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68  structures 118  species 2  interactions 1221  sequences 8  architectures

Family: UPAR_LY6 (PF00021)

Summary: u-PAR/Ly-6 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 "CD59 antigen". More...

CD59 antigen Edit Wikipedia article

u-PAR/Ly-6 domain
Cd59b.png
Identifiers
Symbol UPAR_LY6
Pfam PF00021
InterPro IPR001526
PROSITE PDOC00756
SCOP 1erg
SUPERFAMILY 1erg
CDD cd00117

CD59 antigen (also called 1F-5Ag, H19, HRF20, MACIF, MIRL, P-18 or protectin) inhibits formation of membrane attack complex (MAC), thus protecting cells from complement-mediated lysis. It has a signaling role, as a GPI anchored molecule, in T cell activation and appears to have some role in cell adhesion through CD2 (controversial). CD59 associates with C9, inhibiting incorporation into C5b-8 preventing terminal steps in polymerization of the (MAC) in plasma membranes. Genetic defects in GPI-anchor attachment that cause a reduction or loss of both CD59 and CD55 on erythrocytes produce the symptoms of the disease paroxysmal nocturnal hemoglobinuria (PNH).

A variety of GPI-linked cell-surface glycoproteins are composed of one or more copies of a conserved domain of about 100 amino-acid residues.[2][3] Among these proteins, U-PAR contains three tandem copies of the domain, while all the others are made up of a single domain.

As shown in the following schematic, this conserved domain contains 10 cysteine residues involved in five disulfide bonds - in U-PAR, the first copy of the domain lacks the fourth disulfide bond.

    +------+     +------------------------+                    +---+
    |      |     |                        |                    |   |
xCxxCxxxxxxCxxxxxCxxxxxCxxxxxxxxxxxxxxxxxxCxxxxCxxxxxxxxxxxxxxCCxxxCxxxxxxxx
 |                     |                       |              |
 +---------------------+                       +--------------+

'C': conserved cysteine involved in a disulfide bond.

CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://mpr.nci.nih.gov/prow/).

Subfamilies[edit]

Human proteins containing this domain[edit]

ARS[disambiguation needed]; CD177; CD59; LY6D; LY6E; LY6H; LYNX1; LYPD2; LYPD3; LYPD4; LYPD5; LYPD6; PLAUR; PSCA; SLURP2; SLURP1; SPACA4; TEX101;

References[edit]

  1. ^ PDB 2J8B; Leath KJ, Johnson S, Roversi P, Hughes TR, Smith RA, Mackenzie L, Morgan BP, Lea SM (August 2007). "High-resolution structures of bacterially expressed soluble human CD59". Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 63 (Pt 8): 648–52. doi:10.1107/S1744309107033477. PMC 2335151. PMID 17671359. 
  2. ^ Patthy L, Blasi F, Behrendt N, Ploug M, Houen G, Dano K (1991). "The ligand-binding domain of the cell surface receptor for urokinase-type plasminogen activator". J. Biol. Chem. 266 (12): 7842–7847. PMID 1850423. 
  3. ^ Ploug M, Dano K, Kjalke M, Ronne E, Weidle U, Hoyer-Hansen G (1993). "Localization of the disulfide bonds in the NH2-terminal domain of the cellular receptor for human urokinase-type plasminogen activator. A domain structure belonging to a novel superfamily of glycolipid-anchored membrane proteins". J. Biol. Chem. 268 (23): 17539–17546. PMID 8394346. 

This article incorporates text from the public domain Pfam and InterPro IPR001526

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.

u-PAR/Ly-6 domain Provide feedback

This extracellular disulphide bond rich domain is related to PF00087.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001526

CD59 (also called 1F-5Ag, H19, HRF20, MACIF, MIRL, P-18 or protectin) inhibits formation of membrane attack complex (MAC), thus protecting cells from complement mediated lysis. It has a signalling role, as a GPI-anchored molecule, in T cell activation and appears to have some role in cell adhesion through CD2 (controversial). CD59 associates with C9, inhibiting incorporation into C5b-8 preventing terminal steps in polymerisation of the (MAC) in plasma membranes. Genetic defects in GPI-anchor attachment that cause a reduction or loss of both CD59 and CD55 on erythrocytes produce the symptoms of the disease paroxysmal nocturnal haemoglobinuria (PNH).

A variety of GPI-linked cell-surface glycoproteins are composed of one or more copies of a conserved domain of about 100 amino-acid residues [PUBMED:1850423], [PUBMED:8394346]. Among these proteins, U-PAR contains three tandem copies of the domain, while all the others are made up of a single domain.

As shown in the following schematic, this conserved domain contains 10 cysteine residues involved in five disulphide bonds - in U-PAR, the first copy of the domain lacks the fourth disulphide bond.

     +------+     +------------------------+                    +---+
     |      |     |                        |                    |   |
 xCxxCxxxxxxCxxxxxCxxxxxCxxxxxxxxxxxxxxxxxxCxxxxCxxxxxxxxxxxxxxCCxxxCxxxxxxxx
  |                     |                       |              |
  +---------------------+                       +--------------+
'C': conserved cysteine involved in a disulphide bond.

Domain organisation

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

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Pfam Clan

This family is a member of clan uPAR_Ly6_toxin (CL0117), which has the following description:

This superfamily contains snake toxins as well as extracellular cysteine rich domains.

The clan contains the following 5 members:

Activin_recp BAMBI PLA2_inh Toxin_1 UPAR_LY6

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
(40)
Full
(1221)
Representative proteomes NCBI
(1327)
Meta
(0)
RP15
(39)
RP35
(65)
RP55
(185)
RP75
(543)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(40)
Full
(1221)
Representative proteomes NCBI
(1327)
Meta
(0)
RP15
(39)
RP35
(65)
RP55
(185)
RP75
(543)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(40)
Full
(1221)
Representative proteomes NCBI
(1327)
Meta
(0)
RP15
(39)
RP35
(65)
RP55
(185)
RP75
(543)
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.

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: Prosite
Previous IDs: none
Type: Domain
Author: Sonnhammer ELL, Bateman A
Number in seed: 40
Number in full: 1221
Average length of the domain: 74.40 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 55.41 %

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 17.7 10.0
Trusted cut-off 17.7 10.2
Noise cut-off 17.6 9.9
Model length: 77
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There are 2 interactions for this family. More...

UPAR_LY6 Kringle

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 UPAR_LY6 domain has been found. There are 68 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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