Summary: Type IV secretion system proteins
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Secretion Edit Wikipedia article
Secretion is the movement of material from one point to another chemicals, or a secreted chemical substance from a cell or gland. In contrast to excretion, it is the removal of certain substances or waste products. The classical mechanism of cell secretion is via secretory portals at the cell plasma membrane called porosomes. Porosomes are permanent cup-shaped lipoprotein structure at the cell plasma membrane, where secretory vesicles transiently dock and fuse to release intra-vesicular contents from the cell.
Secretion in bacterial species means the transport or translocation of effector molecules for example: proteins, enzymes or toxins (such as cholera toxin in pathogenic bacteria for example Vibrio cholerae) from across the interior (cytoplasm or cytosol) of a bacterial cell to its exterior. Secretion is a very important mechanism in bacterial functioning and operation in their natural surrounding environment for adaptation and survival.
- 1 Secretion in eukaryotic cells
- 2 Secretion in Gram negative bacteria
- 2.1 Type I secretion system (T1SS or TOSS)
- 2.2 Type II secretion system (T2SS)
- 2.3 Type III secretion system (T3SS or TTSS)
- 2.4 Type IV secretion system (T4SS or TFSS)
- 2.5 Type V secretion system (T5SS)
- 2.6 Type VI secretion system (T6SS)
- 2.7 Release of outer membrane vesicles
- 3 Secretion in Gram positive bacteria
- 4 See also
- 5 References
- 6 Bibliography
- 7 External links
Secretion in eukaryotic cells
Eukaryotic cells, including human cells, have a highly evolved process of secretion. Proteins targeted for the outside are synthesized by ribosomes docked to the rough endoplasmic reticulum (ER). As they are synthesized, these proteins translocate into the ER lumen, where they are glycosylated and where molecular chaperones aid protein folding. Misfolded proteins are usually identified here and retrotranslocated by ER-associated degradation to the cytosol, where they are degraded by a proteasome. The vesicles containing the properly folded proteins then enter the Golgi apparatus.
In the Golgi apparatus, the glycosylation of the proteins is modified and further posttranslational modifications, including cleavage and functionalization, may occur. The proteins are then moved into secretory vesicles which travel along the cytoskeleton to the edge of the cell. More modification can occur in the secretory vesicles (for example insulin is cleaved from proinsulin in the secretory vesicles).
Strict biochemical control is maintained over this sequence by usage of a pH gradient: the pH of the cytosol is 7.4, the ER's pH is 7.0, and the cis-golgi has a pH of 6.5. Secretory vesicles have pHs ranging between 5.0 and 6.0; some secretory vesicles evolve into lysosomes, which have a pH of 4.8.
There are many proteins like FGF1 (aFGF), FGF2 (bFGF), interleukin-1 (IL1) etc. which do not have a signal sequence. They do not use the classical ER-golgi pathway. These are secreted through various nonclassical pathways.
At least four nonclassical (unconventional) protein secretion pathways have been described. They include 1) direct translocation of proteins across the plasma membrane likely through membrane transporters, 2) blebbing, 3) lysosomal secretion, and 4) release via exosomes derived from multivesicular bodies. In addition, proteins can be released from cells by mechanical or physiological wounding and through nonlethal, transient oncotic pores in the plasma membrane induced by washing cells with serum-free media or buffers.
Secretion in human tissues
Many human cell types have the ability to be secretory cells. They have a well-developed endoplasmic reticulum and Golgi apparatus to fulfill their function. Tissues in humans that produce secretions include the gastrointestinal tract which secretes digestive enzymes and gastric acid, the lung which secretes surfactants, and sebaceous glands which secrete sebum to lubricate the skin and hair. Meibomian glands in the eyelid secrete sebum to lubricate and protect the eye.
Secretion in Gram negative bacteria
Secretion is not unique to eukaryotes alone, it is present in bacteria and archaea as well. ATP binding cassette (ABC) type transporters are common to all the three domains of life. The Sec system constituting the Sec Y-E-G complex (see Type II secretion system (T2SS), below) is another conserved secretion system, homologous to the translocon in the eukaryotic endoplasmic reticulum and the Sec 61 translocon complex of yeast. Some secreted proteins are translocated across the cytoplasmic membrane by the Sec translocon, which requires the presence of an N-terminal signal peptide on the secreted protein. Others are translocated across the cytoplasmic membrane by the twin-arginine translocation pathway (Tat). Gram negative bacteria have two membranes, thus making secretion topologically more complex. There are at least six specialized secretion systems in Gram negative bacteria. Many secreted proteins are particularly important in bacterial pathogenesis.
