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25  structures 1429  species 0  interactions 5914  sequences 152  architectures

Family: MIT (PF04212)

Summary: MIT (microtubule interacting and transport) domain

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

MIT (microtubule interacting and transport) domain Provide feedback

The MIT domain forms an asymmetric three-helix bundle [3] and binds ESCRT-III (endosomal sorting complexes required for transport) substrates [2].

Literature references

  1. Phillips SA, Barr VA, Haft DH, Taylor SI, Haft CR; , J Biol Chem 2001;276:5074-5084.: Identification and characterization of SNX15, a novel sorting nexin involved in protein trafficking. PUBMED:11085978 EPMC:11085978

  2. Scott A, Chung HY, Gonciarz-Swiatek M, Hill GC, Whitby FG, Gaspar J, Holton JM, Viswanathan R, Ghaffarian S, Hill CP, Sundquist WI; , EMBO J. 2005;24:3658-3669.: Structural and mechanistic studies of VPS4 proteins. PUBMED:16193069 EPMC:16193069

  3. Scott A, Gaspar J, Stuchell-Brereton MD, Alam SL, Skalicky JJ, Sundquist WI; , Proc Natl Acad Sci U S A. 2005;102:13813-13818.: Structure and ESCRT-III protein interactions of the MIT domain of human VPS4A. PUBMED:16174732 EPMC:16174732


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007330

The MIT domain forms an asymmetric three-helix bundle. It is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking.

A 'variant' MIT domain has been described at the N-terminal region of a related AAA-ATPase, mammalian katanin p60 [ PUBMED:20339000 ].

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(145)
Full
(5914)
Representative proteomes UniProt
(10481)
RP15
(979)
RP35
(2386)
RP55
(4778)
RP75
(6512)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(145)
Full
(5914)
Representative proteomes UniProt
(10481)
RP15
(979)
RP35
(2386)
RP55
(4778)
RP75
(6512)
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
(145)
Full
(5914)
Representative proteomes UniProt
(10481)
RP15
(979)
RP35
(2386)
RP55
(4778)
RP75
(6512)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Crosby A, Patel H
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 145
Number in full: 5914
Average length of the domain: 65.50 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 12.68 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.0 30.0
Trusted cut-off 30.0 30.0
Noise cut-off 29.9 29.9
Model length: 65
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Selections

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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...

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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 MIT domain has been found. There are 25 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2KB60 View 3D Structure Click here
A0A0P0UY01 View 3D Structure Click here
A0A0R0H530 View 3D Structure Click here
A0A0R4IA57 View 3D Structure Click here
A0A0R4IA57 View 3D Structure Click here
A0A0R4IE18 View 3D Structure Click here
A0A0R4IPK7 View 3D Structure Click here
A0A0R4IPK7 View 3D Structure Click here
A0A0R4ITC8 View 3D Structure Click here
A0A0R4IV01 View 3D Structure Click here
A0A1D6FE31 View 3D Structure Click here
A4I4W4 View 3D Structure Click here
A4I963 View 3D Structure Click here
A9JT54 View 3D Structure Click here
B0S8J9 View 3D Structure Click here
B8A2W9 View 3D Structure Click here
D3ZHP7 View 3D Structure Click here
D3ZHP7 View 3D Structure Click here
D4AAT5 View 3D Structure Click here
E7FF70 View 3D Structure Click here
F4HW05 View 3D Structure Click here
I1LKT2 View 3D Structure Click here
I1LRE7 View 3D Structure Click here
I1LTU5 View 3D Structure Click here
O75351 View 3D Structure Click here
P46467 View 3D Structure Click here
P52917 View 3D Structure Click here
Q08BZ6 View 3D Structure Click here
Q09803 View 3D Structure Click here
Q20821 View 3D Structure Click here
Q22143 View 3D Structure Click here
Q3U3Q1 View 3D Structure Click here
Q3U3Q1 View 3D Structure Click here
Q499T5 View 3D Structure Click here
Q499T5 View 3D Structure Click here
Q4D9C2 View 3D Structure Click here
Q4E658 View 3D Structure Click here
Q4KLL7 View 3D Structure Click here
Q4V896 View 3D Structure Click here
Q54CX7 View 3D Structure Click here
Q54CX7 View 3D Structure Click here
Q54CX7 View 3D Structure Click here
Q54JG4 View 3D Structure Click here
Q54KQ7 View 3D Structure Click here
Q54PT2 View 3D Structure Click here
Q54RJ5 View 3D Structure Click here
Q55GN8 View 3D Structure Click here
Q55GN8 View 3D Structure Click here
Q5AG40 View 3D Structure Click here
Q5I0J5 View 3D Structure Click here
Q5ZEN9 View 3D Structure Click here
Q6ETH5 View 3D Structure Click here
Q6PHR2 View 3D Structure Click here
Q6PHR2 View 3D Structure Click here
Q793F9 View 3D Structure Click here
Q8BLK9 View 3D Structure Click here
Q8IKQ5 View 3D Structure Click here
Q8R2S1 View 3D Structure Click here
Q8T127 View 3D Structure Click here
Q8VDV8 View 3D Structure Click here
Q8VEJ9 View 3D Structure Click here
Q8WV92 View 3D Structure Click here
Q91WE1 View 3D Structure Click here
Q96S38 View 3D Structure Click here
Q9BL83 View 3D Structure Click here
Q9NRS6 View 3D Structure Click here
Q9R1S8 View 3D Structure Click here
Q9R1S8 View 3D Structure Click here
Q9UN37 View 3D Structure Click here
Q9VEA9 View 3D Structure Click here
Q9VHF6 View 3D Structure Click here
Q9VHF6 View 3D Structure Click here
Q9VZK1 View 3D Structure Click here
Q9Y162 View 3D Structure Click here
Q9Y6S9 View 3D Structure Click here
Q9Y6W3 View 3D Structure Click here
Q9Y6W3 View 3D Structure Click here
Q9ZNT0 View 3D Structure Click here
X1WG66 View 3D Structure Click here