Summary: Major Vault Protein repeat
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This is the Wikipedia entry entitled "Vault (organelle)". More...
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Vault (organelle) Edit Wikipedia article
Structure of the Vault complex from rat liver.
The vault or vault cytoplasmic ribonucleoprotein is a eukaryotic organelle whose function is not fully understood. Discovered and isolated by cell biologist Nancy Kedersha and biochemist Leonard Rome in 1986, vaults are cytoplasmic organelles which when negative-stained and viewed under an electron microscope resemble the arches of a cathedral vaulted ceiling, with 39-fold symmetry. They are present in many types of eukaryotic cells and appear to be highly conserved amongst eukaryotes.
Vaults are large ribonucleoprotein particles. About 3 times the size of a ribosome and weighing approximately 13 MDa, they are found in most eukaryotic cells and all higher eukaryotes. They measure 34 nm by 60 nm from a negative stain, 26 nm by 49 nm from cryo-electron microscopy, and 35 nm by 59 nm from STEM. The vaults consist primarily of proteins, making it difficult to stain with conventional techniques. The protein structure consists of an outer shell composed of 78 copies of the ~100 KDa major vault protein (MVP). Inside are two associated vault proteins, TEP1 and VPARP. TEP1, also known as the telomerase-associated protein 1, is 290 KDa and VPARP (also known as PARP4) is related to poly-(ADP-ribose) polymerase (PARP) and is 193 KDa. Vaults from higher eukaryotes also contain one or several small vault RNAs (vRNAs, also known as vtRNAs) of 86–141 bases within.
Despite not being fully elucidated, vaults have been associated with the nuclear pore complexes and their octagonal shape appears to support this. Vaults have been implicated in a broad range of cellular functions including nuclear-cytoplasmic transport, mRNA localization, drug resistance, cell signaling, nuclear pore assembly, and innate immunity. The three vault proteins (MVP, VPARP, and TEP1) have each been knocked out individually and in combination (VPARP and TEP1) in mice. All of the knockout mice are viable and no major phenotypic alterations have been observed. Dictyostelium encode three different MVPs, two of which have been knocked out singly and in combination. The only phenotype seen in the Dictyostelium double knockout was growth retardation under nutritional stress. If vaults are involved in an essential cellular functions, it seems likely that redundant systems exist that can ameliorate their loss.
Association with cancer
In the late 1990s, researchers found that vaults (especially the MVP) were over-expressed in cancer patients who were diagnosed with multidrug resistance, that is the resistance against many chemotherapy treatments. Although this does not prove that increased number of vaults led to drug resistance, it does hint at some sort of involvement. This has potential in discovering the mechanisms behind drug-resistance in tumor cells and improving anticancer drugs.
Vaults have been identified in mammals, amphibians, avians and Dictyostelium discoideum. The Vault model used by the Pfam database identifies homologues in Paramecium tetraurelia, Kinetoplastida, many vertebrates, a cnidarian (starlet sea anemone), molluscs, Trichoplax adhaerens, flatworms, Echinococcus granulosus and Choanoflagellate.
Although vaults have been observed in many eukaryotic species, a few species do not appear to have the protein. These include:
- Arabidopsis thaliana—a small flowering plant related to cabbage and mustard.
- Caenorhabditis elegans—a free-living nematode that lives in soil.
- Drosophila melanogaster—a two-winged insect also known as a fruit fly.
- Saccharomyces cerevisiae—a species of yeast.
These four species are model organisms for plants, nematodes, animal genetics and fungi respectively. Despite these exceptions, the high degree of similarity of vaults in organisms that do have them implies some sort of evolutionary importance.
The Rome lab at UCLA has collaborated with a number of groups to use the baculovirus system to produce large quantities of vaults. When the major vault protein (MVP) is expressed in insect cells, vault particles are assembled on polyribosomes in the cytoplasm. By using molecular genetic techniques to modify the gene encoding the major vault protein, vault particles have been produced with chemically active peptides attached to their sequence. These modified proteins are incorporated into the inside of the vault particle without altering its basic structure. Proteins and peptides can also be packaged into vaults by attachment of a packaging domain derived from the VPARP protein. A number of modified vault particles have been produced in order to test the concept that vaults can be bio-engineered to allow their use in a wide variety of biological applications including drug delivery, biological sensors, enzyme delivery, controlled release, and environmental remediation.
