Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
20  structures 850  species 0  interactions 1129  sequences 19  architectures

Family: Dynamitin (PF04912)

Summary: Dynamitin

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

Dynactin Edit Wikipedia article

Dynactin is a 23 subunit protein complex that acts as a co-factor for the microtubule motor cytoplasmic dynein-1.  It is built around a short filament of actin related protein-1 (Arp1).[1][2]

Discovery

Dynactin was identified as an activity that allowed purified cytoplasmic dynein to move membrane vesicles along microtubules in vitro.[3] It was shown to be a multiprotein complex and named dynactin because of its role in dynein activation.[4]

The main features of dynactin were visualized by quick-freeze, deep-etch, rotary shadow electron microscopy. It appears as a short filament, 37-nm in length, which resembles F-actin, plus a thinner, laterally oriented arm.[5] Antibody labelling was used to map the location of the dynactin subunits.[5][6]

Structure

Dynactin consists of three major structural domains: (1) sidearm-shoulder: DCTN1/p150Glued, DCTN2/p50/dynamitin, DCTN3/p24/p22;(2)the Arp1 filament: ACTR1A/Arp1/centractin, actin, CapZ; and (3) the pointed end complex: Actr10/Arp11, DCTN4/p62, DCTN5/p25, and DCTN6/p27[1].

A 4Å cryo-EM structure of dynactin [7] revealed that its filament contains eight Arp1 molecules, one β-actin and one Arp11. In the pointed end complex p62/DCTN4 binds to Arp11 and β-actin and p25 and p27 bind both p62 and Arp11. At the barbed end the capping protein (CapZαβ) binds the Arp1 filament in the same way that it binds actin, although with more charge complementarity, explaining why it binds dynactin more tightly than actin.[8]

The shoulder contains two copies of p150Glued/DCTN1, four copies of p50/DCTN2 and two copies of p24/DCTN3.[1] These proteins form long bundles of alpha helices, which wrap over each other and contact the Arp1 filament[7]. The N-termini of p50/DCTN2 emerge from the shoulder and coat the filament, providing a mechanism for controlling the filament length.[7] The C-termini of the p150Glued/DCTN1 dimer are embedded in the shoulder, whereas the N-terminal 1227 amino acids form the projecting arm. The arm consists of an N-terminal CAPGly domain which can bind the C-terminal tails of microtubules and the microtubule plus end binding protein EB1. This is followed by a basic region, also involved in microtubule binding, a folded-back coiled coil (CC1), the intercoiled domain (ICD) and a second coiled coil domain (CC2)[7]. The p150Glued arm can dock into against the side of the Arp1 filament and pointed end complex[7].

DCTN2 (dynamitin) is also involved in anchoring microtubules to centrosomes and may play a role in synapse formation during brain development.[9] Arp1 has been suggested as the domain for dynactin binding to membrane vesicles (such as Golgi or late endosome) through its association with β-spectrin.[10][11][12][13] The pointed end complex (PEC) has been shown to be involved in selective cargo binding. PEC subunits p62/DCTN4 and Arp11/Actr10 are essential for dynactin complex integrity and dynactin/dynein targeting to the nuclear envelope before mitosis.[14][15][16] Dynactin p25/DCTN5 and p27/DCTN6 are not essential for dynactin complex integrity, but are required for early and recycling endosome transport during the interphase and regulation of the spindle assembly checkpoint in mitosis.[16][17][18]

Interaction with dynein

Dynein and dynactin were reported to interact directly by the binding of dynein intermediate chains with p150Glued.[19] The affinity of this interaction is around 3.5μM.[20] Dynein and dynactin do not run together in a sucrose gradient, but can be induced to form a tight complex in the presence of the N-terminal 400 amino acids of Bicaudal D2 (BICD2), a cargo adaptor that links dynein and dynactin to Golgi derived vesicles.[21] In the presence of BICD2, dynactin binds to dynein and activates it to move for long distances along microtubules.[22][23]

