Summary: Hexon, adenovirus major coat protein, C-terminal domain
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Hexon protein Edit Wikipedia article
|SCOP2||1dhx / SCOPe / SUPFAM|
|SCOP2||1dhx / SCOPe / SUPFAM|
In molecular biology, the hexon protein is a major coat protein found in Adenoviruses. Hexon coat proteins are synthesised during late infection and form homo-trimers. The 240 copies of the hexon trimer that are produced are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and penton base (holding in place a fibre), lie at each of the 12 vertices. The hexon coat protein is a duplication consisting of two domains with a similar fold packed together like the nucleoplasmin subunits. Within a hexon trimer, the domains are arranged around a pseudo 6-fold axis. The domains have a beta-sandwich structure consisting of 8 strands in two sheets with a jelly-roll topology; each domain is heavily decorated with many insertions. Some hexon proteins contain a distinct C-terminal domain.
Hexon directly recruits the cellular motor protein dynein in a pH-dependent manner. The dynein-regulatory protein, dynactin, was found to play a clear role in regulating the dynein-adenovirus complex transport to the nucleus.
- Athappilly FK, Murali R, Rux JJ, Cai Z, Burnett RM (September 1994). "The refined crystal structure of hexon, the major coat protein of adenovirus type 2, at 2.9 A resolution". Journal of Molecular Biology. 242 (4): 430â€“55. doi:10.1006/jmbi.1994.1593. PMIDÂ 7932702.
- Rux JJ, Kuser PR, Burnett RM (September 2003). "Structural and phylogenetic analysis of adenovirus hexons by use of high-resolution x-ray crystallographic, molecular modeling, and sequence-based methods". Journal of Virology. 77 (17): 9553â€“66. doi:10.1128/jvi.77.17.9553-9566.2003. PMCÂ 187380. PMIDÂ 12915569.
- Bremner KH, Scherer J, Yi J, Vershinin M, Gross SP, Vallee RB (December 2009). "Adenovirus transport via direct interaction of cytoplasmic dynein with the viral capsid hexon subunit". Cell Host & Microbe. 6 (6): 523â€“35. doi:10.1016/j.chom.2009.11.006. PMCÂ 2810746. PMIDÂ 20006841.
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Hexon, adenovirus major coat protein, C-terminal domain Provide feedback
Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer. The 240 copies of the hexon trimer are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices . The N and C-terminal domains adopt the same PNGase F-like fold although they are significantly different in length.
Athappilly FK, Murali R, Rux JJ, Cai Z, Burnett RM; , J Mol Biol 1994;242:430-455.: The refined crystal structure of hexon, the major coat protein of adenovirus type 2, at 2.9 A resolution. PUBMED:7932702 EPMC:7932702
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR016108
Hexon is a major coat protein found in various species-specific Adenoviruses, which are type II dsDNA viruses. Hexon coat proteins are synthesised during late infection and form homo-trimers. The 240 copies of the hexon trimer that are produced are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices [ PUBMED:7932702 ]. The hexon coat protein is a duplication consisting of two domains with a similar fold packed together like the nucleoplasmin subunits. Within a hexon trimer, the domains are arranged around a pseudo 6-fold axis. The domains have a beta-sandwich structure consisting of 8 strands in two sheets with a jelly-roll topology; each domain is heavily decorated with many insertions [ PUBMED:12915569 ].
This entry represents the C-terminal domain of hexon coat proteins.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||viral capsid (GO:0019028)|
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
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This large superfamily includes nucleoplasmin as well as a wide range of viral coat and capsid proteins that share a jelly roll topology.
The clan contains the following 42 members:Adeno_hexon_C Astro_capsid_N Birna_VP2 Bromo_coat Calici_coat Calici_coat_C Capsid-VNN Capsid_N Carmo_coat_C Circo_capsid Como_LCP Como_SCP CRPV_capsid Cucumo_coat Dicistro_VP4 DUF2961 DUF4621 HAV_VP IHHNV_capsid Ilar_coat Late_protein_L1 Luteo_coat Nepo_coat Nepo_coat_C Nepo_coat_N NPL Nucleoplasmin Peptidase_A21 Peptidase_A6 Pico_P1A Polyhedrin Polyoma_coat Pox_Rif Rhv SP2 TGFb_propeptide TNV_CP TT_ORF1 Tymo_coat Viral_coat VP4_2 Waikav_capsid_1
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 and the UniProtKB sequence database. More...
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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.
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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.
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|Seed source:||Pfam-B_885 (release 3.0)|
|Author:||Finn RD , Bateman A , Griffiths-Jones SR|
|Number in seed:||3|
|Number in full:||65|
|Average length of the domain:||230.60 aa|
|Average identity of full alignment:||61 %|
|Average coverage of the sequence by the domain:||24.75 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|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.
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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.
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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.
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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.
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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 Adeno_hexon_C domain has been found. There are 108 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 sequence.
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