In 2003 a company called Vault Pharma Inc. was established to move the first vault therapeutic into a phase I clinical trial. This vault is packaged with a chemokine and will be used to activate the immune system to attack lung cancer. Vault Pharma is currently working with Protein Sciences Corp. to develop the GLP/cGMP manufacture of this vault-based therapeutic
- Tanaka H, Kato K, Yamashita E, Sumizawa T, Zhou Y, Yao M, Iwasaki K, Yoshimura M, Tsukihara T (January 2009). "The structure of rat liver vault at 3.5 angstrom resolution". Science 323 (5912): 384–8. doi:10.1126/science.1164975. PMID 19150846.
- Kedersha NL, Rome LH (September 1986). "Isolation and characterization of a novel ribonucleoprotein particle: large structures contain a single species of small RNA". The Journal of Cell Biology 103 (3): 699–709. PMC 2114306. PMID 2943744.
- Kedersha NL, Miquel MC, Bittner D, Rome LH (April 1990). "Vaults. II. Ribonucleoprotein structures are highly conserved among higher and lower eukaryotes". The Journal of Cell Biology 110 (4): 895–901. doi:10.1083/jcb.110.4.895. PMC 2116106. PMID 1691193.
- Kedersha NL, Heuser JE, Chugani DC, Rome LH (January 1991). "Vaults. III. Vault ribonucleoprotein particles open into flower-like structures with octagonal symmetry". The Journal of Cell Biology 112 (2): 225–35. doi:10.1083/jcb.112.2.225. PMC 2288824. PMID 1988458.
- Kickhoefer VA, Stephen AG, Harrington L, Robinson MO, Rome LH (November 1999). "Vaults and telomerase share a common subunit, TEP1". The Journal of Biological Chemistry 274 (46): 32712–7. PMID 10551828.
- Kickhoefer VA, Siva AC, Kedersha NL, Inman EM, Ruland C, Streuli M, Rome LH (September 1999). "The 193-kD vault protein, VPARP, is a novel poly(ADP-ribose) polymerase". The Journal of Cell Biology 146 (5): 917–28. PMC 2169495. PMID 10477748.
- van Zon A, Mossink MH, Scheper RJ, Sonneveld P, Wiemer EA (September 2003). "The vault complex". Cellular and Molecular Life Sciences 60 (9): 1828–37. doi:10.1007/s00018-003-3030-y. PMID 14523546.
- Chugani DC, Rome LH, Kedersha NL (September 1993). "Evidence that vault ribonucleoprotein particles localize to the nuclear pore complex". Journal of Cell Science. 106 ( Pt 1): 23–9. PMID 8270627.
- Unwin PN, Milligan RA (April 1982). "A large particle associated with the perimeter of the nuclear pore complex". The Journal of Cell Biology 93 (1): 63–75. doi:10.1083/jcb.93.1.63. PMC 2112107. PMID 7068761.
- Berger W, Steiner E, Grusch M, Elbling L, Micksche M (January 2009). "Vaults and the major vault protein: novel roles in signal pathway regulation and immunity". Cellular and Molecular Life Sciences 66 (1): 43–61. doi:10.1007/s00018-008-8364-z. PMID 18759128.
- Kickhoefer VA, Liu Y, Kong LB, Snow BE, Stewart PL, Harrington L, Rome LH (January 2001). "The Telomerase/vault-associated protein TEP1 is required for vault RNA stability and its association with the vault particle". The Journal of Cell Biology 152 (1): 157–64. PMC 2193651. PMID 11149928.
- Liu Y, Snow BE, Hande MP, Baerlocher G, Kickhoefer VA, Yeung D, Wakeham A, Itie A, Siderovski DP, Lansdorp PM, Robinson MO, Harrington L (November 2000). "Telomerase-associated protein TEP1 is not essential for telomerase activity or telomere length maintenance in vivo". Molecular and Cellular Biology 20 (21): 8178–84. PMC 86427. PMID 11027287.
- Mossink MH, van Zon A, Fränzel-Luiten E, Schoester M, Kickhoefer VA, Scheffer GL, Scheper RJ, Sonneveld P, Wiemer EA (December 2002). "Disruption of the murine major vault protein (MVP/LRP) gene does not induce hypersensitivity to cytostatics". Cancer Research 62 (24): 7298–304. PMID 12499273.
- Kickhoefer VA, Vasu SK, Rome LH (May 1996). "Vaults are the answer, what is the question?". Trends in Cell Biology 6 (5): 174–8. doi:10.1016/0962-8924(96)10014-3. PMID 15157468.
- Rome LH, Kickhoefer VA (February 2013). "Development of the vault particle as a platform technology". ACS Nano 7 (2): 889–902. doi:10.1021/nn3052082. PMID 23267674.