A cryo-EM structure of dynein, dynactin and BICD2 [7] showed that the BICD2 coiled coil runs along the dynactin filament. The tail of dynein also binds to the Arp1 filament, sitting in the equivalent site that myosin uses to bind actin. The contacts between the dynein tail and dynactin all involve BICD, explaining why it is needed to bring them together. The dynein/dynactin/BICD2 (DDB) complex has also been observed, by negative stain EM, on microtubules. This shows that the cargo (Rab6) binding end of BICD2 extends out through the pointed end complex at the opposite end away from the dynein motor domains.[24]

Functions

Dynactin is often essential for dynein activity[1][25] and can be thought of as a "dynein receptor"[19] that modulates binding of dynein to cell organelles which are to be transported along microtubules.[26][27] Dynactin also enhances the processivity of cytoplasmic dynein[28] and kinesin-2 motors.[29] Dynactin is involved in various processes like chromosome alignment and spindle organization[30] in cell division.[31] Dynactin contributes to mitotic spindle pole focusing through its binding to nuclear mitotic apparatus protein (NuMA).[32][33] Dynactin also targets to the kinetochore through binding between DCTN2/dynamitin and zw10 and has a role in mitotic spindle checkpoint inactivation.[34][35] During prometaphase, dynactin also helps target polo-like kinase 1 (Plk1) to kinetochores through cyclin dependent kinase 1 (Cdk1)-phosphorylated DCTN6/p27, which is involved in proper microtubule-kinetochore attachment and recruitment of spindle assembly checkpoint protein Mad1.[18] In addition, dynactin has been shown to play an essential role in maintaining nuclear position in Drosophila,[36] zebrafish[37] or in different fungi.[38][39] Dynein and dynactin concentrate on the nuclear envelope during the prophase and facilitate nuclear envelope breakdown via its DCTN4/p62 and Arp11 subunits.[16][40] Dynactin is also required for microtubule anchoring at centrosomes and centrosome integrity.[41] Destabilization of the centrosomal pool of dynactin also causes abnormal G1 centriole separation and delayed entry into S phase, suggesting that dynactin contributes to the recruitment of important cell cycle regulators to centrosomes.[42] In addition to transport of various organelles in the cytoplasm, dynactin also links kinesin II to organelles.[43]

