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59  structures 153  species 3  interactions 945  sequences 57  architectures

Family: Integrin_beta (PF00362)

Summary: Integrin, beta chain

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Integrin alphavbeta3 extracellular domains
PDB 1jv2 EBI.jpg
Structure of the extracellular segment of integrin alpha Vbeta3.[1]
Identifiers
Symbol Integrin_alphaVbeta3
Pfam PF08441
Pfam clan CL0159
InterPro IPR013649
SCOP 1jv2
SUPERFAMILY 1jv2
Integrin alpha cytoplasmic region
PDB 1dpk EBI.jpg
Structure of chaperone protein PAPD.[2]
Identifiers
Symbol Integrin_alpha
Pfam PF00357
InterPro IPR000413
PROSITE PDOC00215
SCOP 1dpk
SUPERFAMILY 1dpk
OPM superfamily 197
OPM protein 2knc
Integrin, beta chain
Integrinalpha.png
Identifiers
Symbol Integrin_beta
Pfam PF00362
InterPro IPR002369
SMART SM00187
PROSITE PDOC00216
SCOP 1jv2
SUPERFAMILY 1jv2
Integrin beta 7 cytoplasmic domain: complex with filamin
PDB 2brq EBI.jpg
crystal structure of the filamin a repeat 21 complexed with the integrin beta7 cytoplasmic tail peptide
Identifiers
Symbol Integrin_b_cyt
Pfam PF08725
InterPro IPR014836
SCOP 1m8O
SUPERFAMILY 1m8O

Integrins are transmembrane receptors that mediate the attachment between a cell and its surroundings, such as other cells or the extracellular matrix (ECM). In signal transduction, integrins pass information about the chemical composition and mechanical status of the ECM into the cell. Therefore, in addition to transmitting mechanical forces across otherwise vulnerable membranes, they are involved in cell signaling and the regulation of cell cycle, shape, and motility.

Typically, receptors inform a cell of the molecules in its environment and the cell responds. Not only do integrins perform this outside-in signaling, but they also operate an inside-out mode. Thus, they transduce information from the ECM to the cell, as well as reveal the status of the cell to the outside, allowing rapid and flexible responses to changes in the environment, for example to allow blood coagulation by platelets.

There are many types of integrin, and many cells have multiple types on their surface. Integrins are of vital importance to all animals and have been found in all animals investigated, from sponges to mammals. Integrins have been extensively studied in humans.

Integrins work alongside other proteins such as cadherins, immunoglobulin superfamily cell adhesion molecules, selectins and syndecans to mediate cell–cell and cell–matrix interaction and communication. Integrins bind cell surface and ECM components such as fibronectin, vitronectin, collagen, and laminin.

Structure[edit]

Integrins are obligate heterodimers containing two distinct chains, called the α (alpha) and β (beta) subunits. In mammals, eighteen α and eight β subunits have been characterized, whereas the Drosophila genome encodes only five α and two β subunits, and Caenorhabditis nematodes possess genes for two α subunits and one β.[3] The α and β subunits each penetrate the plasma membrane and possess small cytoplasmic domains.[4]

alpha

gene protein synonyms are
ITGA1 CD49a VLA1
ITGA2 CD49b VLA2
ITGA3 CD49c VLA3
ITGA4 CD49d VLA4
ITGA5 CD49e VLA5
ITGA6 CD49f VLA6
ITGA7 ITGA7 FLJ25220
ITGA8 ITGA8
ITGA9 ITGA9 RLC
ITGA10 ITGA10
ITGA11 ITGA11 HsT18964
ITGAD CD11D FLJ39841
ITGAE CD103 HUMINAE
ITGAL CD11a LFA1A
ITGAM CD11b MAC-1
ITGAV CD51 VNRA, MSK8
ITGA2B CD41 GPIIb
ITGAX CD11c

beta

gene protein synonyms
ITGB1 CD29 FNRB, MSK12, MDF2
ITGB2 CD18 LFA-1, MAC-1, MFI7
ITGB3 CD61 GP3A, GPIIIa
ITGB4 CD104
ITGB5 ITGB5 FLJ26658
ITGB6 ITGB6
ITGB7 ITGB7
ITGB8 ITGB8

