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33  structures 1303  species 0  interactions 3339  sequences 25  architectures

Family: GRASP55_65 (PF04495)

Summary: GRASP55/65 PDZ-like domain

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GRASP55/65 PDZ-like domain Provide feedback

GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system [1]. This region appears to be related to the PDZ domain.

Literature references

  1. Shorter J, Watson R, Giannakou ME, Clarke M, Warren G, Barr FA; , EMBO J 1999;18:4949-4960.: GRASP55, a second mammalian GRASP protein involved in the stacking of Golgi cisternae in a cell-free system. PUBMED:10487747 EPMC:10487747

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024958

The Golgi apparatus is a highly dynamic organelle responsible for sorting out proteins and other biomolecules to the cell surface and to the extracellular milieu. The Golgi apparatus is comprised of flattened membrane-bound compartments called cisternae, which are apposed to one another to form a Golgi stack. The structural organization of the cisternae into stacks and their lateral connection, building the Golgi ribbon, requires a family of proteins called Golgi ReAssembly and Stacking Proteins (GRASP). Two homologues (GRASP55 and GRASP65) have been described in vertebrates and their functions have been associated to Golgi phosphorylation-regulated assembly/disassembly, protein secretion , Golgi remodeling in migrating cells, among others. There is only one gene for GRASP in lower eukaryotes. Essentially all GRASPs contain a conserved N-terminal GRASP region, which comprises two tandem PDZ domains (PDZ1 and PDZ2), a classical protein-peptide interaction domain, and is responsible for GRASP homo-oligomerization and for the attachment to the Golgi membrane. The C-terminal half which is not conserved between species but is rich in proline and serines residues, as well as glutamine and asparagine residues [ PUBMED:27436376 , PUBMED:21235525 , PUBMED:23940043 , PUBMED:21515684 ].

The GRASP-type PDZ domains adopt a canonical PDZ fold with a beta-sandwich of five beta-strands and two alpha-helices. The PDZ1 and PDZ2 domains are nearly superimposable. The peptide-binding pockets of both PDZ domains are formed by alpha2 and beta5. A typical ligand peptide is predicted to form antiparallel beta-strand interactions with beta5 and insert hydrophobic side chains between alpha2 and beta5. The two PDZ domains cooperate to achieve dimerization and oligomerization. In the dimers the PDZ2 domains interact in a way that positions the peptide-binding pockets facing each other. In addition, the dimers are linked through interactions between the two C-terminal tails (CTs) of one dimer and two peptide-binding pockets of the PDZ1 domains in the next dimer [ PUBMED:23940043 , PUBMED:21515684 ].

This entry represents the GRASP-type PDZ domain.

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 PDZ-like (CL0466), which has the following description:

This superfamily comprises families of PDZ domains, which are peptide binding sites.

The clan contains the following 11 members:

DUF6288 EBP50_C GRASP55_65 PDZ PDZ_1 PDZ_2 PDZ_3 PDZ_4 PDZ_5 PDZ_6 Tricorn_PDZ


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...

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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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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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...


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: Pfam-B_3985 (release 7.5)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 18
Number in full: 3339
Average length of the domain: 116 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 47.6 %

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 27.7 27.7
Trusted cut-off 27.7 27.7
Noise cut-off 27.6 27.6
Model length: 138
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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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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 GRASP55_65 domain has been found. There are 33 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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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
A0A044S2T5 View 3D Structure Click here
A0A077ZC22 View 3D Structure Click here
A0A0D2F0S7 View 3D Structure Click here
A0A0H2UJY9 View 3D Structure Click here
A0A0K0E1R1 View 3D Structure Click here
A0A0N4U7B2 View 3D Structure Click here
A0A175VRY0 View 3D Structure Click here
A0A1C1CCX2 View 3D Structure Click here
A0A1D8PD30 View 3D Structure Click here
A0A3P7DUG6 View 3D Structure Click here
A0A3Q0KSK0 View 3D Structure Click here
B0S774 View 3D Structure Click here
C0NCU2 View 3D Structure Click here
C1GRG7 View 3D Structure Click here
C6S3C8 View 3D Structure Click here
E9AHQ6 View 3D Structure Click here
F1RBF9 View 3D Structure Click here
F6T071 View 3D Structure Click here
O35254 View 3D Structure Click here
Q04410 View 3D Structure Click here
Q10149 View 3D Structure Click here
Q386P4 View 3D Structure Click here
Q4D0L6 View 3D Structure Click here
Q4E2Q1 View 3D Structure Click here
Q54C46 View 3D Structure Click here
Q8IJM6 View 3D Structure Click here
Q91X51 View 3D Structure Click here
Q99JX3 View 3D Structure Click here
Q9BQQ3 View 3D Structure Click here
Q9H8Y8 View 3D Structure Click here
Q9N3Y1 View 3D Structure Click here
Q9R064 View 3D Structure Click here
Q9VW57 View 3D Structure Click here
U7PSR4 View 3D Structure Click here