which has a structure consisting of five alpha helices that fold into a bundle. It contains a Vinculin binding site (VBS) composed of a hydrophobic surface spanning five turns of helix four.

[edit] Function

Activation of the VBS leads to the recruitment of Vinculin, talin to form a complex with the integrins which aids stable cell adhesion. Formation of the complex between VBS and Vinculin requires prior unfolding of this middle domain: once released from the talin hydrophobic core, the VBS helix is then available to induce the 'bundle conversion' conformational change within the vinculin head domain thereby displacing the intramolecular interaction with the vinculin tail, allowing vinculin to bind actin.^[16]

[edit] Vinculin binding site

VBS

human vinculin head (1-258) in complex with talin's vinculin binding site 3 (residues 1944-1969)

Identifiers

Symbol

VBS

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

[edit] Function

Vinculin binding sites are protein domains predominantly found in talin and talin-like molecules, enabling binding of vinculin to talin, stabilising integrin-mediated cell-matrix junctions. Talin, in turn, links integrins to the actin cytoskeleton.

[edit] Structure

The consensus sequence for Vinculin binding sites is LxxAAxxVAxxVxxLIxxA, with a secondary structure prediction of four amphipathic helices. The hydrophobic residues that define the VBS are themselves 'masked' and are buried in the core of a series of helical bundles that make up the talin rod.^[19]

[edit] Activation the integrin αIIbβ3

Model of talin-induced integrin activation

A structure–function analysis reported recently^[20] provides a cogent structural model (see top right) to explain talin-dependent integrin activation in three steps:

The talin F3 domain (surface representation; colored by charge), freed from its autoinhibitory interactions in the full-length protein, becomes available for binding to the integrin.
F3 engages the membrane-distal part of the β3-integrin tail (in red), which becomes ordered, but the α–β integrin interactions that hold the integrin in the low-affinity conformation remain intact.
In a subsequent step, F3 engages the membrane-proximal portion of the β3 tail while maintaining its membrane–distal interactions.

[edit] Human proteins containing this domain

TLN1; TLN2;

[edit] See also

Actin-binding protein
Merlin (protein) an acronym for "Moesin-Ezrin-Radixin-Like Protein"