See also

References

  1. ^ a b c d Schroer TA (November 2004). "Dynactin". Annual Review of Cell and Developmental Biology. 20: 759–79. doi:10.1146/annurev.cellbio.20.012103.094623. PMID 15473859. 
  2. ^ Carter AP, Diamant AG, Urnavicius L (April 2016). "How dynein and dynactin transport cargos: a structural perspective". Current Opinion in Structural Biology. 37: 62–70. doi:10.1016/j.sbi.2015.12.003. PMID 26773477. 
  3. ^ Schroer TA, Sheetz MP (December 1991). "Two activators of microtubule-based vesicle transport". The Journal of Cell Biology. 115 (5): 1309–18. PMC 2289226Freely accessible. PMID 1835460. 
  4. ^ Gill SR, Schroer TA, Szilak I, Steuer ER, Sheetz MP, Cleveland DW (December 1991). "Dynactin, a conserved, ubiquitously expressed component of an activator of vesicle motility mediated by cytoplasmic dynein". The Journal of Cell Biology. 115 (6): 1639–50. PMC 2289205Freely accessible. PMID 1836789. 
  5. ^ a b Schafer DA, Gill SR, Cooper JA, Heuser JE, Schroer TA (July 1994). "Ultrastructural analysis of the dynactin complex: an actin-related protein is a component of a filament that resembles F-actin". The Journal of Cell Biology. 126 (2): 403–12. doi:10.1083/jcb.126.2.403. PMC 2200042Freely accessible. PMID 7518465. 
  6. ^ Eckley DM, Gill SR, Melkonian KA, Bingham JB, Goodson HV, Heuser JE, Schroer TA (October 1999). "Analysis of dynactin subcomplexes reveals a novel actin-related protein associated with the arp1 minifilament pointed end". The Journal of Cell Biology. 147 (2): 307–20. PMC 2174220Freely accessible. PMID 10525537. 
  7. ^ a b c d e f Urnavicius L, Zhang K, Diamant AG, Motz C, Schlager MA, Yu M, Patel NA, Robinson CV, Carter AP (March 2015). "The structure of the dynactin complex and its interaction with dynein". Science. 347 (6229): 1441–1446. doi:10.1126/science.aaa4080. PMC 4413427Freely accessible. PMID 25814576. 
  8. ^ Cheong FK, Feng L, Sarkeshik A, Yates JR, Schroer TA (July 2014). "Dynactin integrity depends upon direct binding of dynamitin to Arp1". Molecular Biology of the Cell. 25 (14): 2171–80. doi:10.1091/mbc.E14-03-0842. PMC 4091830Freely accessible. PMID 24829381. 
  9. ^ Uetake Y, Terada Y, Matuliene J, Kuriyama R (May 2004). "Interaction of Cep135 with a p50 dynactin subunit in mammalian centrosomes". Cell Motility and the Cytoskeleton. 58 (1): 53–66. doi:10.1002/cm.10175. PMID 14983524. 
  10. ^ Holleran EA, Tokito MK, Karki S, Holzbaur EL (December 1996). "Centractin (ARP1) associates with spectrin revealing a potential mechanism to link dynactin to intracellular organelles". The Journal of Cell Biology. 135 (6 Pt 2): 1815–29. doi:10.1083/jcb.135.6.1815. PMC 2133946Freely accessible. PMID 8991093. 
  11. ^ Holleran EA, Ligon LA, Tokito M, Stankewich MC, Morrow JS, Holzbaur EL (September 2001). "beta III spectrin binds to the Arp1 subunit of dynactin". The Journal of Biological Chemistry. 276 (39): 36598–605. doi:10.1074/jbc.M104838200. PMID 11461920. 
  12. ^ Muresan V, Stankewich MC, Steffen W, Morrow JS, Holzbaur EL, Schnapp BJ (January 2001). "Dynactin-dependent, dynein-driven vesicle transport in the absence of membrane proteins: a role for spectrin and acidic phospholipids". Molecular Cell. 7 (1): 173–83. doi:10.1016/S1097-2765(01)00165-4. PMID 11172722. 
  13. ^ Johansson M, Rocha N, Zwart W, Jordens I, Janssen L, Kuijl C, Olkkonen VM, Neefjes J (February 2007). "Activation of endosomal dynein motors by stepwise assembly of Rab7-RILP-p150Glued, ORP1L, and the receptor betalll spectrin". The Journal of Cell Biology. 176 (4): 459–71. doi:10.1083/jcb.200606077. PMC 2063981Freely accessible. PMID 17283181. 
  14. ^ Salina D, Bodoor K, Eckley DM, Schroer TA, Rattner JB, Burke B (January 2002). "Cytoplasmic dynein as a facilitator of nuclear envelope breakdown". Cell. 108 (1): 97–107. doi:10.1016/S0092-8674(01)00628-6. PMID 11792324. 
  15. ^ Zhang J, Wang L, Zhuang L, Huo L, Musa S, Li S, Xiang X (July 2008). "Arp11 affects dynein-dynactin interaction and is essential for dynein function in Aspergillus nidulans". Traffic. 9 (7): 1073–87. doi:10.1111/j.1600-0854.2008.00748.x. PMC 2586032Freely accessible. PMID 18410488. 
