Summary: ARP2/3 complex ARPC3 (21 kDa) subunit

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This is the Wikipedia entry entitled "ARPC3". More...

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Actin related protein 2/3 complex, subunit 3, 21kDa

PDB rendering based on 1k8k.

Available structures

PDB

Ortholog search: PDBe, RCSB

List of PDB id codes
1k8k, 1tyq, 1u2v, 2p9i, 2p9k, 2p9l, 2p9n, 2p9p, 2p9s, 2p9u

Identifiers

Symbols

ARPC3; ARC21; p21-Arc

External IDs

OMIM: 604225 MGI: 1928375 HomoloGene: 4178 GeneCards: ARPC3 Gene

Gene Ontology
Molecular function	â¢ actin binding â¢ structural constituent of cytoskeleton â¢ protein binding
Cellular component	â¢ cytoplasm â¢ Arp2/3 protein complex â¢ actin cytoskeleton â¢ lamellipodium
Biological process	â¢ cellular component movement â¢ regulation of actin filament polymerization
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 12:
110.87 â 110.89 Mb

Chr 5:
122.39 â 122.41 Mb

PubMed search

[1]

[2]

ARP2/3 complex ARPC3 (21 kDa) subunit

crystal structure of arp2/3 complex with bound adp and calcium

Identifiers

Symbol

P21-Arc

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Actin-related protein 2/3 complex subunit 3 is a protein that in humans is encoded by the ARPC3 gene.^[1]^[2]^[3]

This gene encodes one of seven subunits of the Arp2/3 protein complex. The Arp2/3 protein complex has been implicated in the control of actin polymerization in cells and has been conserved through evolution. The exact role of the protein encoded by this gene, the p21 subunit, has yet to be determined.^[3]

[edit] References

^ Welch MD, DePace AH, Verma S, Iwamatsu A, Mitchison TJ (Aug 1997). "The human Arp2/3 complex is composed of evolutionarily conserved subunits and is localized to cellular regions of dynamic actin filament assembly". J Cell Biol 138 (2): 375â84. doi:10.1083/jcb.138.2.375. PMC 2138188. PMID 9230079.
^ Machesky LM, Reeves E, Wientjes F, Mattheyse FJ, Grogan A, Totty NF, Burlingame AL, Hsuan JJ, Segal AW (Jan 1998). "Mammalian actin-related protein 2/3 complex localizes to regions of lamellipodial protrusion and is composed of evolutionarily conserved proteins". Biochem J 328 (1): 105â12. PMC 1218893. PMID 9359840.
^ ^a ^b "Entrez Gene: ARPC3 actin related protein 2/3 complex, subunit 3, 21kDa".

[edit] Further reading

Welch MD, Iwamatsu A, Mitchison TJ (1997). "Actin polymerization is induced by Arp2/3 protein complex at the surface of Listeria monocytogenes.". Nature 385 (6613): 265â9. doi:10.1038/385265a0. PMID 9000076.
Marchand JB, Kaiser DA, Pollard TD, Higgs HN (2001). "Interaction of WASP/Scar proteins with actin and vertebrate Arp2/3 complex.". Nat. Cell Biol. 3 (1): 76â82. doi:10.1038/35050590. PMID 11146629.
Zhao X, Yang Z, Qian M, Zhu X (2001). "Interactions among subunits of human Arp2/3 complex: p20-Arc as the hub.". Biochem. Biophys. Res. Commun. 280 (2): 513â7. doi:10.1006/bbrc.2000.4151. PMID 11162547.
Robinson RC, Turbedsky K, Kaiser DA, et al. (2001). "Crystal structure of Arp2/3 complex.". Science 294 (5547): 1679â84. doi:10.1126/science.1066333. PMID 11721045.
Gournier H, Goley ED, Niederstrasser H, et al. (2002). "Reconstitution of human Arp2/3 complex reveals critical roles of individual subunits in complex structure and activity.". Mol. Cell 8 (5): 1041â52. doi:10.1016/S1097-2765(01)00393-8. PMID 11741539.
Andersen JS, Lyon CE, Fox AH, et al. (2002). "Directed proteomic analysis of the human nucleolus.". Curr. Biol. 12 (1): 1â11. doi:10.1016/S0960-9822(01)00650-9. PMID 11790298.
Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899â903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
Gevaert K, Goethals M, Martens L, et al. (2004). "Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides.". Nat. Biotechnol. 21 (5): 566â9. doi:10.1038/nbt810. PMID 12665801.
Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).". Genome Res. 14 (10B): 2121â7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334.
Andersen JS, Lam YW, Leung AK, et al. (2005). "Nucleolar proteome dynamics.". Nature 433 (7021): 77â83. doi:10.1038/nature03207. PMID 15635413.
Dubois T, PalÃ©otti O, Mironov AA, et al. (2005). "Golgi-localized GAP for Cdc42 functions downstream of ARF1 to control Arp2/3 complex and F-actin dynamics.". Nat. Cell Biol. 7 (4): 353â64. doi:10.1038/ncb1244. PMID 15793564.
Stelzl U, Worm U, Lalowski M, et al. (2005). "A human protein-protein interaction network: a resource for annotating the proteome.". Cell 122 (6): 957â68. doi:10.1016/j.cell.2005.08.029. PMID 16169070.
Ewing RM, Chu P, Elisma F, et al. (2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry.". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931.

