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.
65  structures 540  species 0  interactions 114972  sequences 4041  architectures

Family: Laminin_EGF (PF00053)

Summary: Laminin EGF domain

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 "Laminin". More...

Laminin Edit Wikipedia article

Laminins are a family of heterotrimeric glycoproteins found in the basal lamina underlying epithelia. Their binding to type IV collagen contributes to the self-assembly of the basal lamina from components secreted by cells, and their recognition by integrins is important to the function of the basal lamina.

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.

Laminin EGF domain Provide feedback

This family is like PF00008 but has 8 conserved cysteines instead of six.

Literature references

  1. Engel J; , Biochemistry 1992;31:10643-10651.: Laminins and other strange proteins. PUBMED:1420180 EPMC:1420180


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002049

Laminins [ PUBMED:2404817 ] are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation. They are composed of distinct but related alpha, beta and gamma chains. The three chains form a cross-shaped molecule that consist of a long arm and three short globular arms. The long arm consist of a coiled coil structure contributed by all three chains and cross-linked by interchain disulphide bonds. Beside different types of globular domains each subunit contains, in its first half, consecutive repeats of about 60 amino acids in length that include eight conserved cysteines [ PUBMED:2666164 ]. The tertiary structure [ PUBMED:8648630 , PUBMED:8648631 ] of this domain is remotely similar in its N-terminal to that of the EGF-like module (see PROSITEDOC ). It is known as a 'LE' or 'laminin-type EGF-like' domain. The number of copies of the LE domain in the different forms of laminins is highly variable; from 3 up to 22 copies have been found. A schematic representation of the topology of the four disulphide bonds in the LE domain is shown below.

         +-------------------+
       +-|-----------+       |  +--------+  +-----------------+
       | |           |       |  |        |  |                 |
     xxCxCxxxxxxxxxxxCxxxxxxxCxxCxxxxxGxxCxxCxxgaagxxxxxxxxxxxCxx
       sssssssssssssssssssssssssssssssssss

'C': conserved cysteine involved in a disulphide bond
'a': conserved aromatic residue
'G': conserved glycine (lower case = less conserved)
's': region similar to the EGF-like domain
In mouse laminin gamma-1 chain, the seventh LE domain has been shown to be the only one that binds with a high affinity to nidogen [ PUBMED:7781764 ]. The binding-sites are located on the surface within the loops C1-C3 and C5-C6 [ PUBMED:8648630 , PUBMED:8648631 ]. Long consecutive arrays of LE domains in laminins form rod-like elements of limited flexibility [ PUBMED:2404817 ], which determine the spacing in the formation of laminin networks of basement membranes [ PUBMED:8349613 ].

Domain organisation

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

Loading domain graphics...

Pfam Clan

This family is a member of clan EGF (CL0001), which has the following description:

Members of this clan all belong to the EGF superfamily. This particular superfamily is characterised as having least 6 cysteine residues. These cysteines form disulphide bonds, in the order 1-3, 2-4, 5-6, which are essential for the stability of the EGF fold. These disulphide bonds are stacked in a ladder-like arrangement. The Laminin EGF family is distinguished by having an an additional disulphide bond. The function of the domains within this family remains unclear, but they are thought to largely perform a structural role. More often than not, these domains are arranged in tandem repeats in extracellular proteins.

The clan contains the following 22 members:

cEGF CFC DSL EGF EGF_2 EGF_3 EGF_alliinase EGF_CA EGF_MSP1_1 EGF_Tenascin Ephrin_rec_like Fibrillin_U_N FOLN FXa_inhibition Gla hEGF I-EGF_1 Laminin_EGF Plasmod_Pvs28 Sushi Sushi_2 Tme5_EGF_like

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
(72)
Full
(114972)
Representative proteomes UniProt
(183606)
RP15
(16230)
RP35
(36232)
RP55
(88373)
RP75
(117318)
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
(72)
Full
(114972)
Representative proteomes UniProt
(183606)
RP15
(16230)
RP35
(36232)
RP55
(88373)
RP75
(117318)
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
(72)
Full
(114972)
Representative proteomes UniProt
(183606)
RP15
(16230)
RP35
(36232)
RP55
(88373)
RP75
(117318)
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: Swissprot_feature_table
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL
Number in seed: 72
Number in full: 114972
Average length of the domain: 49.5 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 18.54 %

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 21.0 13.4
Trusted cut-off 21.0 13.4
Noise cut-off 20.9 13.3
Model length: 49
Family (HMM) version: 27
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 Laminin_EGF domain has been found. There are 65 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...

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
A0A044QTS7 View 3D Structure Click here
A0A044QV60 View 3D Structure Click here
A0A044R0S3 View 3D Structure Click here
A0A044SZK3 View 3D Structure Click here
A0A044T3N3 View 3D Structure Click here
A0A044T4U4 View 3D Structure Click here
A0A044TNI9 View 3D Structure Click here
A0A044TR47 View 3D Structure Click here
A0A044UH70 View 3D Structure Click here
A0A044VF08 View 3D Structure Click here
A0A077YVM5 View 3D Structure Click here
A0A077YVX9 View 3D Structure Click here
A0A077YZ19 View 3D Structure Click here
A0A077Z0H1 View 3D Structure Click here
A0A077Z1F0 View 3D Structure Click here
A0A077Z4D6 View 3D Structure Click here
A0A077Z4D8 View 3D Structure Click here
A0A077Z685 View 3D Structure Click here
A0A077ZE42 View 3D Structure Click here
A0A0G2JTN7 View 3D Structure Click here
A0A0G2K023 View 3D Structure Click here
A0A0G2K5E2 View 3D Structure Click here
A0A0G2KI51 View 3D Structure Click here
A0A0H5SBB2 View 3D Structure Click here
A0A0I9N8S5 View 3D Structure Click here
A0A0K0DVQ8 View 3D Structure Click here
A0A0K0DZ23 View 3D Structure Click here
A0A0K0E060 View 3D Structure Click here
A0A0K0EAE9 View 3D Structure Click here
A0A0K0EC03 View 3D Structure Click here
A0A0K0EGE7 View 3D Structure Click here
A0A0K0EM36 View 3D Structure Click here
A0A0K0EQ15 View 3D Structure Click here
A0A0K0JC11 View 3D Structure Click here
A0A0K0JLL5 View 3D Structure Click here
A0A0N4U3X3 View 3D Structure Click here
A0A0N4U6N6 View 3D Structure Click here
A0A0N4U6P2 View 3D Structure Click here
A0A0N4U6Q3 View 3D Structure Click here
A0A0N4U928 View 3D Structure Click here