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130  structures 1480  species 0  interactions 106776  sequences 728  architectures

Family: LIM (PF00412)

Summary: LIM domain

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This is the Wikipedia entry entitled "LIM domain". More...

LIM domain Edit Wikipedia article

LIM domain
Structure of the 4th LIM domain of Pinch protein. Zinc atoms are shown in grey

LIM domains are protein structural domains, composed of two contiguous zinc finger domains, separated by a two-amino acid residue hydrophobic linker.[1] They are named after their initial discovery in the proteins Lin11, Isl-1 & Mec-3.[2] LIM-domain containing proteins have been shown to play roles in cytoskeletal organisation, organ development and oncogenesis. LIM-domains mediate protein–protein interactions that are critical to cellular processes.

LIM domains have highly divergent sequences, apart from certain key residues. The sequence divergence allow a great many different binding sites to be grafted onto the same basic domain. The conserved residues are those involved in zinc binding or the hydrophobic core of the protein. The sequence signature of LIM domains is as follows:


LIM domain organisation

LIM domains frequently occur in multiples, as seen in proteins such as TES, LMO4, and can also be attached to other domains in order to confer a binding or targeting function upon them, such as LIM-kinase.

The LIM superclass of genes have been classified into 14 classes: ABLIM, CRP, ENIGMA, EPLIN, LASP, LHX, LMO, LIMK, LMO7, MICAL, PXN, PINCH, TES, and ZYX. Six of these classes (i.e., ABLIM, MICAL, ENIGMA, ZYX, LHX, LM07) originated in the stem lineage of animals, and this expansion is thought to have made a major contribution to the origin of animal multicellularity.[3]

LIM domains are also found in various bacterial lineages where they are typically fused to a metallopeptidase domain. Some versions show fusions to an inactive P-loop NTPase at their N-terminus and a single transmembrane helix. These domain fusions suggest that the prokaryotic LIM domains are likely to regulate protein processing at the cell membrane. The domain architectural syntax is remarkably parallel to those of the prokaryotic versions of the B-box zinc finger and the AN1 zinc finger domains.[4]


  1. ^ Kadrmas JL, Beckerle MC (2004). "The LIM domain: from the cytoskeleton to the nucleus". Nat. Rev. Mol. Cell Biol. 5 (11): 920–31. doi:10.1038/nrm1499. PMID 15520811.
  2. ^ Bach I (2000). "The LIM domain: regulation by association". Mech. Dev. 91 (1–2): 5–17. doi:10.1016/S0925-4773(99)00314-7. PMID 10704826.
  3. ^ Koch BJ, Ryan JF, Baxevanis AD (March 2012). "The Diversification of the LIM Superclass at the Base of the Metazoa Increased Subcellular Complexity and Promoted Multicellular Specialization". PLoS ONE. 7 (3): e33261. Bibcode:2012PLoSO...733261K. doi:10.1371/journal.pone.0033261. PMC 3305314. PMID 22438907.
  4. ^ Burroughs AM, Iyer LM, Aravind L (July 2011). "Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system". Mol. Biosyst. 7 (1): 2261–77. doi:10.1039/C1MB05061C. PMC 5938088. PMID 21547297.

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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.

LIM domain Provide feedback

This family represents two copies of the LIM structural domain.

Literature references

  1. Perez-Alvarado GC, Miles C, Michelsen JW, Louis HA, Winge DR, Beckerle MC, Summers MF; , Nat Struct Biol 1994;1:388-398.: Structure of the carboxy-terminal Lim domain from the cysteine rich protein Crp. PUBMED:7664053 EPMC:7664053

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001781

This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [ PUBMED:1970421 , PUBMED:1467648 ]. Protein containing LIM Znf domains include:

  • Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode.
  • C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells.
  • Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene.
  • Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3.
  • Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene.
  • Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types.
  • Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs.
  • Vertebrate protein kinases LIMK-1 and LIMK-2.
  • Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia.
  • Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin.
  • Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein.
  • Vertebrate paxillin, a cytoskeletal focal adhesion protein.
  • Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see INTERPRO ).
  • Helianthus annuus (Common sunflower) pollen specific protein SF3.
  • Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP.
  • Yeast protein LRG1 which is involved in sporulation [ PUBMED:8065929 ].
  • Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1.
  • C. elegans homeobox protein ceh-14.
  • C. elegans homeobox protein unc-97.
  • S. cerevisiae hypothetical protein YKR090w.
  • C. elegans hypothetical proteins C28H8.6.

These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains.

LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is:


LIM domains bind two zinc ions [ PUBMED:8506279 ]. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction.

Domain organisation

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

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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...

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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.

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

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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...


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.

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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.

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Seed source: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 34
Number in full: 106776
Average length of the domain: 57.10 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 21.18 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.9 22.9
Trusted cut-off 22.9 22.9
Noise cut-off 22.8 22.8
Model length: 58
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence


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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 LIM domain has been found. There are 130 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
A0A061AD47 View 3D Structure Click here
A0A0G2JYM0 View 3D Structure Click here
A0A0G2K688 View 3D Structure Click here
A0A0G2K8R3 View 3D Structure Click here
A0A0G2K919 View 3D Structure Click here
A0A0G2K995 View 3D Structure Click here
A0A0G2KAE1 View 3D Structure Click here
A0A0G2KJM7 View 3D Structure Click here
A0A0G2QC60 View 3D Structure Click here
A0A0K3AQM0 View 3D Structure Click here
A0A0P0VM79 View 3D Structure Click here
A0A0R0GAE0 View 3D Structure Click here
A0A0R0H662 View 3D Structure Click here
A0A0R0I6V2 View 3D Structure Click here
A0A0R0K9J7 View 3D Structure Click here
A0A0R0LB42 View 3D Structure Click here
A0A0R4ICT4 View 3D Structure Click here
A0A0R4IJJ4 View 3D Structure Click here
A0A0R4IJP7 View 3D Structure Click here
A0A0R4IN44 View 3D Structure Click here
A0A0R4INF7 View 3D Structure Click here
A0A0R4IVV2 View 3D Structure Click here
A0A0R4IWT9 View 3D Structure Click here
A0A0R4IXJ5 View 3D Structure Click here
A0A1D5NSS7 View 3D Structure Click here
A0A1D6E4S2 View 3D Structure Click here
A0A1D6HEG9 View 3D Structure Click here
A0A1D6JXK9 View 3D Structure Click here
A0A1D6KF85 View 3D Structure Click here
A0A1D6KXJ5 View 3D Structure Click here
A0A1D6LVZ7 View 3D Structure Click here
A0A1D6PDX4 View 3D Structure Click here
A0A1D8PPS6 View 3D Structure Click here
A0A1D8PRQ6 View 3D Structure Click here
A0A1L8F1M4 View 3D Structure Click here
A0A2R8PVS7 View 3D Structure Click here
A0A2R8Q2U1 View 3D Structure Click here
A0A2R8Q4Q0 View 3D Structure Click here
A0A2R8Q887 View 3D Structure Click here
A0A2R8QEF4 View 3D Structure Click here