[edit] External links

ARPC3 human gene location in the UCSC Genome Browser.
ARPC3 human gene details in the UCSC Genome Browser.

PDB gallery

1k8k: Crystal Structure of Arp2/3 Complex

1tyq: Crystal structure of Arp2/3 complex with bound ATP and calcium

1u2v: Crystal structure of Arp2/3 complex with bound ADP and calcium

2p9i: Crystal Structure of bovine Arp2/3 Complex co-crystallized with ADP and crosslinked with gluteraldehyde

2p9k: Crystal structure of bovine Arp2/3 complex co-crystallized with ATP and crosslinked with glutaraldehyde

2p9l: Crystal Structure of bovine Arp2/3 complex

2p9n: Crystal Structure of bovine Arp2/3 complex co-crystallized with ADP

2p9p: Crystal Structure of bovine Arp2/3 complex co-crystallized with ADP

2p9s: Structure of bovine Arp2/3 complex co-crystallized with ATP/Mg2+

2p9u: Crystal structure of bovine Arp2/3 complex co-crystallized with AMP-PNP and calcium

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ARP2/3 complex ARPC3 (21 kDa) subunit Provide feedback

The seven component ARP2/3 actin-organising complex is involved in actin assembly and function.

Literature references

Gournier H, Goley ED, Niederstrasser H, Trinh T, Welch MD; , Mol Cell 2001;8:1041-1052.: Reconstitution of human Arp2/3 complex reveals critical roles of individual subunits in complex structure and activity. PUBMED:11741539 EPMC:11741539

External database links

PANDIT:	PF04062
Pseudofam:	PF04062
SYSTERS:	P21-Arc

This tab holds annotation information from the InterPro database.

InterPro entry IPR007204

The Arp2/3 complex is a seven-protein assembly that is critical for actin nucleation and branching in cells. Arp2/3 nucleates new actin filaments while bound to existing filaments, thus creating a branched network [PUBMED:15040784]. The complex consists of Arp2, Arp3, p41, p34, p21, p20 and p16. Subunits p34 and p20 constitute the core of the structure, with the remaining subunits located peripherally [PUBMED:11741539]. This entry describes the p21 subunit. Proteins such as WASp and Scar1 may mediate receptor signalling through interactions with p21-Arc, resulting in the activation of Arc2/3 complex activity [PUBMED:11162547].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Cellular component	cytoskeleton (GO:0005856)
Biological process	regulation of actin filament polymerization (GO:0030833)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

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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.

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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 (29)	Full (364)	Representative proteomes				NCBI (331)	Meta (3)
	Seed (29)	Full (364)	RP15 (73)	RP35 (121)	RP55 (183)	RP75 (231)	NCBI (331)	Meta (3)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (29)	Full (364)	Representative proteomes				NCBI (331)	Meta (3)
	Seed (29)	Full (364)	RP15 (73)	RP35 (121)	RP55 (183)	RP75 (231)	NCBI (331)	Meta (3)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

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.

	Seed (29)	Full (364)	Representative proteomes				NCBI (331)	Meta (3)
	Seed (29)	Full (364)	RP15 (73)	RP35 (121)	RP55 (183)	RP75 (231)	NCBI (331)	Meta (3)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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_6413 (release 7.3);

Previous IDs:

none

Type:

Family

Author:

Wood V, Finn RD

Number in seed:

29

Number in full:

364

Average length of the domain:

170.20 aa

Average identity of full alignment:

48 %

Average coverage of the sequence by the domain:

94.42 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	25.0	25.0
Trusted cut-off	40.0	40.0
Noise cut-off	18.3	16.9

Model length:

175

Family (HMM) version:

9

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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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 adjacent tab. 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.

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kingdom
phylum
class
order
family
genus
species

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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.

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Sub-species

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.

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Species trees

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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.

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Interactive tree

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.

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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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Interactions

There is 1 interaction for this family. More...

Actin

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 P21-Arc domain has been found. There are 15 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...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: P21-Arc (PF04062)

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