Type I secretion system (T1SS or TOSS)
Type I secretion is a chaperone dependent secretion system employing the Hly and Tol gene clusters. The process begins as a leader sequence HlyA is recognized and binds HlyB on the membrane. This signal sequence is extremely specific for the ABC transporter. The HlyAB complex stimulates HlyD which begins to uncoil and reaches the outer membrane where TolC recognizes a terminal molecule or signal on HlyD. HlyD recruits TolC to the inner membrane and HlyA is excreted outside of the outer membrane via a long-tunnel protein channel.
Type I secretion system transports various molecules, from ions, drugs, to proteins of various sizes (20 - 900 kDa). The molecules secreted vary in size from the small Escherichia coli peptide colicin V, (10 kDa) to the Pseudomonas fluorescens cell adhesion protein LapA of 520 kDa. The best characterized are the RTX toxins and the lipases. Type I secretion is also involved in export of non-proteinaceous substrates like cyclic β-glucans and polysaccharides.
Type II secretion system (T2SS)
Proteins secreted through the type II system, or main terminal branch of the general secretory pathway, depend on the Sec or Tat system for initial transport into the periplasm. Once there, they pass through the outer membrane via a multimeric (12-14 subunits) complex of pore forming secretin proteins. In addition to the secretin protein, 10-15 other inner and outer membrane proteins compose the full secretion apparatus, many with as yet unknown function. Gram-negative type IV pili use a modified version of the type II system for their biogenesis, and in some cases certain proteins are shared between a pilus complex and type II system within a single bacterial species.
Type III secretion system (T3SS or TTSS)
It is homologous to the basal body in bacterial flagella. It is like a molecular syringe through which a bacterium (e.g. certain types of Salmonella, Shigella, Yersinia, Vibrio) can inject proteins into eukaryotic cells. The low Ca2+ concentration in the cytosol opens the gate that regulates T3SS. One such mechanism to detect low calcium concentration has been illustrated by the lcrV (Low Calcium Response) antigen utilized by Yersinia pestis, which is used to detect low calcium concentrations and elicits T3SS attachment. The Hrp system in plant pathogens inject harpins and pathogen effector proteins through similar mechanisms into plants. This secretion system was first discovered in Yersinia pestis and showed that toxins could be injected directly from the bacterial cytoplasm into the cytoplasm of its host's cells rather than simply be secreted into the extracellular medium.
Type IV secretion system (T4SS or TFSS)
It is homologous to conjugation machinery of bacteria. It is capable of transporting both DNA and proteins. It was discovered in Agrobacterium tumefaciens, which uses this system to introduce the T-DNA portion of the Ti plasmid into the plant host, which in turn causes the affected area to develop into a crown gall (tumor). Helicobacter pylori uses a type IV secretion system to deliver CagA into gastric epithelial cells, which is associated with gastric carcinogenesis. Bordetella pertussis, the causative agent of whooping cough, secretes the pertussis toxin partly through the type IV system. Legionella pneumophila, the causing agent of legionellosis (Legionnaires' disease) utilizes a type IVB secretion system, known as the icm/dot (intracellular multiplication / defect in organelle trafficking genes) system, to translocate numerous effector proteins into its eukaryotic host. The prototypic Type IVA secretion system is the VirB complex of Agrobacterium tumefaciens.
crystal structure of trac
Protein members of this family are components of the type IV secretion system. They mediate intracellular transfer of macromolecules via a mechanism ancestrally related to that of bacterial conjugation machineries.
In short, Type IV secretion system (T4SS), is the general mechanism by which bacterial cells secrete or take up macromolecules. Their precise mechanism remains unknown. T4SS is encoded on Gram-negative conjugative elements in bacteria.T4SS are cell envelope-spanning complexes or in other words 11-13 core proteins that form a channel through which DNA and proteins can travel from the cytoplasm of the donor cell to the cytoplasm of the recipient cell. Additionally, T4SS also secrete virulence factor proteins directly into host cells as well as taking up DNA from the medium during natural transformation, which shows the versatility of this macromolecular secretion apparatus.
As shown in the above figure, TraC, in particular consists of a three helix bundle and a loose globular appendage.
T4SS has two effector proteins: firstly, ATS-1, which stands for Anaplasma translocated substrate 1, and secondly AnkA, which stands for ankyrin repeat domain-containing protein A. Additionally, T4SS coupling proteins are VirD4, which bind to VirE2.
Type V secretion system (T5SS)
Also called the autotransporter system, type V secretion involves use of the Sec system for crossing the inner membrane. Proteins which use this pathway have the capability to form a beta-barrel with their C-terminus which inserts into the outer membrane, allowing the rest of the peptide (the passenger domain) to reach the outside of the cell. Often, autotransporters are cleaved, leaving the beta-barrel domain in the outer membrane and freeing the passenger domain. Some researchers believe remnants of the autotransporters gave rise to the porins which form similar beta-barrel structures. A common example of an autotransporter that uses this secretion system is the Trimeric Autotransporter Adhesins.
Type VI secretion system (T6SS)
For more on the T6SS, refer to the article Type VI Secretion Systems
Type VI secretion systems were originally identified in 2006 by the group of John Mekalanos at the Harvard Medical School (Boston, USA) in two bacterial pathogens, Vibrio cholerae and Pseudomonas aeruginosa. These were identified when mutations in the Hcp and VrgG genes in Vibrio Cholerae led to decreased virulence and pathogenicity. Since then, Type VI secretion systems have been found in a quarter of all proteobacterial genomes, including animal, plant, human pathogens, as well as soil, environmental or marine bacteria. While most of the early studies of Type VI secretion focused on its role in the pathogenesis of higher organisms, more recent studies suggested a broader physiological role in defense against simple eukaryotic predators and its role in inter-bacteria interactions. The Type VI secretion system gene clusters contain from 15 to more than 20 genes, two of which, Hcp and VgrG, have been shown to be nearly universally secreted substrates of the system. Structural analysis of these and other proteins in this system bear a striking resemblance to the tail spike of the T4 phage, and the activity of the system is thought to functionally resemble phage infection.
Release of outer membrane vesicles
In addition to the use of the multiprotein complexes listed above, Gram-negative bacteria possess another method for release of material: the formation of bacterial outer membrane vesicles. Portions of the outer membrane pinch off, forming nano-scale spherical structures made of a lipopolysaccharide-rich lipid bilayer enclosing periplasmic materials, and are deployed for membrane vesicle trafficking to manipulate environment or invade at host-pathogen interface. Vesicles from a number of bacterial species have been found to contain virulence factors, some have immunomodulatory effects, and some can directly adhere to and intoxicate host cells. While release of vesicles has been demonstrated as a general response to stress conditions, the process of loading cargo proteins seems to be selective.
Secretion in Gram positive bacteria
In some Staphylococcus and Streptococcus species, the accessory secretory system handles the export of highly repetitive adhesion glycoproteins.
- Secretory proteins
- Trimeric Autotransporter Adhesins (TAA)
- Secretory pathway
- Membrane vesicle trafficking
- Host-pathogen interface
- Bacterial outer membrane vesicles
- Lee, Jin-Sook; Jeremic, Aleksandar; Shin, Leah; Cho, Won Jin; Chen, Xuequn; Jena, Bhanu P. (2012). "Neuronal porosome proteome: Molecular dynamics and architecture". Journal of Proteomics 75 (13): 3952–62. doi:10.1016/j.jprot.2012.05.017. PMID 22659300.
- Anderson, L. L. (2006). "Discovery of the 'porosome' The universal secretory machinery in cells". Journal of Cellular and Molecular Medicine 10 (1): 126–31. doi:10.1111/j.1582-4934.2006.tb00294.x. PMID 16563225.
- Nickel, Walter; Seedorf, Matthias (2008). "Unconventional Mechanisms of Protein Transport to the Cell Surface of Eukaryotic Cells". Annual Review of Cell and Developmental Biology 24: 287–308. doi:10.1146/annurev.cellbio.24.110707.175320. PMID 18590485.
- McNeil, Paul L.; Steinhardt, Richard A. (2003). "Plasma membrane disruption: repair, prevention, adaptation". Annual Review of Cell and Developmental Biology 19: 697–731. doi:10.1146/annurev.cellbio.19.111301.140101. PMID 14570587.
- Chirico, William J (2011). "Protein release through nonlethal oncotic pores as an alternative nonclassical secretory pathway". BMC Cell Biology 12: 46. doi:10.1186/1471-2121-12-46. PMC 3217904. PMID 22008609.
- Wooldridge, K, ed. (2009). Bacterial Secreted Proteins: Secretory Mechanisms and Role in Pathogenesis. Caister Academic Press. ISBN 978-1-904455-42-4.[page needed]
- Boyd, Chelsea D.; Smith, T. Jarrod; El-Kirat-Chatel, Sofiane; Newell, Peter D.; Dufrêne, Yves F.; O'Toole, George A. (2014-08-01). "Structural Features of the Pseudomonas fluorescens Biofilm Adhesin LapA Required for LapG-Dependent Cleavage, Biofilm Formation, and Cell Surface Localization". Journal of Bacteriology 196 (15): 2775–2788. doi:10.1128/JB.01629-14. ISSN 0021-9193. PMC 4135675. PMID 24837291.
- Salyers, A. A. & Whitt, D. D. (2002). Bacterial Pathogenesis: A Molecular Approach, 2nd ed., Washington, D.C.: ASM Press. ISBN 1-55581-171-X[page needed]
- Hatakeyama, Masanori; Higashi, Hideaki (2005). "Helicobacter pylori CagA: A new paradigm for bacterial carcinogenesis". Cancer Science 96 (12): 835–43. doi:10.1111/j.1349-7006.2005.00130.x. PMID 16367902.
- Cascales, Eric; Christie, Peter J. (2003). "The versatile bacterial type IV secretion systems". Nature Reviews Microbiology 1 (2): 137–49. doi:10.1038/nrmicro753. PMID 15035043.
- Christie, Peter J.; Atmakuri, Krishnamohan; Krishnamoorthy, Vidhya; Jakubowski, Simon; Cascales, Eric (2005). "Biogenesis, Architecture, and Function of Bacterial Type Iv Secretion Systems". Annual Review of Microbiology 59: 451–85. doi:10.1146/annurev.micro.58.030603.123630. PMID 16153176.
- Christie, Peter J. (2004). "Type IV secretion: The Agrobacterium VirB/D4 and related conjugation systems". Biochimica et Biophysica Acta 1694 (1–3): 219–34. doi:10.1016/j.bbamcr.2004.02.013. PMID 15546668.
- Yeo, Hye-Jeong; Yuan, Qing; Beck, Moriah R.; Baron, Christian; Waksman, Gabriel (2003). "Structural and functional characterization of the VirB5 protein from the type IV secretion system encoded by the conjugative plasmid pKM101". Proceedings of the National Academy of Sciences 100 (26): 15947–52. Bibcode:2003PNAS..10015947Y. doi:10.1073/pnas.2535211100. JSTOR 3149111. PMC 307673. PMID 14673074.
- Lawley, T.D; Klimke, W.A; Gubbins, M.J; Frost, L.S (2003). "F factor conjugation is a true type IV secretion system". FEMS Microbiology Letters 224 (1): 1–15. doi:10.1016/S0378-1097(03)00430-0. PMID 12855161.
- Rikihisa, Yasuko; Lin, Mingqun; Niu, Hua (2010). "Microreview: Type IV secretion in the obligatory intracellular bacterium Anaplasma phagocytophilum". Cellular Microbiology 12 (9): 1213–21. doi:10.1111/j.1462-5822.2010.01500.x. PMC 3598623. PMID 20670295.
- Thanassi, David G.; Stathopoulos, Christos; Karkal, Aarthi; Li, Huilin (2005). "Protein secretion in the absence of ATP: The autotransporter, two-partner secretion and chaperone/usher pathways of Gram-negative bacteria (Review)". Molecular Membrane Biology 22 (1–2): 63–72. doi:10.1080/09687860500063290. PMID 16092525.
- Gerlach, R; Hensel, M (2007). "Protein secretion systems and adhesins: The molecular armory of Gram-negative pathogens". International Journal of Medical Microbiology 297 (6): 401–15. doi:10.1016/j.ijmm.2007.03.017. PMID 17482513.
- Pukatzki, Stefan; Ma, Amy T.; Sturtevant, Derek; Krastins, Bryan; Sarracino, David; Nelson, William C.; Heidelberg, John F.; Mekalanos, John J. (2006). "Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system". Proceedings of the National Academy of Sciences 103 (5): 1528–33. Bibcode:2006PNAS..103.1528P. doi:10.1073/pnas.0510322103. JSTOR 30048406. PMC 1345711. PMID 16432199.
- Mougous, Joseph D.; Cuff, Marianne E.; Raunser, Stefan; Shen, Aimee; Zhou, Min; Gifford, Casey A.; Goodman, Andrew L.; Joachimiak, Grazyna; et al. (2006). "A Virulence Locus of Pseudomonas aeruginosa Encodes a Protein Secretion Apparatus". Science 312 (5779): 1526–30. Bibcode:2006Sci...312.1526M. doi:10.1126/science.1128393. PMC 2800167. PMID 16763151.
- Bingle, Lewis EH; Bailey, Christopher M; Pallen, Mark J (2008). "Type VI secretion: A beginner's guide". Current Opinion in Microbiology 11 (1): 3–8. doi:10.1016/j.mib.2008.01.006. PMID 18289922.
- Cascales, Eric (2008). "The type VI secretion toolkit". EMBO Reports 9 (8): 735–41. doi:10.1038/embor.2008.131. PMC 2515208. PMID 18617888.
- Schwarz, Sandra; Hood, Rachel D.; Mougous, Joseph D. (2010). "What is type VI secretion doing in all those bugs?". Trends in Microbiology 18 (12): 531–7. doi:10.1016/j.tim.2010.09.001. PMC 2991376. PMID 20961764.
- Coulthurst, S. (2013). "The type VI secretion system - A widespread and versatile cell targeting system". Research in Microbiology 164 (6): 640–54. doi:10.1016/j.resmic.2013.03.017. PMID 23542428.
- Silverman, J.; Brunet, Y.; Cascales, E. P.; Mougous, J. (2012). "Structure and Regulation of the Type VI Secretion System". Annual Review of Microbiology 66: 453–472. doi:10.1146/annurev-micro-121809-151619. PMC 3595004. PMID 22746332.
- Kuehn, M. J.; Kesty, NC (2005). "Bacterial outer membrane vesicles and the host-pathogen interaction". Genes & Development 19 (22): 2645–55. doi:10.1101/gad.1299905. PMID 16291643.
- McBroom, Amanda J.; Kuehn, Meta J. (2006). "Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response". Molecular Microbiology 63 (2): 545–58. doi:10.1111/j.1365-2958.2006.05522.x. PMC 1868505. PMID 17163978.
- Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter, eds. (2002). "Search: Secretion". Molecular Biology of the Cell (4th ed.). New York: Garland Science. ISBN 0-8153-3218-1.
- White, David (2000). The Physiology and Biochemistry of Prokaryotes (2nd ed.). Oxford University Press. ISBN 978-0-19-512579-5.
- Avon, David. "Home page". Cells alive!.
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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Type IV secretion system proteins Provide feedback
Members of this family are components of the type IV secretion system. They mediate intracellular transfer of macromolecules via a mechanism ancestrally related to that of bacterial conjugation machineries .
Yeo HJ, Yuan Q, Beck MR, Baron C, Waksman G; , Proc Natl Acad Sci U S A 2003;100:15947-15952.: Structural and functional characterization of the VirB5 protein from the type IV secretion system encoded by the conjugative plasmid pKM101. PUBMED:14673074 EPMC:14673074
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This tab holds annotation information from the InterPro database.
InterPro entry IPR014158
This entry contains VirB5, a protein that is involved in the type IV DNA secretion systems typified by the Agrobacterium Ti plasmid vir system where it interacts with several other proteins essential for proper pilus formation [PUBMED:15901731]. VirB5 is homologous to the IncN (N-type) conjugation system protein TraC [PUBMED:14673074] as well as the P-type protein TrbJ and the F-type protein TraE [PUBMED:12855161].
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|Seed source:||Pfam-B_4497 (release 16.0)|
|Number in seed:||45|
|Number in full:||180|
|Average length of the domain:||191.00 aa|
|Average identity of full alignment:||20 %|
|Average coverage of the sequence by the domain:||54.70 %|
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build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
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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".
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.
The tree shows the occurrence of this domain across different species. More...
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.
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
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.
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 T4SS domain has been found. There are 1 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...