Protein SEC13 homolog (SEC13)
The protein contains 322 amino acids for an estimated molecular weight of 35541 Da.
Functions as a component of the nuclear pore complex (NPC) and the COPII coat. At the endoplasmic reticulum, SEC13 is involved in the biogenesis of COPII-coated vesicles (PubMed:8972206). Required for the exit of adipsin (CFD/ADN), an adipocyte-secreted protein from the endoplasmic reticulum (By similarity).', 'As a component of the GATOR subcomplex GATOR2, functions within the amino acid-sensing branch of the TORC1 signaling pathway. Indirectly activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex (PubMed:23723238). It is negatively regulated by the upstream amino acid sensors SESN2 and CASTOR1 (PubMed:25457612, PubMed:27487210). (updated: Nov. 7, 2018)
Protein identification was indicated in the following studies:
- Goodman and co-workers. (2013) The proteomics and interactomics of human erythrocytes. Exp Biol Med (Maywood) 238(5), 509-518.
- Lange and co-workers. (2014) Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J Proteome Res. 13(4), 2028-2044.
- Hegedűs and co-workers. (2015) Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications. Database (Oxford) 1-8.
Methods
The following articles were analysed to gather the proteome content of erythrocytes.
The gene or protein list provided in the studies were processed using the ID mapping API of Uniprot in September 2018. The number of proteins identified and mapped without ambiguity in these studies is indicated below.
Only Swiss-Prot entries (reviewed) were considered for protein evidence assignation.
| Publication | Identification 1 | Uniprot mapping 2 | Not mapped / Obsolete | TrEMBL | Swiss-Prot |
|---|---|---|---|---|---|
| Goodman (2013) | 2289 (gene list) | 2278 | 53 | 20599 | 2269 |
| Lange (2014) | 1234 | 1234 | 7 | 28 | 1224 |
| Hegedus (2015) | 2638 | 2622 | 0 | 235 | 2387 |
| Wilson (2016) | 1658 | 1528 | 170 | 291 | 1068 |
| d'Alessandro (2017) | 1826 | 1817 | 2 | 0 | 1815 |
| Bryk (2017) | 2090 | 2060 | 10 | 108 | 1942 |
| Chu (2018) | 1853 | 1804 | 55 | 362 | 1387 |
1 as available in the article and/or in supplementary material
2 uniprot mapping returns all protein isoforms as one entry
The compilation of older studies can be retrieved from the Red Blood Cell Collection database.
The data and differentiation stages presented below come from the proteomic study and analysis performed by our partners of the GReX consortium, more details are available in their published work.
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| Variant | Description |
|---|---|
| dbSNP:rs34078590 |
Biological Process
Antigen processing and presentation of exogenous peptide antigen via MHC class II
Antigen processing and presentation of peptide antigen via MHC class I
Cellular protein metabolic process
Cellular response to amino acid starvation
COPII vesicle coating
COPII-coated vesicle budding
COPII-coated vesicle cargo loading
Endoplasmic reticulum to Golgi vesicle-mediated transport
Intracellular protein transport
Intracellular transport of virus
Membrane organization
Mitotic cell cycle
Mitotic nuclear membrane reassembly
Mitotic spindle organization
MRNA export from nucleus
MRNA transport
Nuclear pore distribution
Positive regulation of GTPase activity
Positive regulation of TOR signaling
Positive regulation of TORC1 signaling
Positive regulation of transcription, DNA-templated
Post-translational protein modification
Protein exit from endoplasmic reticulum
Protein import into nucleus
Protein N-linked glycosylation via asparagine
Regulation of cellular response to heat
Regulation of gene silencing by miRNA
Regulation of glycolytic process
Sister chromatid cohesion
TRNA export from nucleus
Ubiquitin-dependent ERAD pathway
Viral life cycle
Viral process
Viral transcription
Cellular Component
COPII vesicle coat
Cytosol
Endoplasmic reticulum exit site
Endoplasmic reticulum membrane
ER to Golgi transport vesicle membrane
Extracellular exosome
GATOR2 complex
Golgi membrane
Host cell
Intracellular membrane-bounded organelle
Lysosomal membrane
Nuclear envelope
