Summary: Arfaptin-like domain
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This is the Wikipedia entry entitled "Arfaptin". More...
Arfaptin Edit Wikipedia article
Arfaptin | |||||||||
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![]() crystal structure analysis of rac1-gdp complexed with arfaptin (p21)
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Identifiers | |||||||||
Symbol | Arfaptin | ||||||||
Pfam | PF06456 | ||||||||
Pfam clan | CL0145 | ||||||||
InterPro | IPR010504 | ||||||||
SCOP | 1i4l | ||||||||
SUPERFAMILY | 1i4l | ||||||||
CDD | cd00011 | ||||||||
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In molecular biology, the arfaptin domain is a protein domain which interacts with ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms an elongated, crescent-shaped dimer of three-helix coiled-coils.[1] The N-terminal region of ICA69 is similar to arfaptin.[2]
References
- ^ Tarricone C, Xiao B, Justin N, Walker PA, Rittinger K, Gamblin SJ, Smerdon SJ (May 2001). "The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways". Nature. 411 (6834): 215–9. doi:10.1038/35075620. PMID 11346801.
- ^ Spitzenberger F, Pietropaolo S, Verkade P, Habermann B, Lacas-Gervais S, Mziaut H, Pietropaolo M, Solimena M (July 2003). "Islet cell autoantigen of 69 kDa is an arfaptin-related protein associated with the Golgi complex of insulinoma INS-1 cells". J. Biol. Chem. 278 (28): 26166–73. doi:10.1074/jbc.M213222200. PMID 12682071.
This article incorporates text from the public domain Pfam and InterPro IPR010504
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
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.
Arfaptin-like domain Provide feedback
Arfaptin interacts with ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms an elongated, crescent-shaped dimer of three-helix coiled-coils [1]. The N-terminal region of ICA69 is similar to arfaptin [2].
Literature references
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Tarricone C, Xiao B, Justin N, Walker PA, Rittinger K, Gamblin SJ, Smerdon SJ; , Nature 2001;411:215-219.: The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways. PUBMED:11346801 EPMC:11346801
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Spitzenberger F, Pietropaolo S, Verkade P, Habermann B, Lacas-Gervais S, Mziaut H, Pietropaolo M, Solimena M; , J Biol Chem 2003;278:26166-26173.: Islet Cell Autoantigen of 69 kDa Is an Arfaptin-related Protein Associated with the Golgi Complex of Insulinoma INS-1 Cells. PUBMED:12682071 EPMC:12682071
Internal database links
SCOOP: | BAR BAR_2 BAR_3 |
Similarity to PfamA using HHSearch: | BAR |
External database links
SCOP: | 1i4l |
This tab holds annotation information from the InterPro database.
InterPro entry IPR010504
The arfaptin homology (AH) domain is a protein domain found in a range of proteins, including arfaptins, protein kinase C-binding protein PICK1 [PUBMED:10623590] and mammalian 69 kDa islet cell autoantigen (ICA69) [PUBMED:12682071]. The AH domain of arfaptin has been shown to dimerise and to bind Arf and Rho family GTPases [PUBMED:11346801, PUBMED:11696355], including ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules.
The AH domain consists of three alpha-helices arranged as an extended antiparallel alpha-helical bundle. Two arfaptin AH domains associate to form a highly elongated, crescent-shaped dimer [PUBMED:11346801, PUBMED:11696355].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | protein domain specific binding (GO:0019904) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Golgi-transport (CL0145), which has the following description:
This clan contains families that are involved in intracellular transport and signalling. Arfaptins are proteins which interact with small GTPases involved in vesicular budding at the Golgi complex. They form an elongated dimer of three helix coiled coils and are structurally very similar to the BAR domain [1][2]. The Sec34 family is involved in tethering vesicles to the Golgi [3].
The clan contains the following 9 members:
Arfaptin BAR BAR_2 BAR_3 BAR_3_WASP_bdg FAM92 FCH IMD Vps5Alignments
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...
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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.
Seed (11) |
Full (1591) |
Representative proteomes | UniProt (2533) |
NCBI (4688) |
Meta (0) |
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RP15 (397) |
RP35 (710) |
RP55 (1132) |
RP75 (1302) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (11) |
Full (1591) |
Representative proteomes | UniProt (2533) |
NCBI (4688) |
Meta (0) |
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RP15 (397) |
RP35 (710) |
RP55 (1132) |
RP75 (1302) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
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...
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.
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.
Curation
Seed source: | Pfam-B_5314 (release 7.5) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 11 |
Number in full: | 1591 |
Average length of the domain: | 204.80 aa |
Average identity of full alignment: | 30 % |
Average coverage of the sequence by the domain: | 54.00 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 229 | ||||||||||||
Family (HMM) version: | 13 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 Arfaptin domain has been found. There are 10 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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