[edit] References

^ ^a ^b Burridge K, Connell L (1983). "A new protein of adhesion plaques and ruffling membranes". J. Cell Biol. 97 (2): 359–67. doi:10.1083/jcb.97.2.359. PMC 2112532. PMID 6684120.
^ Kupfer A, Singer SJ, Dennert G (1986). "On the mechanism of unidirectional killing in mixtures of two cytotoxic T lymphocytes. Unidirectional polarization of cytoplasmic organelles and the membrane-associated cytoskeleton in the effector cell". J. Exp. Med. 163 (3): 489–98. doi:10.1084/jem.163.3.489. PMC 2188060. PMID 3081676.
^ Burn P, Kupfer A, Singer SJ (1988). "Dynamic membrane-cytoskeletal interactions: specific association of integrin and talin arises in vivo after phorbol ester treatment of peripheral blood lymphocytes". Proc. Natl. Acad. Sci. U.S.A. 85 (2): 497–501. doi:10.1073/pnas.85.2.497. PMC 279577. PMID 3124107.
^ Alan D. Michelson (2006). Platelets, Second Edition. Boston: Academic Press. ISBN 0-12-369367-5.
^ Hynes RO (1987). "Integrins: a family of cell surface receptors". Cell 48 (4): 549–54. doi:10.1016/0092-8674(87)90233-9. PMID 3028640.
^ Ruoslahti E, Pierschbacher MD (1987). "New perspectives in cell adhesion: RGD and integrins". Science 238 (4826): 491–7. doi:10.1126/science.2821619. PMID 2821619.
^ Chen WT, Hasegawa E, Hasegawa T, Weinstock C, Yamada KM (1985). "Development of cell surface linkage complexes in cultured fibroblasts". J. Cell Biol. 100 (4): 1103–14. doi:10.1083/jcb.100.4.1103. PMC 2113771. PMID 3884631.
^ Kupfer A, Singer SJ (1989). "The specific interaction of helper T cells and antigen-presenting B cells. IV. Membrane and cytoskeletal reorganizations in the bound T cell as a function of antigen dose". J. Exp. Med. 170 (5): 1697–713. doi:10.1084/jem.170.5.1697. PMC 2189515. PMID 2530300.
^ Horwitz A, Duggan K, Buck C, Beckerle MC, Burridge K (1986). "Interaction of plasma membrane fibronectin receptor with talin—a transmembrane linkage". Nature 320 (6062): 531–3. doi:10.1038/320531a0. PMID 2938015.
^ Burridge K, Mangeat P (1984). "An interaction between vinculin and talin". Nature 308 (5961): 744–6. doi:10.1038/308744a0. PMID 6425696.
^ Geiger B (1979). "A 130K protein from chicken gizzard: its localization at the termini of microfilament bundles in cultured chicken cells". Cell 18 (1): 193–205. doi:10.1016/0092-8674(79)90368-4. PMID 574428.
^ Fox JE, Goll DE, Reynolds CC, Phillips DR (1985). "Identification of two proteins (actin-binding protein and P235) that are hydrolyzed by endogenous Ca2+-dependent protease during platelet aggregation". J. Biol. Chem. 260 (2): 1060–6. PMID 2981831.
^ Beckerle MC, Burridge K, DeMartino GN, Croall DE (1987). "Colocalization of calcium-dependent protease II and one of its substrates at sites of cell adhesion". Cell 51 (4): 569–77. doi:10.1016/0092-8674(87)90126-7. PMID 2824061.
^ Chishti AH, Kim AC, Marfatia SM, Lutchman M, Hanspal M, Jindal H, Liu SC, Low PS, Rouleau GA, Mohandas N, Chasis JA, Conboy JG, Gascard P, Takakuwa Y, Huang SC, Benz EJ, Bretscher A, Fehon RG, Gusella JF, Ramesh V, Solomon F, Marchesi VT, Tsukita S, Tsukita S, Hoover KB (1998). "The FERM domain: a unique module involved in the linkage of cytoplasmic proteins to the membrane". Trends Biochem. Sci. 23 (8): 281–2. doi:10.1016/S0968-0004(98)01237-7. PMID 9757824.
^ García-Alvarez B, de Pereda JM, Calderwood DA, Ulmer TS, Critchley D, Campbell ID, Ginsberg MH, Liddington RC (2003). "Structural determinants of integrin recognition by talin". Mol. Cell 11 (1): 49–58. doi:10.1016/S1097-2765(02)00823-7. PMID 12535520.
^ ^a ^b Papagrigoriou E, Gingras AR, Barsukov IL, Bate N, Fillingham IJ, Patel B, Frank R, Ziegler WH, Roberts GC, Critchley DR, Emsley J (2004). "Activation of a vinculin-binding site in the talin rod involves rearrangement of a five-helix bundle". EMBO J. 23 (15): 2942–51. doi:10.1038/sj.emboj.7600285. PMC 514914. PMID 15272303.
^ Rees DJ, Ades SE, Singer SJ, Hynes RO (1990). "Sequence and domain structure of talin". Nature 347 (6294): 685–9. doi:10.1038/347685a0. PMID 2120593.
^ Calderwood DA, Yan B, de Pereda JM, Alvarez BG, Fujioka Y, Liddington RC, Ginsberg MH (2002). "The phosphotyrosine binding-like domain of talin activates integrins". J. Biol. Chem. 277 (24): 21749–58. doi:10.1074/jbc.M111996200. PMID 11932255.
^ Gingras AR, Vogel KP, Steinhoff HJ, Ziegler WH, Patel B, Emsley J, Critchley DR, Roberts GC, Barsukov IL (February 2006). "Structural and dynamic characterization of a vinculin binding site in the talin rod". Biochemistry 45 (6): 1805–17. doi:10.1021/bi052136l. PMID 16460027.
^ Wegener KL, Partridge AW, Han J, Pickford AR, Liddington RC, Ginsberg MH, Campbell ID (2007). "Structural basis of integrin activation by talin". Cell 128 (1): 171–82. doi:10.1016/j.cell.2006.10.048. PMID 17218263.