Nuclear pore outer ring
Nucleoplasm
The reference OMIM entry for this protein is 600152
Sec13-like protein 1; sec13l1
Sec13, yeast, homolog of; sec13
Sec13-related protein; sec13r
D3s1231e
DESCRIPTION
Bidirectional transport of macromolecules between the cytoplasm and nucleus occurs through nuclear pore complexes (NPCs) embedded in the nuclear envelope. NPCs are composed of subcomplexes, and SEC13L1 is part of one such subcomplex, Nup107-160 (Loiodice et al., 2004).CLONING
Gieser and Swaroop (1992) described sequence tagged sites (STSs) from 58 novel directionally cloned human cDNAs from an enriched retinal pigment epithelial cell line library. The nucleotide sequence of one of the cDNA clones, AA35 (D3S1231E), showed strong homology to the yeast SEC13 gene, which is required for vesicle biogenesis from endoplasmic reticulum during the transport of proteins. Swaroop et al. (1994) designated the human gene SEC13R. The predicted amino acid sequence of the SEC13R gene product shows 70% similarity to the yeast protein. The deduced polypeptide sequence contains several beta-transducin-like WD40 repeats and is rich in serine and threonine residues. A 1.4-kb transcript of SEC13R was detected by Northern analysis of many human tissues. However, RT-PCR analysis using 2 primer sets from different regions of the gene suggested differential expression of alternatively spliced transcripts in various tissues. Using the N-terminal region of NUP96 (601021) as bait in a yeast 2-hybrid screen of B-cell, breast, and placenta cDNA libraries, Enninga et al. (2003) cloned SEC13L1, which they called SEC13. The full-length protein contains 322 amino acids. Western blot analysis detected endogenous SEC13L1 at an apparent molecular mass of about 36 kD. Immunoelectron microscopy detected SEC13L1 and NUP96 on both the cytoplasmic and nucleoplasmic sides of the NPC, in addition to other intracellular sites. By proteomic analysis and mass spectrometry, Cronshaw et al. (2002) identified 94 proteins associated with NPCs purified from rat liver nuclei. Sec13r was relatively abundant, with 16 to 32 copies per NPC.GENE FUNCTION
By mutation analysis, Enninga et al. (2003) determined that the SEC13L1-NUP96 interaction required the WD repeat region of SEC13L1 and residues 201 to 378 of NUP96. SEC13L1 did not bind NUP98 (601021). In mitosis, SEC13L1 was dispersed throughout the cell, whereas a pool of NUP96 colocalized with the spindle apparatus. Photobleaching experiments showed that SEC13L1 shuttled between intranuclear sites and the cytoplasm, and a fraction of SEC13L1 stably associated with NPCs. Cotransfection of SEC13L1 and the SEC13L1-binding site of NUP96 decreased the mobile pool of SEC13L1. Targeting and mutation studies showed that SEC13L1 is actively transported into the nucleus and contains a C-terminal nuclear localization signal. Loiodice et al. (2004) transfected HeLa cells with cDNAs encoding the constituents of the Nup107-160 subcomplex. All proteins were properly targeted at the nuclear envelope after 2 or 3 days, except for SEC13, which gave an additional signal typical for endoplasmic reticulum (ER) and ER exit sites. Coimmunoprecipitation of SEC13 with NUP37 (609264) confirmed that SEC13 interacts with Nup107-160. The fraction of SEC13 associated with Nup107-160 was targeted to kinetochores from prophase to anaphase during mitosis. Bar-Peled et al. (2013) identified the octameric GATOR (GTPase-activating protein (GAP) activity toward RAGs) complex as a critical regulator of the pathway that signals amino acid sufficiency to mTORC1 (see 601231). GATOR is composed of 2 subcomplexes, GATOR1 and GATOR2. Inhi ... More on the omim web site
Nov. 16, 2018: Protein entry updated
Automatic update: Entry updated from uniprot information.
Feb. 10, 2018: Protein entry updated
Automatic update: Entry updated from uniprot information.
Feb. 2, 2018: Protein entry updated
Automatic update: Uniprot description updated
Dec. 19, 2017: Protein entry updated
Automatic update: Uniprot description updated
March 16, 2016: Protein entry updated
Automatic update: OMIM entry 600152 was added.