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24  structures 312  species 1  interaction 5482  sequences 292  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

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

A large "ZP domain" region, 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.[2] Functional and crystallographic studies revealed that the "ZP domain" region common to all these proteins is a protein polymerization module that consists of two distinct but structurally related immunoglobulin-like domains, ZP-N and ZP-C.[3][4][5][6][7][8][9] The ZP module is located in the C-terminal portion of the extracellular region and - with the exception of non-polymeric family member ENG[10] - contains 8 or 10 conserved Cys residues involved in disulfide bonds.[5][6][9]

Additional copies of isolated ZP-N domains are found in the N-terminal region of egg coat protein subunits involved in fertilization in both vertebrates and invertebrates, such as human zona pellucida components ZP1, ZP2 and ZP4 and mollusk vitelline envelope receptor for egg lysin (VERL).[5][11][12]

Examples

Humans genes encoding proteins containing this domain include:

References

  1. ^ a b Bork P, Sander C (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. ^ a b 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 395899Freely accessible. PMID 15079052. 
  5. ^ a b c 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, 3D4G, 3EF7
  6. ^ a b 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, 3NK4
  7. ^ Lin SJ, Hu Y, Zhu J, Woodruff TK, Jardetzky TS (2011). "Structure of betaglycan zona pellucida (ZP)-C domain provides insights into ZP-mediated protein polymerization and TGF-beta binding". Proc Natl Acad Sci U S A. 108 (13): 5232–6. doi:10.1073/pnas.1010689108. PMC 3069177Freely accessible. PMID 21402931.  PDB: 3QW9
  8. ^ Diestel U, Resch M, Meinhardt K, Weiler S, Hellmann TV, Mueller TD, Nickel J, Eichler J, Muller YA (2013). "Identification of a Novel TGF-β-Binding Site in the Zona Pellucida C-terminal (ZP-C) Domain of TGF-β-Receptor-3 (TGFR-3)". PLOS ONE. 8 (6): e67214. doi:10.1371/journal.pone.0067214. PMC 3695229Freely accessible. PMID 23826237.  PDB: 4AJV
  9. ^ a b Bokhove M, Nishimura K, Brunati M, Han L, de Sanctis D, Rampoldi L, Jovine L (2016). "A structured interdomain linker directs self-polymerization of human uromodulin". Proc. Natl. Acad. Sci. U.S.A. 113 (6): 1552–1557. doi:10.1073/pnas.1519803113. PMC 4760807Freely accessible. PMID 26811476.  PDB: 4WRN, 5BUP
  10. ^ Saito T, Bokhove M, Croci R, Zamora-Caballero S, Han L, Letarte M, de Sanctis D, Jovine L (2017). "Structural Basis of the Human Endoglin-BMP9 Interaction: Insights into BMP Signaling and HHT1". Cell Reports. 19 (9): 1917–1928. doi:10.1016/j.celrep.2017.05.011. PMC 5464963Freely accessible. PMID 28564608.  PDB: 5HZV
  11. ^ Callebaut I, Mornon JP, Monget P (2007). "Isolated ZP-N domains constitute the N-terminal extensions of Zona Pellucida proteins". Bioinformatics. 23: 1871–1874. doi:10.1093/bioinformatics/btm265. PMID 17510169. 
  12. ^ Raj I, Sadat Al Hosseini H, Dioguardi E, Nishimura K, Han L, Villa A, de Sanctis D, Jovine L (2017). "Structural Basis of Egg Coat-Sperm Recognition at Fertilization". Cell. 169 (7): 1315–1326. doi:10.1016/j.cell.2017.05.033. PMC 5480393Freely accessible. PMID 28622512.  PDB: 5II4, 5II5, 5II6, 5MR2, 5IIC, 5IIA, 5IIB, 5MR3

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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No Pfam abstract.

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

The zona pellucida (ZP) domain is a protein polymerisation module of ~260 amino acid module, which is found at the C terminus of many secreted eukaryotic glycoproteins that play fundamental roles in development, hearing, immunity, and cancer [PUBMED:1313375, PUBMED:12021773, PUBMED:12878193, PUBMED:15079052]. Proteins containing a ZP domain include:

  • Sperm receptor proteins ZP2 and ZP3. Along with protein ZP1, proteins ZP2 and ZP3 are responsible for sperm-adhesion to the zona pellucida. ZP3 first binds to specific sperm proteins, thus mediating sperm contacts with the oocyte. ZP2 acts as a second sperm receptor reinforcing the interactions. ZP1 cross-links the polymers formed by ZP2 and ZP3.
  • Zona pellucida sperm-binding protein B (ZP-B) (also known as ZP-X in rabbit and ZP-3 alpha in pig).
  • Glycoprotein GP2, the major component of pancreatic secretory granule membranes.
  • TGF-beta receptor type III (also known as betaglycan). This protein is a proteoglycan that binds to TGF-beta and could be involved in capturing and retaining TGF-beta for presentation to the signalling receptors.
  • Uromodulin (also known as Tamm-Horsfall urinary glycoprotein). The function of this protein, which is the most abundant in human urine, is not yet clear.
  • Chicken beta-tectorin, a major glycoprotein of avian tectorial membrane.

Most ZP domain proteins are synthesized as precursors with carboxy-terminal transmembrane domains or glycosyl phosphatidylinositol (GPI) anchors [PUBMED:12021773].