- Mossink MH, van Zon A, Scheper RJ, Sonneveld P, Wiemer EA (October 2003). "Vaults: a ribonucleoprotein particle involved in drug resistance?". Oncogene 22 (47): 7458–67. doi:10.1038/sj.onc.1206947. PMID 14576851.
- http://pfam.sanger.ac.uk/family/PF01505 Major Vault Protein repeat Pfam family
- Rome L, Kedersha N, Chugani D (August 1991). "Unlocking vaults: organelles in search of a function". Trends in Cell Biology 1 (2-3): 47–50. doi:10.1016/0962-8924(91)90088-Q. PMID 14731565.
- Mrazek, Jan; Toso, Daniel; Ryazantsev, Sergey; Zhang, Xing; Zhou, Z. Hong; Fernandez, Beatriz Campo; Kickhoefer, Valerie A.; Rome, Leonard H. (2014-11-25). "Polyribosomes are molecular 3D nanoprinters that orchestrate the assembly of vault particles". ACS nano 8 (11): 11552–11559. doi:10.1021/nn504778h. ISSN 1936-086X. PMC 4245718. PMID 25354757.
- Sharma, Sherven; Zhu, Li; Srivastava, Minu K.; Harris-White, Marni; Huang, Min; Lee, Jay M.; Rosen, Fran; Lee, Gina; Wang, Gerald (2013-01-01). "CCL21 Chemokine Therapy for Lung Cancer". International Trends in Immunity 1 (1): 10–15. ISSN 2326-3121. PMC 4175527. PMID 25264541.
- Kar, Upendra K.; Srivastava, Minu K.; Andersson, Asa; Baratelli, Felicita; Huang, Min; Kickhoefer, Valerie A.; Dubinett, Steven M.; Rome, Leonard H.; Sharma, Sherven (2011-01-01). "Novel CCL21-vault nanocapsule intratumoral delivery inhibits lung cancer growth". PloS One 6 (5): e18758. doi:10.1371/journal.pone.0018758. ISSN 1932-6203. PMC 3086906. PMID 21559281.
- Vault website (UCLA)
- Vault Pharma Inc.
- Vault Ribonucleoprotein Particles at the US National Library of Medicine Medical Subject Headings (MeSH)
- Page for Vault RNA at Rfam
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Major Vault Protein repeat Provide feedback
The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 mDa of unknown function . This family corresponds to a repeat found in the amino terminal half of the major vault protein.
This tab holds annotation information from the InterPro database.
InterPro entry IPR002499
Vaults are the largest ribonucleoprotein particles known, having a mass of approximately 13 MDa. They are multi-subunit structures that may act as scaffolds for proteins involved in signal transduction and may also play a role in nucleo-cytoplasmic transport. Vaults are present in most normal tissues, but are more highly expressed in epithelial cells with secretory and excretory functions, as well as in cells chronically exposed to xenobiotics, such as bronchial cells and cells lining the intestine [PUBMED:16918321]. Overexpression of these proteins is linked with multidrug-resistance in cancer cells.
The mammalian vault structure is highly regular and consists of approximately 96 molecules of the 100 kDa major vault protein (MVP), 2 molecules of the 240 kDa minor vault protein TEP1, 8 molecules of the 193 kDa minor vault protein VPARP and at least 6 copies of a small untranslated RNA of 88-141 bases. The MVP molecules form the core of the complex, which is a barrel-like structure with an invaginated waist and two protruding caps. The complex can unfold into two symmetrical flower-like structures with 8 petals each supposedly consisting of 6 MVP molecules [PUBMED:10196123].
The MVP protein is composed of two distinct domains [PUBMED:16373071]. The N-terminal domain contains ~8 copies of the vault repeat (or MVP repeat) in tandem. The MVP repeat is composed of ~53 amino acids and forms a structural part of the vault wall. The C-terminal part of MVP may be involved in oligomerization and be located in the vault cap, while the MVP repeats in the N-terminal part can be packed like staves in a barrel to form the vault wall. The 3D structure of the repeat forms a fold that consists of a three stranded (B) antiparallel beta-sheet in a unique topology B2-B1-B3 and two loops. MVP repeats can be interaction-mediating modules, as MVP repeats 3 and 4 bind VPARP, which is one of the other vault proteins.
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
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Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
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We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
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You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
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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.
|Seed source:||Bateman A|
|Number in seed:||164|
|Number in full:||555|
|Average length of the domain:||42.60 aa|
|Average identity of full alignment:||38 %|
|Average coverage of the sequence by the domain:||20.41 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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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 More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
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:
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".
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:
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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.
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Vault domain has been found. There are 187 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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