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17  structures 237  species 0  interactions 2880  sequences 163  architectures

Family: Zona_pellucida (PF00100)

Summary: Zona pellucida-like domain

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This is the Wikipedia entry entitled "Zona pellucida-like domain". More...

Zona pellucida-like domain Edit Wikipedia article

Zona pellucida-like domain
Identifiers
Symbol Zona_pellucida
Pfam PF00100
InterPro IPR001507
SMART SM00241
PROSITE PDOC00577

Zona pellucida-like domain (ZP domain / ZP-like domain) is a family of evolutionarily related proteins.[1][2]

A large domain, containing around 260 amino acids, has been recognised in a variety of receptor-like eukaryotic glycoproteins.[1] All of these proteins are mosaic proteins composed of various domains and that all have a large extracellular region, often followed by either a transmembrane region and a very short cytoplasmic region or by a GPI-anchor. The domain common to all these proteins is a bipartite protein polymerization module [3][4] that is located in the C-terminal portion of the extracellular region and contains 8 or 10 conserved Cys residues involved in disulfide bonds. [5][6]

Examples[edit]

Humans genes encoding proteins containing this domain include:

References[edit]

  1. ^ a b Bork P, Sander C (April 1992). "A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor". FEBS Lett. 300 (3): 237–40. doi:10.1016/0014-5793(92)80853-9. PMID 1313375. 
  2. ^ Jovine L, Darie CC, Litscher ES, Wassarman PM (2005). "Zona pellucida domain proteins". Annu. Rev. Biochem. 74: 83–114. doi:10.1146/annurev.biochem.74.082803.133039. PMID 15952882. 
  3. ^ Jovine L, Qi H, Williams Z, Litscher E, Wassarman PM (2002). "The ZP domain is a conserved module for polymerization of extracellular proteins". Nat Cell Biol. 4 (6): 457–61. doi:10.1038/ncb802. PMID 12021773. 
  4. ^ Jovine L, Qi H, Williams Z, Litscher ES, Wassarman PM (2004). "A duplicated motif controls assembly of zona pellucida domain proteins". Proc. Natl. Acad. Sci. U.S.A. 101 (16): 5922–7. doi:10.1073/pnas.0401600101. PMC 395899. PMID 15079052. 
  5. ^ Monné M, Han L, Schwend T, Burendahl S, Jovine L (2008). "Crystal structure of the ZP-N domain of ZP3 reveals the core fold of animal egg coats". Nature 456 (7222): 653–7. doi:10.1038/nature07599. PMID 19052627.  PDB 3D4C PDB 3D4G PDB 3EF7
  6. ^ Han L, Monné M, Okumura, H, Schwend, T, Cherry, AL, Flot, D, Matsuda, T, Jovine, L (2010). "Insights into egg coat assembly and egg-sperm interaction from the X-ray structure of full-length ZP3". Cell 143 (3): 404–15. doi:10.1016/j.cell.2010.09.041. PMID 20970175.  PDB 3NK3 PDB 3NK4

This article incorporates text from the public domain Pfam and InterPro IPR001507

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.

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Literature references

  1. Bork P, Sander C; , FEBS Lett 1992;300:237-240.: A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor. PUBMED:1313375 EPMC:1313375


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001507

A large domain, containing around 260 amino acids, has been recognised in a variety of receptor-like eukaryotic glycoproteins [PUBMED:1313375]. All of these proteins are mosaic proteins composed of various domains and that all have a large extracellular region followed by either a transmembrane region and a very short cytoplasmic region or by a GPI-anchor. The domain common to all these proteins is located in the C-terminal portion of the extracellular region, and contains 8 conserved Cys residues, which are probably involved in disulphide bond formation.

This entry includes a domain found in the zona pellucida proteins. The zona pellucida is a specialised extracellular matrix of mammailian eggs, which plays a crucial role in fertilisation by directly mediating species-restricted recongition between gametes. In mammals, up to four zona pellucida subnits are known, named ZP1-4. The full-length crystal structure of murine ZP3 has been solved [PUBMED:20970175].

This entry is also found in other glycoproteins, such as CD105 (also called endoglin) which is the regulatory component of the TGF-beta receptor complex. It is a modulator of cellular responses to TGF-beta 1.

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 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
(143)
Full
(2880)
Representative proteomes NCBI
(2596)
Meta
(0)
RP15
(525)
RP35
(708)
RP55
(1302)
RP75
(1681)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(143)
Full
(2880)
Representative proteomes NCBI
(2596)
Meta
(0)
RP15
(525)
RP35
(708)
RP55
(1302)
RP75
(1681)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(143)
Full
(2880)
Representative proteomes NCBI
(2596)
Meta
(0)
RP15
(525)
RP35
(708)
RP55
(1302)
RP75
(1681)
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: Swissprot_feature_table
Previous IDs: zona_pellucida;
Type: Family
Author: Sonnhammer ELL, Bateman A
Number in seed: 143
Number in full: 2880
Average length of the domain: 221.40 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 41.22 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 265
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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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 Zona_pellucida 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 seqence.

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