Summary: Vitamin D binding protein, domain III
This is the Wikipedia entry entitled "Vitamin D binding protein domain III". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at email@example.com and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
Vitamin D binding protein domain III Edit Wikipedia article
|This article is an orphan, as no other articles link to it. Please introduce links to this page from related articles; try the Find links tool for suggestions. (July 2012)|
crystal structure of uncomplexed vitamin d-binding protein
In molecular biology, Vitamin D binding protein domain III protein domain is predominantly found in Vitamin D binding proteins (DBP). Vitamin D-binding protein (DBP)(also referred to as Gc-globulin) is synthesized primarily in the liver. This entry outlines the domain III of DBP. Domain III (amino acid 379–458) is G-actin binding region located in the C-terminal. Domain (amino acids 373 to 403). This protein is found ubiquitously in vivo in significant quantities and can be detected in all fluid compartments. During acute phase inflammatory respose, DBP levels tend to increase.
DBP domain III has a multihelical structure. It is required for formation of an actin 'clamp', allowing the protein to bind to actin. This protein is a member of the albumin gene family and has the characteristic multiple disulfide-bonded, triple domain structure.
- Zhang J, Habiel DM, Ramadass M, Kew RR (2010). "Identification of two distinct cell binding sequences in the vitamin D binding protein.". Biochim Biophys Acta 1803 (5): 623–9. doi:10.1016/j.bbamcr.2010.02.010. PMC 2856814. PMID 20211661.
- Otterbein LR, Cosio C, Graceffa P, Dominguez R (June 2002). "Crystal structures of the vitamin D-binding protein and its complex with actin: structural basis of the actin-scavenger system". Proc. Natl. Acad. Sci. U.S.A. 99 (12): 8003–8. doi:10.1073/pnas.122126299. PMC 123010. PMID 12048248.
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.
Vitamin D binding protein, domain III Provide feedback
Members of this family are predominantly found in Vitamin D binding protein, and adopt a multihelical structure. They are required for formation of an actin 'clamp', allowing the protein to bind to actin .
Otterbein LR, Cosio C, Graceffa P, Dominguez R; , Proc Natl Acad Sci U S A. 2002;99:8003-8008.: Crystal structures of the vitamin D-binding protein and its complex with actin: structural basis of the actin-scavenger system. PUBMED:12048248 EPMC:12048248
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR015247
This domain is predominantly found in Vitamin D binding proteins, and adopts a multihelical structure. It is required for formation of an actin 'clamp', allowing the protein to bind to actin [PUBMED:12048248].
- 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
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- 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:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||6|
|Number in full:||46|
|Average length of the domain:||67.30 aa|
|Average identity of full alignment:||58 %|
|Average coverage of the sequence by the domain:||14.43 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||5|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
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
There are 3 interactions 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 VitD-bind_III domain has been found. There are 9 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...