In addition, variants of some of the subunits are formed by differential splicing; for example, four variants of the beta-1 subunit exist. Through different combinations of the α and β subunits, some 24 unique integrins are generated, although the number varies according to different studies.[5]

Integrin subunits span the plasma membrane and in general have short cytoplasmic domains of about 40–70 amino acids. The exception is the beta-4 subunit, which has a cytoplasmic domain of 1088 amino acids, one of the largest known cytoplasmic domains of any membrane protein. Outside the cell plasma membrane, the α and β chains lie close together along a length of about 23 nm; the final 5 nm N-termini of each chain forms a ligand-binding region for the extracellular matrix (ECM).

The molecular mass of the integrin subunits can vary from 90 kDa to 160 kDa. Beta subunits have four cysteine-rich repeated sequences. Both α and β subunits bind several divalent cations. The role of divalent cations in the α subunit is unknown, but may stabilize the folds of the protein. The cations in the β subunits are more interesting: they are directly involved in coordinating at least some of the ligands that integrins bind.

There are various ways of categorizing the integrins. For example, a subset of the α chains has an additional structural element (or "domain") inserted toward the N-terminal, the alpha-A domain (so called because it has a similar structure to the A-domains found in the protein von Willebrand factor; it is also termed the α-I domain). Integrins carrying this domain either bind to collagens (e.g. integrins α1 β1, and α2 β1), or act as cell-cell adhesion molecules (integrins of the β2 family). This α-I domain is the binding site for ligands of such integrins. Those integrins that don't carry this inserted domain also have an A-domain in their ligand binding site, but this A-domain is found on the β subunit.

In both cases, the A-domains carry up to three divalent cation binding sites. One is permanently occupied in physiological concentrations of divalent cations, and carries either a calcium or magnesium ion, the principal divalent cations in blood at median concentrations of 1.4 mM (calcium) and 0.8 mM (magnesium). The other two sites become occupied by cations when ligands bind—at least for those ligands involving an acidic amino acid in their interaction sites. An acidic amino acid features in the integrin-interaction site of many ECM proteins, for example as part of the amino acid sequence Arginine-Glycine-Aspartic acid ("RGD" in the one-letter amino acid code).

High resolution structure[edit]

Despite many years of effort, discovering the high-resolution structure of integrins proved to be challenging: membrane proteins are classically difficult to purify, and integrins are also large, complex and linked to many sugar trees ("highly glycosylated"). Low-resolution images of detergent extracts of intact integrin GPIIbIIIa, obtained using electron microscopy, and even data from indirect techniques that investigate the solution properties of integrins using ultracentrifugation and light scattering, were combined with fragmentary high-resolution crystallographic or NMR data from single or paired domains of single integrin chains, and molecular models postulated for the rest of the chains.

Despite these wide-ranging efforts, the X-ray crystal structure obtained for the complete extracellular region of one integrin, αvβ3, was a surprise.[6] It showed the molecule to be folded into an inverted V-shape that potentially brings the ligand-binding sites close to the cell membrane. Perhaps more importantly, the crystal structure was also obtained for the same integrin bound to a small ligand containing the RGD-sequence, the drug cilengitide.[7] As detailed above, this finally revealed why divalent cations (in the A-domains) are critical for RGD-ligand binding to integrins. The interaction of such sequences with integrins is believed to be a primary switch by which ECM exerts its effects on cell behaviour.

The structure poses many questions, especially regarding ligand binding and signal transduction. The ligand binding site is directed towards the C-terminal of the integrin, the region where the molecule emerges from the cell membrane. If it emerges orthogonally from the membrane, the ligand binding site would apparently be obstructed, especially as integrin ligands are typically massive and well cross-linked components of the ECM. In fact, little is known about the angle that membrane proteins subtend to the plane of the membrane; this is a problem difficult to address with available technologies. The default assumption is that they emerge rather like little lollipops, but the evidence for this sweet supposition is noticeable by its absence. The integrin structure has drawn attention to this problem, which may have general implications for how membrane proteins work. It appears that the integrin transmembrane helices are tilted (see "Activation" below), which hints that the extracellular chains may also not be orthogonal with respect to the membrane surface.

Although the crystal structure changed surprisingly little after binding to cilengitide, the current hypothesis is that integrin function involves changes in shape to move the ligand-binding site into a more accessible position, away from the cell surface, and this shape change also triggers intracellular signaling. There is a wide body of cell-biological and biochemical literature that supports this view. Perhaps the most convincing evidence involves the use of antibodies that only recognize integrins when they have bound to their ligands, or are activated. As the "footprint" that an antibody makes on its binding target is roughly a circle about 3 nm in diameter, the resolution of this technique is low. Nevertheless, these so-called LIBS (Ligand-Induced-Binding-Sites) antibodies unequivocally show that dramatic changes in integrin shape routinely occur. However, how the changes detected with antibodies look on the structure is still unknown.

Activation[edit]

When released into the cell membrane, newly synthesized integrin dimers are speculated to be found in the same "bent" conformation revealed by the structural studies described above. One school of thought claims that this bent form prevents them from interacting with their ligands, although bent forms can predominate in high-resolution EM structures of integrin bound to an ECM ligands. Therefore, at least in biochemical experiments, integrin dimers must apparently not be 'unbent' in order to prime them and allow their binding to the ECM. In cells, the priming is accomplished by a protein talin, which binds to the β tail of the integrin dimer and changes its conformation.[8][9] The α and β integrin chains are both class-I transmembrane proteins: they pass the plasma membrane as single transmembrane alpha-helices. Unfortunately, the helices are too long, and recent studies suggest that, for integrin gpIIbIIIa, they are tilted with respect both to one another and to the plane of the membrane. Talin binding alters the angle of tilt of the β3 chain transmembrane helix in model systems and this may reflect a stage in the process of inside-out signalling which primes integrins.[10] Moreover, talin proteins are able to dimerize[11] and thus are thought to intervene in the clustering of integrin dimers which leads to the formation of a focal adhesion. Recently, the Kindlin-1 and Kindlin-2 proteins have also been found to interact with integrin and activate it.[12]

Function[edit]

Integrins have two main functions:

  • Attachment of the cell to the ECM
  • Signal transduction from the ECM to the cell

However, they are also involved in a wide range of other biological activities, including immune patrolling, cell migration, and binding to cells by certain viruses, such as adenovirus, echovirus, hantavirus, and foot and mouth disease viruses.

A prominent function of the integrins is seen in the molecule GPIIbIIIa, an integrin on the surface of blood platelets (thrombocytes) responsible for attachment to fibrin within a developing blood clot. This molecule dramatically increases its binding affinity for fibrin/fibrinogen through association of platelets with exposed collagens in the wound site. Upon association of platelets with collagen, GPIIbIIIa changes shape, allowing it to bind to fibrin and other blood components to form the clot matrix and stop blood loss.

Attachment of cell to the ECM[edit]

Integrins couple the ECM outside a cell to the cytoskeleton (in particular, the microfilaments) inside the cell. Which ligand in the ECM the integrin can bind to is defined by which α and β subunits the integrin is made of. Among the ligands of integrins are fibronectin, vitronectin, collagen, and laminin. The connection between the cell and the ECM may help the cell to endure pulling forces without being ripped out of the ECM. The ability of a cell to create this kind of bond is also of vital importance in ontogeny.

Cell attachment to the ECM is a basic requirement to build a multicellular organism. Integrins are not simply hooks, but give the cell critical signals about the nature of its surroundings. Together with signals arising from receptors for soluble growth factors like VEGF, EGF, and many others, they enforce a cellular decision on what biological action to take, be it attachment, movement, death, or differentiation. Thus integrins lie at the heart of many cellular biological processes. The attachment of the cell takes place through formation of cell adhesion complexes, which consist of integrins and many cytoplasmic proteins, such as talin, vinculin, paxillin, and alpha-actinin. These act by regulating kinases such as FAK (focal adhesion kinase) and Src kinase family members to phosphorylate substrates such as p130CAS thereby recruiting signaling adaptors such as CRK. These adhesion complexes attach to the actin cytoskeleton. The integrins thus serve to link two networks across the plasma membrane: the extracellular ECM and the intracellular actin filamentous system. Integrin alpha6beta4 is an exception: it links to the keratin intermediate filament system in epithelial cells.

Focal adhesions are large molecular complexes, which are generated following interaction of integrins with ECM, then their clustering. The clusters likely provide sufficient intracellular binding sites to permit the formation of stable signaling complexes on the cytoplasmic side of the cell membrane. So the focal adhesions contain integrin ligand, integrin molecule, and associate plaque proteins. Binding is propelled by changes in free energy.[13] As previously stated, these complexes connect the extracellular matrix to actin bundles. Cryo-electron tomography reveals that the adhesion contains particles on the cell membrane with diameter of 25 +/- 5 nm and spaced at approximately 45 nm.[14] Treatment with Rho-kinase inhibitor Y-27632 reduces the size of the particle, and it is extremely mechanosensitive.[15]

One important function of integrins on cells in tissue culture is their role in cell migration. Cells adhere to a substrate through their integrins. During movement, the cell makes new attachments to the substrate at its front and concurrently releases those at its rear. When released from the substrate, integrin molecules are taken back into the cell by endocytosis; they are transported through the cell to its front by the endocytic cycle, where they are added back to the surface. In this way they are cycled for reuse, enabling the cell to make fresh attachments at its leading front. It is not yet clear whether cell migration in tissue culture is an artefact of integrin processing, or whether such integrin-dependent cell migration also occurs in living organisms.

Signal transduction[edit]

Integrins play an important role in cell signaling by modulating the cell signaling pathways of transmembrane protein kinases such as receptor tyrosine kinases (RTK). While the interaction between integrin and receptor tyrosine kinases originally was thought of as uni-directional and supportive, recent studies Indicate that integrins have additional, multi-faceted roles in cell signaling. Integrins can regulate the receptor tyrosine kinase signaling by recruiting specific adaptors to the plasma membrane. For example, β1c integrin recruits Gab1/Shp2 and presents Shp2 to IGF1R, resulting in dephosphorylation of the receptor.[16] In a reverse direction, when a receptor tyrosine kinase is activated, integrins co-localise at focal adhesion with the receptor tyrosine kinases and their associated signaling molecules.

The repertoire of integrins expressed on a particular cell can specify the signaling pathway due to the differential binding affinity of ECM ligands for the integrins. The tissue stiffness and matrix composition can initiate specific signaling pathways regulating cell behavior. Clustering and activation of the integrins/actin complexes strengthen the focal adhesion interaction and initiate the framework for cell signaling through assembly of adhesomes.[17]

Depending on the integrin's regulatory impact on specific receptor tyrosine kinases, the cell can experience:

Knowledge of the relationship between integrins and receptor tyrosine kinase has laid a foundation for new approaches to cancer therapy. Specifically, targeting integrins associated with RTKs is an emerging approach for inhibiting angiogenesis.[18]

Vertebrate integrins[edit]

The following are some of the integrins found in vertebrates:

Name Synonyms Distribution Ligands
α1β1 VLA-1 Many Collagens, laminins[19]
α2β1 VLA-2 Many Collagens, laminins[19]
α3β1 VLA-3 Many Laminin-5
α4β1 VLA-4[19] Hematopoietic cells Fibronectin, VCAM-1[19]
α5β1 VLA-5; fibronectin receptor widespread fibronectin[19] and proteinases
α6β1 VLA-6; laminin receptor widespread laminins
α7β1 muscle, glioma laminins
αLβ2 LFA-1[19] T-lymphocytes ICAM-1, ICAM-2[19]
αMβ2 Mac-1, CR3[19] Neutrophils and monocytes Serum proteins, ICAM-1[19]
αIIbβ3 Fibrinogen receptor; gpIIbIIIa [20] Platelets[19] fibrinogen, fibronectin[19]
αVβ1 ocular melanoma; neurologial tumors vitronectin; fibrinogen
αVβ3 vitronectin receptor[21] activated endothelial cells, melanoma, glioblastoma vitronectin,[21] fibronectin, fibrinogen, osteopontin, Cyr61
αVβ5 widespread, esp. fibroblasts, epithelial cells vitronectin and adenovirus
αVβ6 proliferating epithelia, esp. lung and mammary gland fibronectin; TGFβ1+3
αVβ8 neural tissue; peripheral nerve fibronectin; TGFβ1+3
α6β4 Epithelial cells[19] Laminin[19]

Beta-1 integrins interact with many alpha integrin chains. Gene knockouts of integrins in mice are not always lethal, which suggests that during embryonal development, one integrin may substitute its function for another in order to allow survival. Some integrins are on the cell surface in an inactive state, and can be rapidly primed, or put into a state capable of binding their ligands, by cytokines. Integrins can assume several different well-defined shapes or "conformational states". Once primed, the conformational state changes to stimulate ligand binding, which then activates the receptors — also by inducing a shape change — to trigger outside-in signal transduction.

References[edit]

  1. ^ Xiong JP, Stehle T, Diefenbach B et al. (October 2001). "Crystal structure of the extracellular segment of integrin alpha Vbeta3". Science 294 (5541): 339–45. doi:10.1126/science.1064535. PMC 2885948. PMID 11546839. 
  2. ^ Sauer FG, Fütterer K, Pinkner JS, Dodson KW, Hultgren SJ, Waksman G (August 1999). "Structural basis of chaperone function and pilus biogenesis". Science 285 (5430): 1058–61. doi:10.1126/science.285.5430.1058. PMID 10446050. 
  3. ^ Humphries M.J. (2000). "Integrin structure". Biochem. Soc. Trans. 28 (4): 311–339. doi:10.1042/0300-5127:0280311. PMID 10961914. 
  4. ^ Nermut MV, Green NM, Eason P, Yamada SS, Yamada KM (December 1988). "Electron microscopy and structural model of human fibronectin receptor". EMBO J. 7 (13): 4093–9. PMC 455118. PMID 2977331. 
  5. ^ Hynes R (2002). "Integrins: bidirectional, allosteric signaling machines". Cell 110 (6): 673–87. doi:10.1016/S0092-8674(02)00971-6. PMID 12297042. 
  6. ^ Xiong JP; Stehle, T; Diefenbach, B; Zhang, R; Dunker, R; Scott, DL; Joachimiak, A; Goodman, SL; Arnaout, MA (2001). "Crystal structure of the extracellular segment of integrin αvβ3". Science 294 (5541): 339–345. doi:10.1126/science.1064535. PMC 2885948. PMID 11546839. 
  7. ^ Smith J (2003). "Cilengitide Merck". Curr Opin Investig Drugs 4 (6): 741–5. PMID 12901235. 
  8. ^ Calderwood DA (June 2004). "Talin controls integrin activation". Biochem. Soc. Trans. 32 (Pt3): 434–7. doi:10.1042/BST0320434. PMID 15157154. 
  9. ^ Calderwood DA, Zent R, Grant R, Rees DJ, Hynes RO, Ginsberg MH (October 1999). "The Talin head domain binds to integrin beta subunit cytoplasmic tails and regulates integrin activation". J. Biol. Chem. 274 (40): 28071–4. doi:10.1074/jbc.274.40.28071. PMID 10497155. 
  10. ^ Shattil SJ, Kim C, Ginsberg MH (2010). "The final steps of integrin activation: the end game". Nature Reviews Molecular Cell Biology 11 (4): 288–300. doi:10.1038/nrm2871. PMID 20308986. 
  11. ^ Goldmann WH, Bremer A, Häner M, Aebi U, Isenberg G (1994). "Native talin is a dumbbell-shaped homodimer when it interacts with actin". J. Struct. Biol. 112 (1): 3–10. doi:10.1006/jsbi.1994.1002. PMID 8031639. 
  12. ^ Harburger DS, Bouaouina M, Calderwood DA (April 2009). "Kindlin-1 and −2 directly bind the C-terminal region of beta integrin cytoplasmic tails and exert integrin-specific activation effects". J. Biol. Chem. 284 (17): 11485–97. doi:10.1074/jbc.M809233200. PMC 2670154. PMID 19240021. 
  13. ^ Olberding JE, Thouless MD, Arruda EM, Garikipati K (2010). "The non-equilibrium thermodynamics and kinetics of focal adhesion dynamics". In Buehler, Markus J. PLoS ONE 5 (8): e12043. doi:10.1371/journal.pone.0012043. PMC 2923603. PMID 20805876. 
  14. ^ Patla I, Volberg T, Elad N, Hirschfeld-Warneken V, Grashoff C, Fässler R, Spatz JP, Geiger B, Medalia O (September 2010). "Dissecting the molecular architecture of integrin adhesion sites by cryo-electron tomography". Nat. Cell Biol. 12 (9): 909–15. doi:10.1038/ncb2095. PMID 20694000. 
  15. ^ Gullingsrud J, Sotomayor M. "Mechanosensitive channels". Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology: University of Illinois at Urbana-Champaign. 
  16. ^ Goel, H. L.; Breen, M; Zhang, J; Das, I; Aznavoorian-Cheshire, S; Greenberg, N. M.; Elgavish, A; Languino, L. R. (1 August 2005). "1A Integrin Expression Is Required for Type 1 Insulin-Like Growth Factor Receptor Mitogenic and Transforming Activities and Localization to Focal Contacts". Cancer Research 65 (15): 6692–6700. doi:10.1158/0008-5472.CAN-04-4315. PMID 16061650. 
  17. ^ Kim, Soo-Hyun; Turnbull, Jeremy; Guimond, Scott (2011). "Extracellular matrix and cell signaling: the dynamic cooperation of integrin, proteoglycan and growth factor receptor". Journal of Endocrynology (209): 139–151. 
  18. ^ Carbonell, W. S.; DeLay, M.; Jahangiri, A.; Park, C. C.; Aghi, M. K. (3 May 2013). "1 Integrin Targeting Potentiates Antiangiogenic Therapy and Inhibits the Growth of Bevacizumab-Resistant Glioblastoma". Cancer Research 73 (10): 3145–3154. doi:10.1158/0008-5472.CAN-13-0011. PMID 23644530. 
  19. ^ a b c d e f g h i j k l m Krieger M, Scott MP, Matsudaira PT, Lodish HF, Darnell JE, Zipursky L, Kaiser C, Berk A (2004). Molecular cell biology (fifth ed.). New York: W.H. Freeman and CO. ISBN 0-7167-4366-3. 
  20. ^ http://www.vetpathology.org/cgi/reprint/34/1/61.pdf Vet Path01 34:61-73 (1997)
  21. ^ a b Hermann P, Armant M, Brown E, Rubio M, Ishihara H, Ulrich D, Caspary RG, Lindberg FP, Armitage R, Maliszewski C, Delespesse G, Sarfati M (February 1999). "The vitronectin receptor and its associated CD47 molecule mediates proinflammatory cytokine synthesis in human monocytes by interaction with soluble CD23". J. Cell Biol. 144 (4): 767–75. doi:10.1083/jcb.144.4.767. PMC 2132927. PMID 10037797. 

External links[edit]

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Integrin, beta chain Provide feedback

Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer [1]. The sequences repeats have been trimmed due to an overlap with EGF.

Literature references

  1. May AP, Ponting CP; , Trends Biochem Sci 1999;24:12-13.: Integrin alpha- and beta 4-subunit-domain homologues in cyanobacterial proteins. PUBMED:10087915 EPMC:10087915


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002369

Integrins are the major metazoan receptors for cell adhesion to extracellular matrix proteins and, in vertebrates, also play important roles in certain cell-cell adhesions, make transmembrane connections to the cytoskeleton and activate many intracellular signalling pathways [PUBMED:12297042, PUBMED:12361595]. The integrin receptors are composed of alpha and beta subunit heterodimers. Each subunit crosses the membrane once, with most of the polypeptide residing in the extracellular space, and has two short cytoplasmic domains. Some members of this family have EGF repeats at the C terminus and also have a vWA domain inserted within the integrin domain at the N terminus.

Most integrins recognise relatively short peptide motifs, and in general require an acidic amino acid to be present. Ligand specificity depends upon both the alpha and beta subunits [PUBMED:12234368]. There are at least 18 types of alpha and 8 types of beta subunits recognised in humans [PUBMED:14689578]. Each alpha subunit tends to associate only with one type of beta subunit, but there are exceptions to this rule [PUBMED:2467745]. Each association of alpha and beta subunits has its own binding specificity and signalling properties. Many integrins require activation on the cell surface before they can bind ligands. Integrins frequently intercommunicate, and binding at one integrin receptor activate or inhibit another.

The structure of unliganded alphaV beta3 showed the molecule to be folded, with the head bent over towards the C termini of the legs which would normally be inserted into the membrane [PUBMED:12714499]. The head comprises a beta propeller domain at the end terminus of the alphaV subunit and an I/A domain inserted into a loop on the top of the hybrid domain in the beta subunit. The I/A domain consists of a Rossman fold with a core of beta parallel sheets surrounded by amphipathic alpha helices.

Integrins are important therapeutic targets in conditions such as atherosclerosis, thrombosis, cancer and asthma [PUBMED:2199285].

At the N terminus of the beta subunit is a cysteine-containing domain reminiscent of that found in presenillins and semaphorins, which has hence been termed the PSI domain. C-terminal to the PSI domain is an A-domain, which has been predicted to adopt a Rossmann fold similar to that of the alpha subunit, but with additional loops between the second and third beta strands [PUBMED:9009218]. The murine gene Pactolus shares significant similarity with the beta subunit [PUBMED:9535848], but lacks either one or both of the inserted loops. The C-terminal portion of the beta subunit extracellular domain contains an internally disulphide-bonded cysteine-rich region, while the intracellular tail contains putative sites of interaction with a variety of intracellular signalling and cytoskeletal proteins, such as focal adhesion kinase and alpha-actinin respectively [PUBMED:9818167]. Integrin cytoplasmic domains are normally less than 50 amino acids in length, with the beta-subunit sequences exhibiting greater homology to each other than the alpha-subunit sequences. This is consistent with current evidence that the beta subunit is the principal site for binding of cytoskeletal and signalling molecules, whereas the alpha subunit has a regulatory role. The first 20 amino acids of the beta-subunit cytoplasmic domain are also alpha helical, but the final 25 residues are disordered and, apart from a turn that follows a conserved NPxY motif, appear to lack defined structure, suggesting that this is adopted on effector binding. The two membrane-proximal helices mediate the link between the subunits via a series of hydrophobic and electrostatic contacts.

This entry represents the N-terminal portion of the extracellular region of integrin beta subunits.

Domain organisation

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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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(786)
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(1)
RP15
(104)
RP35
(134)
RP55
(265)
RP75
(425)
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  Seed
(48)
Full
(945)
Representative proteomes NCBI
(786)
Meta
(1)
RP15
(104)
RP35
(134)
RP55
(265)
RP75
(425)
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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

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Seed source: Prosite
Previous IDs: integrin_B;
Type: Family
Author: Finn RD
Number in seed: 48
Number in full: 945
Average length of the domain: 347.30 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 48.53 %

HMM information View help on HMM parameters

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 25.7 25.7
Trusted cut-off 26.2 28.0
Noise cut-off 25.4 25.6
Model length: 426
Family (HMM) version: 13
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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Interactions

There are 3 interactions for this family. More...

FG-GAP Integrin_B_tail EGF_2

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 Integrin_beta domain has been found. There are 59 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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