[edit] External links

MBInfo: Talin
MBInfo: Talin activates integrins
Talin-1 UniProtKB/Swiss-Prot entry Q9Y490
Talin substrate for calpain – PMAP The Proteolysis Map animation.
Talin-1 Info with links in the Cell Migration Gateway
Talin-2 Info with links in the Cell Migration Gateway
Integrins at the US National Library of Medicine Medical Subject Headings (MeSH)

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)

v t e Growth factors

Fibroblast	FGF receptor ligands: FGF1/FGF2/FGF5 · FGF3/FGF4/FGF6 · KGF (FGF7/FGF10/FGF22) · FGF8/FGF17/FGF18 · FGF9/FGF16/FGF20 FGF homologous factors: FGF11 · FGF12 · FGF13 · FGF14 hormone-like: FGF19 · FGF21 · FGF23

EGF-like domain	TGF-α · EGF · HB-EGF

TGFβ pathway	TGF-β (TGF-β1, TGF-β2, TGF-β3)

Insulin-like	IGF-1 · IGF-2

Platelet-derived	PDGFA · PDGFB · PDGFC · PDGFD

Vascular endothelial	VEGF-A · VEGF-B · VEGF-C · VEGF-D · PGF

Other	Nerve · Hepatocyte

B trdu: iter (nrpl/grfl/cytl/horl), csrc (lgic, enzr, gprc, igsr, intg, nrpr/grfr/cytr), itra (adap, gbpr, mapk), calc, lipd; path (hedp, wntp, tgfp+mapp, notp, jakp, fsap, hipp, tlrp)

Transmembrane receptors: Immunoglobulin superfamily immune receptors

Antibody receptor:
Fc receptor

Epsilon (ε)	FcεRI · (FcεRII is C-type lectin)

Gamma (γ)	FcγRI · FcγRII · FcγRIII · Neonatal

Alpha (α)/mu (μ)	FcαRI · Fcα/μR

Secretory	Polymeric immunoglobulin receptor

Antigen receptor

B cells

Antigen receptor	BCR

Co-receptor	stimulate: CD21/CD19/CD81 inhibit: CD22

Accessory molecules	Ig-α/Ig-β (CD79)

T cells

Ligands	MHC (MHC class I and MHC class II)

Antigen receptor	TCR: TRA@ · TRB@ · TRD@ · TRG@

Co-receptors	CD8 (with two glycoprotein chains CD8α and CD8β) · CD4

Accessory molecules	CD3 · CD3γ · CD3δ · CD3ε · ζ-chain (also called CD3ζ and TCRζ)

Cytokine receptor

see cytokine receptors

Killer-cell IG-like receptors

KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL4, KIR2DL5A, KIR2DL5B, KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS4, KIR2DS5, KIR3DL1, KIR3DL2, KIR3DL3, KIR3DS1

Leukocyte IG-like receptors

LILRA1 · LILRA2 · LILRA3 · LILRA4 · LILRA5 · LILRA6 · LILRB1 · LILRB2 · LILRB3 · LILRB4 · LILRB5 · LILRA6 · LILRA5

B trdu: iter (nrpl/grfl/cytl/horl), csrc (lgic, enzr, gprc, igsr, intg, nrpr/grfr/cytr), itra (adap, gbpr, mapk), calc, lipd; path (hedp, wntp, tgfp+mapp, notp, jakp, fsap, hipp, tlrp)

M: LMC

cell/phys/auag/auab/comp, igrc

imdf/ipig/hyps/tumr

proc, drug (L3/4)

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.

