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13  structures 1162  species 0  interactions 2747  sequences 40  architectures

Family: CDC50 (PF03381)

Summary: LEM3 (ligand-effect modulator 3) family / CDC50 family

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LEM3 (ligand-effect modulator 3) family / CDC50 family Provide feedback

Members of this family have been predicted to contain transmembrane helices. The family member LEM3 (P42838) is a ligand-effect modulator, mutation of which increases glucocorticoid receptor activity in response to dexamethasone and also confers increased activity on other intracellular receptors including the progesterone, oestrogen and mineralocorticoid receptors. LEM3 is thought to affect a downstream step in the glucocorticoid receptor pathway. Factors that modulate ligand responsiveness are likely to contribute to the context-specific actions of the glucocorticoid receptor in mammalian cells [1]. The products of genes YNR048w (P53740), YNL323w (P42838) and YCR094w (P25656) (CDC50) show redundancy of function and are involved in regulation of transcription via CDC39 [2]. CDC39 (also known as NOT1) is normally a negative regulator of transcription either by affecting the general RNA polymerase II machinery or by altering chromatin structure [4]. One function of CDC39 is to block activation of the mating response pathway in the absence of pheromone, and mutation causes arrest in G1 by activation of the pathway [3]. It may be that the cold-sensitive arrest in G1 noticed in CDC50 mutants [2] may be due to inactivation of CDC39. The effects of LEM3 on glucocorticoid receptor activity may also be due to effects on transcription via CDC39.

Literature references

  1. Sitcheran R, Emter R, Kralli A, Yamamoto KR; , Genetics 2000;156:963-972.: A genetic analysis of glucocorticoid receptor signaling. Identification and characterization of ligand-effect modulators in Saccharomyces cerevisiae. PUBMED:11063677 EPMC:11063677

  2. Radji M, Kim JM, Togan T, Yoshikawa H, Shirahige K; , Yeast 2001;18:195-205.: The cloning and characterization of the CDC50 gene family in Saccharomyces cerevisiae. PUBMED:11180453 EPMC:11180453

  3. Neiman AM, Chang F, Komachi K, Herskowitz I; , Cell Regul 1990;1:391-401.: CDC36 and CDC39 are negative elements in the signal transduction pathway of yeast. PUBMED:2099190 EPMC:2099190

  4. Collart MA, Struhl K; , EMBO J 1993;12:177-186.: CDC39, an essential nuclear protein that negatively regulates transcription and differentially affects the constitutive and inducible HIS3 promoters. PUBMED:8428577 EPMC:8428577

  5. Misu K, Fujimura-Kamada K, Ueda T, Nakano A, Katoh H, Tanaka K; , Mol Biol Cell 2003;14:730-747.: Cdc50p, a Conserved Endosomal Membrane Protein, Controls Polarized Growth in Saccharomyces cerevisiae. PUBMED:12589066 EPMC:12589066


This tab holds annotation information from the InterPro database.

InterPro entry IPR005045

CDC50/LEM3 is a family of membrane proteins whose members include cell cycle control protein 50, alkylphosphocholine resistance protein LEM3, which is is required for phospholipid translocation across the plasma membrane in Saccharomyces cerevisiae [PUBMED:12133835], and several ALA-interacting subunits, which are plant proteins involved in lipid translocation and secretory vesicle formation [PUBMED:18344284].

Gene Ontology

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Domain organisation

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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
(297)
Full
(2747)
Representative proteomes UniProt
(4686)
NCBI
(5424)
Meta
(9)
RP15
(486)
RP35
(1265)
RP55
(2081)
RP75
(2792)
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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
(297)
Full
(2747)
Representative proteomes UniProt
(4686)
NCBI
(5424)
Meta
(9)
RP15
(486)
RP35
(1265)
RP55
(2081)
RP75
(2792)
Alignment:
Format:
Order:
Sequence:
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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
(297)
Full
(2747)
Representative proteomes UniProt
(4686)
NCBI
(5424)
Meta
(9)
RP15
(486)
RP35
(1265)
RP55
(2081)
RP75
(2792)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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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_2846 (release 6.6)
Previous IDs: DUF284;
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W , Kerrison ND
Number in seed: 297
Number in full: 2747
Average length of the domain: 268.70 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 74.40 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.6 28.6
Trusted cut-off 29.1 28.8
Noise cut-off 27.3 28.3
Model length: 286
Family (HMM) version: 16
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 CDC50 domain has been found. There are 13 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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