The ZP domain contains eight strictly conserved cysteines, which form disulphide bridges. The disulphide bonds within the ZP domains are divided into two groups, suggesting that the ZP domain consists of two subdomains. In addition to the conserved cysteines, only a few aromatic or hydrophobic amino acids are absolutely invariant, probably as a result of structural rather than functional constraints [PUBMED:1313375, PUBMED:12878193, PUBMED:15079052].

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 E-set (CL0159), which has the following description:

This clan includes a diverse range of domains that have an Ig-like fold and appear to be distantly related to each other. The clan includes: PKD domains, cadherins and several families of bacterial Ig-like domains as well as viral tail fibre proteins. it also includes several Fibronectin type III domain-containing families.

The clan contains the following 218 members:

A2M A2M_BRD A2M_recep Adeno_GP19K AlcCBM31 Alpha-amylase_N Alpha_adaptinC2 Alpha_E2_glycop Arch_flagellin Arylsulfotran_N ASF1_hist_chap ATG19_autophagy BACON Big_1 Big_10 Big_11 Big_2 Big_3 Big_3_2 Big_3_3 Big_3_5 Big_4 Big_5 Big_6 Big_7 Big_8 Big_9 Bile_Hydr_Trans BiPBP_C bMG1 bMG10 bMG3 bMG5 bMG6 BslA BsuPI Cadherin Cadherin-like Cadherin_2 Cadherin_3 Cadherin_4 Cadherin_5 Cadherin_pro CagX Calx-beta Candida_ALS_N CARDB CBM39 CBM_X2 CD45 CelD_N Ceramidse_alk_C CHB_HEX_C CHB_HEX_C_1 ChitinaseA_N ChiW_Ig_like CHU_C Coatamer_beta_C COP-gamma_platf CopC Cyc-maltodext_N Cytomega_US3 DsbC DUF11 DUF1410 DUF1425 DUF1929 DUF2271 DUF3244 DUF3327 DUF3416 DUF3458 DUF3501 DUF3823_C DUF3859 DUF3872 DUF4165 DUF4179 DUF4426 DUF4448 DUF4469 DUF4625 DUF4879 DUF4981 DUF4982 DUF5001 DUF5008 DUF5011 DUF5065 DUF5115 DUF525 DUF5643 DUF916 EB_dh ECD EpoR_lig-bind ERAP1_C EstA_Ig_like Filamin FixG_C Flavi_glycop_C FlgD_ig fn3 Fn3-like fn3_2 fn3_4 fn3_5 fn3_6 FN3_7 Fn3_assoc fn3_PAP GBS_Bsp-like Glucodextran_B Glyco_hydro2_C5 Glyco_hydro_2 Glyco_hydro_61 Gmad2 GMP_PDE_delta GPI-anchored Hanta_G1 He_PIG He_PIG_assoc HECW_N HemeBinding_Shp Hemocyanin_C Herpes_BLLF1 HYR IFNGR1 Ig_GlcNase Ig_mannosidase IL12p40_C Il13Ra_Ig IL17R_fnIII_D1 IL17R_fnIII_D2 IL2RB_N1 IL3Ra_N IL4Ra_N IL6Ra-bind Inhibitor_I42 Inhibitor_I71 Integrin_alpha2 Interfer-bind Invasin_D3 IRK_C IrmA Iron_transport LEA_2 Lep_receptor_Ig LIFR_N Lipase_bact_N LPMO_10 LRR_adjacent LTD Mannosidase_ig MG1 MG2 MG3 MG4 Mo-co_dimer N_BRCA1_IG Na_K-ATPase NEAT Neocarzinostat Neurexophilin NPCBM_assoc PapD_C PBP-Tp47_c Peptidase_C25_C Phlebovirus_G2 PhoD_N PKD PKD_2 PKD_3 Pollen_allerg_1 Pox_vIL-18BP Pur_ac_phosph_N Qn_am_d_aII Qn_am_d_aIII RabGGT_insert Reeler REJ RET_CLD1 RET_CLD3 RET_CLD4 RGI_lyase RHD_dimer Rho_GDI Rib SCAB-Ig SKICH SLAM SoxZ SprB SusE SVA SWM_repeat T2SS-T3SS_pil_N Tafi-CsgC TarS_C1 TcA_RBD TcfC TIG TIG_2 TIG_plexin Tissue_fac Top6b_C Transglut_C Transglut_N TRAP_beta Tuberculin UL16 Velvet WIF Wzt_C Y_Y_Y YBD ZirS_C Zona_pellucida

Alignments

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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
(423)
Full
(5482)
Representative proteomes UniProt
(8463)
NCBI
(14915)
Meta
(0)
RP15
(1423)
RP35
(2668)
RP55
(4298)
RP75
(4860)
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Key: ✓ available, x not generated, not available.

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  Seed
(423)
Full
(5482)
Representative proteomes UniProt
(8463)
NCBI
(14915)
Meta
(0)
RP15
(1423)
RP35
(2668)
RP55
(4298)
RP75
(4860)
Alignment:
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  Seed
(423)
Full
(5482)
Representative proteomes UniProt
(8463)
NCBI
(14915)
Meta
(0)
RP15
(1423)
RP35
(2668)
RP55
(4298)
RP75
(4860)
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: zona_pellucida;
Type: Family
Sequence Ontology: SO:0100021
Author: Sonnhammer ELL , Bateman A
Number in seed: 423
Number in full: 5482
Average length of the domain: 225.80 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 41.18 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 256
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Interactions

There is 1 interaction for this family. More...

Zona_pellucida

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 24 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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