Talin, middle domain Provide feedback

Members of this family adopt a structure consisting of five alpha helices that fold into a bundle. They contain a Vinculin binding site (VBS) composed of a hydrophobic surface spanning five turns of helix four. Activation of the VBS causes subsequent recruitment of Vinculin, which enables maturation of small integrin/talin complexes into more stable adhesions. Formation of the complex between VBS and Vinculin requires prior unfolding of this middle domain: once released from the talin hydrophobic core, the VBS helix is then available to induce the 'bundle conversion' conformational change within the vinculin head domain thereby displacing the intramolecular interaction with the vinculin tail, allowing vinculin to bind actin [1].

Literature references

Papagrigoriou E, Gingras AR, Barsukov IL, Bate N, Fillingham IJ, Patel B, Frank R, Ziegler WH, Roberts GC, Critchley DR, Emsley J; , EMBO J. 2004;23:2942-2951.: Activation of a vinculin-binding site in the talin rod involves rearrangement of a five-helix bundle. PUBMED:15272303 EPMC:15272303

External database links

PANDIT:	PF09141
Pseudofam:	PF09141
SCOP:	1sj7
SYSTERS:	Talin_middle

This tab holds annotation information from the InterPro database.

InterPro entry IPR015224

This domain adopts a structure consisting of five alpha helices that fold into a bundle. It contains a Vinculin binding site (VBS) composed of a hydrophobic surface spanning five turns of helix four. Activation of the VBS causes subsequent recruitment of Vinculin, which enables maturation of small integrin/talin complexes into more stable adhesions. Formation of the complex between VBS and Vinculin requires prior unfolding of this middle domain: once released from the talin hydrophobic core, the VBS helix is then available to induce the 'bundle conversion' conformational change within the vinculin head domain thereby displacing the intramolecular interaction with the vinculin tail, allowing vinculin to bind actin [PUBMED:15272303].

Gene Ontology

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

Cellular component	ruffle (GO:0001726)
Cellular component	focal adhesion (GO:0005925)
Molecular function	structural constituent of cytoskeleton (GO:0005200)
Biological process	cytoskeletal anchoring at plasma membrane (GO:0007016)

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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We make a range of alignments for each Pfam-A family:

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full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

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	Seed (6)	Full (194)	Representative proteomes				NCBI (161)	Meta (0)
	Seed (6)	Full (194)	RP15 (33)	RP35 (42)	RP55 (70)	RP75 (108)	NCBI (161)	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 (6)	Full (194)	Representative proteomes				NCBI (161)	Meta (0)
	Seed (6)	Full (194)	RP15 (33)	RP35 (42)	RP55 (70)	RP75 (108)	NCBI (161)	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 (6)	Full (194)	Representative proteomes				NCBI (161)	Meta (0)
	Seed (6)	Full (194)	RP15 (33)	RP35 (42)	RP55 (70)	RP75 (108)	NCBI (161)	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.

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

Seed source:

pdb_1sj7

Previous IDs:

none

Type:

Domain

Author:

Sammut SJ

Number in seed:

6

Number in full:

194

Average length of the domain:

157.90 aa

Average identity of full alignment:

59 %

Average coverage of the sequence by the domain:

6.87 %

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	25.0	25.0
Trusted cut-off	35.3	25.2
Noise cut-off	24.9	23.7

Model length:

161

Family (HMM) version:

5

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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Show

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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How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

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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Tree controls

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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.

Interactions

There is 1 interaction for this family. More...

Talin_middle

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 Talin_middle domain has been found. There are 6 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.

Loading structure mapping...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Talin_middle (PF09141)

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Summary: Talin, middle domain

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Talin protein Edit Wikipedia article

Contents

[edit] Protein domains

[edit] Middle domain

[edit] Structure

[edit] Function

[edit] Vinculin binding site

[edit] Function

[edit] Structure

[edit] Activation the integrin αIIbβ3

[edit] Human proteins containing this domain

[edit] See also

[edit] References

[edit] External links

Talin, middle domain Provide feedback

Literature references

External database links

InterPro entry IPR015224

Gene Ontology

Domain organisation

Alignments

Alignment types

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Reformatting

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View options

Format an alignment

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External links

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Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures