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133  structures 349  species 1  interaction 21182  sequences 452  architectures

Family: Spectrin (PF00435)

Summary: Spectrin repeat

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This is the Wikipedia entry entitled "Spectrin repeat". More...

Spectrin repeat Edit Wikipedia article

Spectrin repeat
PDB 1aj3 EBI.jpg
Structure of the spectrin repeat: a left-handed antiparallel triple-helical coiled-coil.[1]
Identifiers
Symbol Spectrin
Pfam PF00435
InterPro IPR002017
PROSITE PDOC50083
SCOP 1aj3
SUPERFAMILY 1aj3
OPM superfamily 79
OPM protein 2spc
CDD cd00176

Spectrin repeats[2] are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin, dystrophin and more recently the plakin family. The spectrin repeat forms a three-helix bundle. These conform to the rules of the heptad repeat. Spectrin repeats give rise to linear proteins. This however may be due to sample bias in which linear and rigid structures are more amenable to crystallization. There are hints however, that some proteins harbouring spectrin repeats may also be flexible. This is most likely due to specifically evolved functional purposes.

Human proteins containing this domain[edit]

ACTN1; ACTN2; ACTN3; ACTN4; AKAP6; C14orf49; CATX-15; DMD; DRP2; DST; KALRN; MACF1; MCF2L; SPNB4; SPTA1; SPTAN1; SPTB; SPTBN1; SPTBN2; SPTBN3; SPTBN4; SPTBN5; SYNE1; SYNE2; TRIO; UTRN;

References[edit]

  1. ^ Pascual J, Pfuhl M, Walther D, Saraste M, Nilges M (October 1997). "Solution structure of the spectrin repeat: a left-handed antiparallel triple-helical coiled-coil". J. Mol. Biol. 273 (3): 740–51. doi:10.1006/jmbi.1997.1344. PMID 9356261. 
  2. ^ Harrison SC, Yan Y, Winograd E, Viel A, Cronin T, Branton D (1993). "Crystal structure of the repetitive segments of spectrin". Science 262 (5142): 2027–2030. doi:10.1126/science.8266097. PMID 8266097. 

Further reading[edit]

  • Djinovic-Carugo K, Gautel M, Ylänne J, Young P (February 2002). "The spectrin repeat: a structural platform for cytoskeletal protein assemblies". FEBS Lett. 513 (1): 119–23. doi:10.1016/S0014-5793(01)03304-X. PMID 11911890. 
  • Pascual J, Castresana J, Saraste M (September 1997). "Evolution of the spectrin repeat". BioEssays 19 (9): 811–7. doi:10.1002/bies.950190911. PMID 9297972. 
  • Al-Jassar, C; Knowles, T, Jeeves, M, Kami, K, Behr, E, Bikker, H, Overduin, M, Chidgey, M (Jul 2, 2011). "The Nonlinear Structure of the Desmoplakin Plakin Domain and the Effects of Cardiomyopathy-Linked Mutations.". Journal of Molecular Biology 411 (5): 1049–61. doi:10.1016/j.jmb.2011.06.047. PMID 21756917. 


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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.

Spectrin repeat Provide feedback

Spectrin repeat-domains are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference [2]. The spectrin domain- repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C. Although the domain occurs in ultiple repeats along sequences, the domains are actually stable on their own - ie they act, biophysically, like domains rather than repeats that along function when aggregated.

Literature references

  1. Hartwig JH; , Protein Profile 1995;2:732-732.: Actin-binding proteins. 1: Spectrin super family. PUBMED:7584474 EPMC:7584474

  2. Yan Y, Winograd E, Viel A, Cronin T, Harrison SC, Branton D; , Science 1993;262:2027-2030.: Crystal structure of the repetitive segments of spectrin. PUBMED:8266097 EPMC:8266097


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002017

Spectrin repeats [PUBMED:8266097] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [PUBMED:12672815, PUBMED:15062087], alpha-actinin [PUBMED:10481917] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.

Gene Ontology

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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...

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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
(83)
Full
(21182)
Representative proteomes NCBI
(19145)
Meta
(10)
RP15
(2238)
RP35
(2954)
RP55
(5943)
RP75
(9769)
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Format an alignment

  Seed
(83)
Full
(21182)
Representative proteomes NCBI
(19145)
Meta
(10)
RP15
(2238)
RP35
(2954)
RP55
(5943)
RP75
(9769)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(83)
Full
(21182)
Representative proteomes NCBI
(19145)
Meta
(10)
RP15
(2238)
RP35
(2954)
RP55
(5943)
RP75
(9769)
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.

Pfam alignments:

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_1 (release 1.0)
Previous IDs: spectrin;
Type: Domain
Author: Bateman A, Finn RD, Stabach P
Number in seed: 83
Number in full: 21182
Average length of the domain: 103.80 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 36.64 %

HMM information View help on HMM parameters

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 24.2 24.2
Trusted cut-off 24.2 24.2
Noise cut-off 24.1 24.1
Model length: 105
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Spectrin

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 Spectrin domain has been found. There are 133 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.

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