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5  structures 1289  species 0  interactions 1864  sequences 38  architectures

Family: RINT1_TIP1 (PF04437)

Summary: RINT-1 / TIP-1 family

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

RINT-1 / TIP-1 family Provide feedback

This family includes RINT-1, a Rad50 interacting protein which participates in radiation induced checkpoint control [1] as well as the TIP-1 protein from yeast that seems to be involved in a complex with Sec20p that is required for Golgi transport [2].

Literature references

  1. Xiao J, Liu CC, Chen PL, Lee WH; , J Biol Chem 2001;276:6105-6111.: RINT-1, a novel Rad50-interacting protein, participates in radiation-induced G(2)/M checkpoint control. PUBMED:11096100 EPMC:11096100

  2. Sweet DJ, Pelham HR; , EMBO J 1993;12:2831-2840.: The TIP1 gene of Saccharomyces cerevisiae encodes an 80 kDa cytoplasmic protein that interacts with the cytoplasmic domain of Sec20p. PUBMED:8334998 EPMC:8334998


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007528

This entry includes PINT-1 from animals, Tip20 from yeasts and MAIGO2 (Mag2) from plants. They play a role in anterograde transport from the endoplasmic reticulum (ER) to the Golgi and/or retrograde transport from the Golgi to the ER share sequence similarity. They share a similar domain organisation with an N-terminal leucine heptad repeat rich coiled coil and an ~500-residue C-terminal RINT1/TIP20 domain, which might be a protein-protein interaction module necessary for the formation of functional complexes.

RINT-1 interacts with Rad50 only during late S and G2/M phases and participates in radiation induced checkpoint control [ PUBMED:11096100 ]. RINT-1 also functions in membrane trafficking from the endoplasmic reticulum(ER) to the Golgi complex in interphase cells [ PUBMED:11096100 , PUBMED:16600870 , PUBMED:16571679 ].

Tip20 is involved in the retrograde transport from the Golgi to the ER [ PUBMED:19151722 , PUBMED:8334998 ].

Arabidopsis Mag2 functions in the transport of storage protein precursors between the ER and Golgi complex in plants [ PUBMED:17194767 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 (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.

  Seed
(59)
Full
(1864)
Representative proteomes UniProt
(3098)
RP15
(368)
RP35
(897)
RP55
(1496)
RP75
(1986)
Jalview 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
(59)
Full
(1864)
Representative proteomes UniProt
(3098)
RP15
(368)
RP35
(897)
RP55
(1496)
RP75
(1986)
Alignment:
Format:
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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
(59)
Full
(1864)
Representative proteomes UniProt
(3098)
RP15
(368)
RP35
(897)
RP55
(1496)
RP75
(1986)
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.

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: Bateman A, Wood V
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Wood V
Number in seed: 59
Number in full: 1864
Average length of the domain: 451.80 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 62.09 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.0 30.0
Trusted cut-off 30.1 30.1
Noise cut-off 29.9 29.9
Model length: 513
Family (HMM) version: 15
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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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 RINT1_TIP1 domain has been found. There are 5 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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