  16. ^ a b c Yeh TY, Quintyne NJ, Scipioni BR, Eckley DM, Schroer TA (October 2012). "Dynactin's pointed-end complex is a cargo-targeting module". Molecular Biology of the Cell. 23 (19): 3827–37. doi:10.1091/mbc.E12-07-0496. PMC 3459859Freely accessible. PMID 22918948. 
  17. ^ Zhang J, Yao X, Fischer L, Abenza JF, Peñalva MA, Xiang X (June 2011). "The p25 subunit of the dynactin complex is required for dynein-early endosome interaction". The Journal of Cell Biology. 193 (7): 1245–55. doi:10.1083/jcb.201011022. PMC 3216330Freely accessible. PMID 21708978. 
  18. ^ a b Yeh TY, Kowalska AK, Scipioni BR, Cheong FK, Zheng M, Derewenda U, Derewenda ZS, Schroer TA (April 2013). "Dynactin helps target Polo-like kinase 1 to kinetochores via its left-handed beta-helical p27 subunit". The EMBO Journal. 32 (7): 1023–35. doi:10.1038/emboj.2013.30. PMC 3616283Freely accessible. PMID 23455152. 
  19. ^ a b Vaughan KT, Vallee RB (December 1995). "Cytoplasmic dynein binds dynactin through a direct interaction between the intermediate chains and p150Glued". The Journal of Cell Biology. 131 (6 Pt 1): 1507–16. doi:10.1083/jcb.131.6.1507. PMC 2120689Freely accessible. PMID 8522607. 
  20. ^ Morgan JL, Song Y, Barbar E (November 2011). "Structural dynamics and multiregion interactions in dynein-dynactin recognition". The Journal of Biological Chemistry. 286 (45): 39349–59. doi:10.1074/jbc.M111.296277. PMC 3234759Freely accessible. PMID 21931160. 
  21. ^ Splinter D, Razafsky DS, Schlager MA, Serra-Marques A, Grigoriev I, Demmers J, Keijzer N, Jiang K, Poser I, Hyman AA, Hoogenraad CC, King SJ, Akhmanova A (November 2012). "BICD2, dynactin, and LIS1 cooperate in regulating dynein recruitment to cellular structures". Molecular Biology of the Cell. 23 (21): 4226–41. doi:10.1091/mbc.E12-03-0210. PMC 3484101Freely accessible. PMID 22956769. 
  22. ^ Schlager MA, Hoang HT, Urnavicius L, Bullock SL, Carter AP (September 2014). "In vitro reconstitution of a highly processive recombinant human dynein complex". The EMBO Journal. 33 (17): 1855–68. doi:10.15252/embj.201488792. PMC 4158905Freely accessible. PMID 24986880. 
  23. ^ McKenney RJ, Huynh W, Tanenbaum ME, Bhabha G, Vale RD (July 2014). "Activation of cytoplasmic dynein motility by dynactin-cargo adapter complexes". Science. 345 (6194): 337–41. doi:10.1126/science.1254198. PMC 4224444Freely accessible. PMID 25035494. 
  24. ^ Chowdhury S, Ketcham SA, Schroer TA, Lander GC (April 2015). "Structural organization of the dynein-dynactin complex bound to microtubules". Nature Structural & Molecular Biology. 22 (4): 345–7. doi:10.1038/nsmb.2996. PMC 4385409Freely accessible. PMID 25751425. 
  25. ^ Schroer TA, Sheetz MP (December 1991). "Two activators of microtubule-based vesicle transport". The Journal of Cell Biology. 115 (5): 1309–18. doi:10.1083/jcb.115.5.1309. PMC 2289226Freely accessible. PMID 1835460. 
  26. ^ Waterman-Storer CM, Karki SB, Kuznetsov SA, Tabb JS, Weiss DG, Langford GM, Holzbaur EL (October 1997). "The interaction between cytoplasmic dynein and dynactin is required for fast axonal transport". Proceedings of the National Academy of Sciences of the United States of America. 94 (22): 12180–5. doi:10.1073/pnas.94.22.12180. PMC 23743Freely accessible. PMID 9342383. 
  27. ^ McGrail M, Gepner J, Silvanovich A, Ludmann S, Serr M, Hays TS (October 1995). "Regulation of cytoplasmic dynein function in vivo by the Drosophila Glued complex". The Journal of Cell Biology. 131 (2): 411–25. doi:10.1083/jcb.131.2.411. PMC 2199972Freely accessible. PMID 7593168. 
  28. ^ King SJ, Schroer TA (January 2000). "Dynactin increases the processivity of the cytoplasmic dynein motor". Nature Cell Biology. 2 (1): 20–4. doi:10.1038/71338. PMID 10620802. 
  29. ^ Berezuk MA, Schroer TA (February 2007). "Dynactin enhances the processivity of kinesin-2". Traffic. 8 (2): 124–9. doi:10.1111/j.1600-0854.2006.00517.x. PMID 17181772. 
