Y-box-binding protein 3 (YBX3)

The protein contains 372 amino acids for an estimated molecular weight of 40090 Da.

 

Binds to the GM-CSF promoter. Seems to act as a repressor. Binds also to full-length mRNA and to short RNA sequences containing the consensus site 5'-UCCAUCA-3'. May have a role in translation repression (By similarity). (updated: Sept. 12, 2018)

Protein identification was indicated in the following studies:

  1. Goodman and co-workers. (2013) The proteomics and interactomics of human erythrocytes. Exp Biol Med (Maywood) 238(5), 509-518.
  2. 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.
  3. 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.
  4. Wilson and co-workers. (2016) Comparison of the Proteome of Adult and Cord Erythroid Cells, and Changes in the Proteome Following Reticulocyte Maturation. Mol Cell Proteomics. 15(6), 1938-1946.
  5. Bryk and co-workers. (2017) Quantitative Analysis of Human Red Blood Cell Proteome. J Proteome Res. 16(8), 2752-2761.
  6. D'Alessandro and co-workers. (2017) Red blood cell proteomics update: is there more to discover? Blood Transfus. 15(2), 182-187.
  7. Chu and co-workers. (2018) Quantitative mass spectrometry of human reticulocytes reveal proteome-wide modifications during maturation. Br J Haematol. 180(1), 118-133.

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.

PublicationIdentification 1Uniprot mapping 2Not mapped /
Obsolete		TrEMBLSwiss-Prot
Goodman (2013)2289 (gene list)227853205992269
Lange (2014)123412347281224
Hegedus (2015)2638262202352387
Wilson (2016)165815281702911068
d'Alessandro (2017)18261817201815
Bryk (2017)20902060101081942
Chu (2018)18531804553621387

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.

No sequence conservation computed yet.
Protein sequence (FASTA)
Protein coevolution profile (FreeContact)
Multiple Sequence Alignment (Muscle)

Interpro domains
Total structural coverage: 23%
Model score: 0
No model available.

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VariantDescription
dbSNP:rs1126501

The reference OMIM entry for this protein is 603437

Cold-shock domain protein a; csda
Dna-binding protein a; dbpa

DESCRIPTION

Cold-shock domain (CSD) proteins, such as CSDA, are characterized by a highly conserved central domain of approximately 100 amino acids that is homologous to bacterial cold-shock proteins (summary by Sakura et al., 1988).

CLONING

To identify cDNAs encoding DNA-binding proteins (DBPs), Sakura et al. (1988) screened a human placenta cDNA expression library with DNA fragments containing either the human epidermal growth factor receptor (EGFR; 131550) enhancer or the human c-erbB2 (164870) promoter. They isolated cDNAs encoding DBPA and DBPB (154030). The DBPA cDNAs consisted of 2 forms that differ by an internal 207-bp deletion. Northern blot analysis of HeLa cell RNA detected a major 2.5-kb DBPA transcript and a minor 2.3-kb DBPA transcript. The deduced DBPA and DBPB proteins share a central region in which 100 of 109 amino acids are identical between the 2 proteins. Kudo et al. (1995) isolated full-length human cDNAs encoding DBPA and DBPB by screening for proteins that bind to the human leukosialin (182160) promoter. The deduced 342-amino acid DBPA protein has a cold-shock domain and a DNA-binding domain. Northern blot analysis of human tissues demonstrated highest levels of DBPA transcription in skeletal muscle and heart. Immunofluorescence detected DBPA protein expression in both the cytoplasm and nucleus of HeLa cells. Independently, Coles et al. (1996) isolated DBPA and DBPB cDNAs by screening for proteins that are able to bind to the repressor element in the human GMCSF (138960) promoter. They determined that their DBPA cDNA has a variant sequence compared to the previously reported DBPA cDNA sequences, resulting in a deduced 372-amino acid protein with 4 amino acid substitutions and a 30-amino acid C-terminal extension. Overexpression of this variant DBPA led to repression of the GMCSF promoter.

GENE STRUCTURE

Kudo et al. (1995) isolated the DBPA genomic sequence and found that it contains 10 exons spanning 24 kb; exon 6, which encodes 69 amino acids, is alternatively spliced.

MAPPING

Kudo et al. (1995) mapped the CSDA gene to chromosome 12p13.1 by in situ hybridization. ... More on the omim web site

Subscribe to this protein entry history

July 1, 2020: Protein entry updated
Automatic update: OMIM entry 603437 was added.

Oct. 19, 2018: Additional information
Initial protein addition to the database. This entry was referenced in Bryk and co-workers. (2017).