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.
17  structures 315  species 5  interactions 3407  sequences 437  architectures

Family: Laminin_N (PF00055)

Summary: Laminin N-terminal (Domain VI)

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...

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 N-terminal (Domain VI) Provide feedback

No Pfam abstract.

Literature references

  1. Vuolteenaho R, Chow LT, Tryggvason K; , J Biol Chem 1990;265:15611-15616.: Structure of the human laminin B1 chain gene. PUBMED:1975589 EPMC:1975589


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008211

Laminin is a large molecular weight glycoprotein present only in basement membranes in almost every animal tissue. It is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components [PUBMED:1975589]. Each laminin is a heterotrimer assembled from alpha, beta and gamma chain subunits, secreted and incorporated into cell-associated extracellular matrices [PUBMED:10842354].

Basement membrane assembly is a cooperative process in which laminins polymerise through their N-terminal domain (LN or domain VI) and anchor to the cell surface through their G domains. Netrins may also associate with this network through heterotypic LN domain interactions [PUBMED:8349613]. This leads to cell signalling through integrins and dystroglycan (and possibly other receptors) recruited to the adherent laminin. This LN domain dependent self-assembly is considered to be crucial for the integrity of basement membranes, as highlighted by genetic forms of muscular dystrophy containing the deletion of the LN module from the alpha 2 laminin chain [PUBMED:7874173]. The laminin N-terminal domain is found in all laminin and netrin subunits except laminin alpha 3A, alpha 4 and gamma 2.

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 GBD (CL0202), which has the following description:

This large superfamily contains beta sandwich domains with a jelly roll topology. Many of these families are involved in carbohydrate recognition. Despite sharing little sequence similarity they do share a weak sequence motif, with a conserved bulge in the C-terminal beta sheet. The probable role of this bulge is in bending of the beta sheet that contains the bulge. This enables the curvature of the sheet forming the sugar binding site [1].

The clan contains the following 70 members:

7TMR-DISMED2 Agarase_CBM Allantoicase ANAPC10 Arabino_trans_C Bac_rhamnosid_N BcsB BetaGal_dom4_5 BPA_C Calpain_III CBM-like CBM27 CBM32 CBM46 CBM60 CBM65_1 CBM_11 CBM_15 CBM_17_28 CBM_26 CBM_35 CBM_4_9 CBM_6 CE2_N CIA30 Clenterotox Cry1Ac_D5 DUF4465 DUF4627 DUF5000 DUF5010_C DUF5077 DUF5625 DUF642 Endotoxin_C Ephrin_lbd Exop_C F5_F8_type_C FBA FlhE GH101_N GH115_C Glft2_N Glyco_hydro_2_N GxDLY HA70_C Laminin_B Laminin_N Lectin_like Lipl32 Lyase_N Malectin Malectin_like Muskelin_N NPCBM P_proprotein PA-IL PAW PCMD PepX_C PINIT PITH PPC PulA_N1 Sad1_UNC SGBP_B_XBD TcA_TcB_BD Thioredoxin_10 XRCC1_N YpM

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
(160)
Full
(3407)
Representative proteomes UniProt
(5213)
NCBI
(9546)
Meta
(0)
RP15
(734)
RP35
(1482)
RP55
(2508)
RP75
(2944)
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
(160)
Full
(3407)
Representative proteomes UniProt
(5213)
NCBI
(9546)
Meta
(0)
RP15
(734)
RP35
(1482)
RP55
(2508)
RP75
(2944)
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
(160)
Full
(3407)
Representative proteomes UniProt
(5213)
NCBI
(9546)
Meta
(0)
RP15
(734)
RP35
(1482)
RP55
(2508)
RP75
(2944)
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: Swissprot_feature_table
Previous IDs: laminin_Nterm;
Type: Family
Sequence Ontology: SO:0100021
Author: Sonnhammer ELL
Number in seed: 160
Number in full: 3407
Average length of the domain: 216.50 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 14.71 %

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 25.9 25.9
Trusted cut-off 26.2 25.9
Noise cut-off 25.8 25.6
Model length: 234
Family (HMM) version: 17
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.

Interactions

There are 5 interactions for this family. More...

LRR_8 Laminin_EGF LRR_5 LRR_1 Laminin_EGF

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_N domain has been found. There are 17 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...