  30. ^ Echeverri CJ, Paschal BM, Vaughan KT, Vallee RB (February 1996). "Molecular characterization of the 50-kD subunit of dynactin reveals function for the complex in chromosome alignment and spindle organization during mitosis". The Journal of Cell Biology. 132 (4): 617–33. doi:10.1083/jcb.132.4.617. PMC 2199864Freely accessible. PMID 8647893. 
  31. ^ Karki S, Holzbaur EL (February 1999). "Cytoplasmic dynein and dynactin in cell division and intracellular transport". Current Opinion in Cell Biology. 11 (1): 45–53. doi:10.1016/S0955-0674(99)80006-4. PMID 10047518. 
  32. ^ Gaglio T, Saredi A, Bingham JB, Hasbani MJ, Gill SR, Schroer TA, Compton DA (October 1996). "Opposing motor activities are required for the organization of the mammalian mitotic spindle pole". The Journal of Cell Biology. 135 (2): 399–414. doi:10.1083/jcb.135.2.399. PMC 2121053Freely accessible. PMID 8896597. 
  33. ^ Merdes A, Heald R, Samejima K, Earnshaw WC, Cleveland DW (May 2000). "Formation of spindle poles by dynein/dynactin-dependent transport of NuMA". The Journal of Cell Biology. 149 (4): 851–62. doi:10.1083/jcb.149.4.851. PMC 2174573Freely accessible. PMID 10811826. 
  34. ^ Howell BJ, McEwen BF, Canman JC, Hoffman DB, Farrar EM, Rieder CL, Salmon ED (December 2001). "Cytoplasmic dynein/dynactin drives kinetochore protein transport to the spindle poles and has a role in mitotic spindle checkpoint inactivation". The Journal of Cell Biology. 155 (7): 1159–72. doi:10.1083/jcb.200105093. PMC 2199338Freely accessible. PMID 11756470. 
  35. ^ Starr DA, Williams BC, Hays TS, Goldberg ML (August 1998). "ZW10 helps recruit dynactin and dynein to the kinetochore". The Journal of Cell Biology. 142 (3): 763–74. doi:10.1083/jcb.142.3.763. PMC 2148168Freely accessible. PMID 9700164. 
  36. ^ Whited JL, Cassell A, Brouillette M, Garrity PA (October 2004). "Dynactin is required to maintain nuclear position within postmitotic Drosophila photoreceptor neurons". Development. 131 (19): 4677–86. doi:10.1242/dev.01366. PMC 2714772Freely accessible. PMID 15329347. 
  37. ^ Tsujikawa M, Omori Y, Biyanwila J, Malicki J (September 2007). "Mechanism of positioning the cell nucleus in vertebrate photoreceptors". Proceedings of the National Academy of Sciences of the United States of America. 104 (37): 14819–24. doi:10.1073/pnas.0700178104. PMC 1976238Freely accessible. PMID 17785424. 
  38. ^ Xiang X, Han G, Winkelmann DA, Zuo W, Morris NR (May 2000). "Dynamics of cytoplasmic dynein in living cells and the effect of a mutation in the dynactin complex actin-related protein Arp1". Current Biology. 10 (10): 603–6. doi:10.1016/S0960-9822(00)00488-7. PMID 10837229. 
  39. ^ Bruno KS, Tinsley JH, Minke PF, Plamann M (May 1996). "Genetic interactions among cytoplasmic dynein, dynactin, and nuclear distribution mutants of Neurospora crassa". Proceedings of the National Academy of Sciences of the United States of America. 93 (10): 4775–80. doi:10.1073/pnas.93.10.4775. PMC 39355Freely accessible. PMID 8643479. 
  40. ^ Salina D, Bodoor K, Eckley DM, Schroer TA, Rattner JB, Burke B (January 2002). "Cytoplasmic dynein as a facilitator of nuclear envelope breakdown". Cell. 108 (1): 97–107. doi:10.1016/S0092-8674(01)00628-6. PMID 11792324. 
  41. ^ Quintyne NJ, Gill SR, Eckley DM, Crego CL, Compton DA, Schroer TA (October 1999). "Dynactin is required for microtubule anchoring at centrosomes". The Journal of Cell Biology. 147 (2): 321–34. doi:10.1083/jcb.147.2.321. PMC 2174233Freely accessible. PMID 10525538. 
  42. ^ Quintyne NJ, Schroer TA (October 2002). "Distinct cell cycle-dependent roles for dynactin and dynein at centrosomes". The Journal of Cell Biology. 159 (2): 245–54. doi:10.1083/jcb.200203089. PMC 2173046Freely accessible. PMID 12391026. 
  43. ^ Deacon SW, Serpinskaya AS, Vaughan PS, Lopez Fanarraga M, Vernos I, Vaughan KT, Gelfand VI (February 2003). "Dynactin is required for bidirectional organelle transport". The Journal of Cell Biology. 160 (3): 297–301. doi:10.1083/jcb.200210066. PMC 2172679Freely accessible. PMID 12551954. 

Further reading

This article incorporates text from the public domain Pfam and InterPro IPR008603

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.

Dynamitin Provide feedback

Dynamitin is a subunit of the microtubule-dependent motor complex and in implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS) [1].

Literature references

  1. Jin T, Li J; , J Biol Chem 2002;277:32963-32969.: Dynamitin controls Beta 2 integrin avidity by modulating cytoskeletal constraint on integrin molecules. PUBMED:12082093 EPMC:12082093


This tab holds annotation information from the InterPro database.

InterPro entry IPR028133

Dynactin is a multiprotein complex necessary for the function of microtubule motor protein dynein. The dynein-dynactin complex is involved in a variety of cellular events, including membrane vesicle transport, mitotic spindle assembly and centrosome separation [PUBMED:19935668, PUBMED:9522459, PUBMED:10047518].

Dynamitin (dynactin subunit 2, DCTN2) is a subunit of the dynactin complex. In Saccharomyces cerevisiae it is also known as Jnm1. Dynactin contains two distinct structural domains: a projecting sidearm that interacts with dynein and an actin-like minifilament backbone that is thought to bind cargo. Dynamitin holds together both structural domains [PUBMED:10525537]. Dynamitin is implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS) [PUBMED:12082093]. In mice, DCTN2 is involved in anchoring microtubules to centrosomes and may play a role in synapse formation during brain development [PUBMED:9144527].

Gene Ontology

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

Domain organisation

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

Loading domain graphics...

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 (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...

View options

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
(53)
Full
(1129)
Representative proteomes UniProt
(1692)
NCBI
(2002)
Meta
(0)
RP15
(326)
RP35
(615)
RP55
(862)
RP75
(1074)
Jalview View  View  View  View  View  View  View  View   
HTML View  View               
PP/heatmap 1 View               

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

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(53)
Full
(1129)
Representative proteomes UniProt
(1692)
NCBI
(2002)
Meta
(0)
RP15
(326)
RP35
(615)
RP55
(862)
RP75
(1074)
Alignment:
Format:
Order:
Sequence:
Gaps:
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
(53)
Full
(1129)
Representative proteomes UniProt
(1692)
NCBI
(2002)
Meta
(0)
RP15
(326)
RP35
(615)
RP55
(862)
RP75
(1074)
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.

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 View help on the curation process

Seed source: Pfam-B_5757 (release 7.6)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 53
Number in full: 1129
Average length of the domain: 322.30 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 87.44 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.9 30.9
Trusted cut-off 31.1 31.1
Noise cut-off 30.2 30.8
Model length: 388
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

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.

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 Dynamitin domain has been found. There are 20 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.

Loading structure mapping...