Nuclease-sensitive element-binding protein 1 - P67809 (YBOX1_HUMAN)


Protein Feature View of PDB entries mapped to a UniProtKB sequence  

DNA- and RNA-binding protein involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation (PubMed:8188694, PubMed:10817758, PubMed:11698476, PubMed:14718551, PubMed:18809583, PubMed:31358969). Predominantly acts as a RNA-binding protein: binds preferentially to the 5'-[CU]CUGCG-3' RNA motif and specifically recognizes mRNA transcripts modified by C5-methylcytosine (m5C) (PubMed:19561594, PubMed:31358969). Promotes mRNA stabilization: acts by binding to m5C-containing mRNAs and recruiting the mRNA stability maintainer ELAVL1, thereby preventing mRNA decay (PubMed:10817758, PubMed:11698476, PubMed:31358969). Component of the CRD-mediated complex that promotes MYC mRNA stability (PubMed:19029303). Contributes to the regulation of translation by modulating the interaction between the mRNA and eukaryotic initiation factors (By similarity). Plays a key role in RNA composition of extracellular exosomes by defining the sorting of small non-coding RNAs, such as tRNAs, Y RNAs, Vault RNAs and miRNAs (PubMed:27559612, PubMed:29073095). Probably sorts RNAs in exosomes by recognizing and binding C5-methylcytosine (m5C)-containing RNAs (PubMed:28341602, PubMed:29073095). Acts as a key effector of epidermal progenitors by preventing epidermal progenitor senescence: acts by regulating the translation of a senescence-associated subset of cytokine mRNAs, possibly by binding to m5C-containing mRNAs (PubMed:29712925). Also involved in pre-mRNA alternative splicing regulation: binds to splice sites in pre-mRNA and regulates splice site selection (PubMed:12604611). Also able to bind DNA: regulates transcription of the multidrug resistance gene MDR1 is enhanced in presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7' (PubMed:18809583). Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes (PubMed:8188694, PubMed:18809583). Promotes separation of DNA strands that contain mismatches or are modified by cisplatin (PubMed:14718551). Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA, suggesting a role in DNA repair (PubMed:14718551). The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation (PubMed:19483673). UniProt
Pathway Maps
      ESCHER  BiGG
Subunit Structure
Homodimer in the presence of ATP (PubMed:10817758, PubMed:11851341). Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1 (PubMed:19029303). Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs (PubMed:17289661). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (PubMed:15146077). Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1 (By similarity). Interacts with IGF2BP1 and RBBP6 (PubMed:17289661, PubMed:18851979). Component of cytoplasmic messenger ribonucleoprotein particles (mRNPs) (PubMed:19029303). Interacts with AKT1, MBNL1, SFRS9, SFRS12, ALYREF/THOC4, MSH2, XRCC5, WRN and NCL (PubMed:12604611, PubMed:14559993, PubMed:14718551, PubMed:15806160, PubMed:18335541). Interacts (via C-terminus) with APEX1 (via N-terminus); the interaction is increased with APEX1 acetylated at 'Lys-6' and 'Lys-7' (PubMed:18809583). Interacts with AGO1 and AGO2 (PubMed:17932509). Interacts with ANKRD2 (PubMed:15136035). Interacts with DERA (PubMed:25229427). Interacts with FMR1; this interaction occurs in association with polyribosome (By similarity). Interacts with ZBTB7B (By similarity). Interacts with HDGF (isoform 1) (PubMed:26845719). Interacts with ELAVL1; leading to ELAVL1 recruitment on C5-methylcytosine (m5C)-containing mRNAs and subsequent mRNA stability (PubMed:31358969). UniProt
In the CSD domain, Trp-65 specifically recognizes C5-methylcytosine (m5C) modification through its indole ring. UniProt
The Protein Feature View requires a browser that supports SVG (Scalable Vector Graphics). Mouse over tracks and labels for more information.
Data origin/color codes
The vertical color bar on the left side indicates data provenance.
Data in green originates from UniProtKB  
Variation data (sourced from UniProt) shows non-genetic variation from the ExPASy   and dbSNP   websites.
Data in yellow originates from Pfam  , by interacting with the HMMER3 web site  
Data in purple originates from Phosphosite  .
Data in orange originates from the SCOP   (version 1.75) and SCOPe   (version 2.04) classifications.
Data in grey has been calculated using BioJava  . Protein disorder predictions are based on JRONN (Troshin, P. and Barton, G. J. unpublished), a Java implementation of RONN  
  • Red: potentially disorderd region
  • Blue: probably ordered region.
Hydropathy has been calculated using a sliding window of 15 residues and summing up scores from standard hydrophobicity tables.
  • Red: hydrophobic
  • Blue: hydrophilic.
Data in lilac represent the genomic exon structure projected onto the UniProt sequence.
Data in blue originates from PDB
  • Secstruc: Secondary structure projected from representative PDB entries onto the UniProt sequence.
Sequence Mismatches It is now possible to see information about expression tags, cloning artifacts, and many other details related to sequence mismatches.
Icons represent a number of different sequence modifications that can be observed in PDB files. For example the 'T' icon T represents expression tags that have been added to the sequence. The 'E' icon E represents an engineered mutation. However, besides these two, there are many other icons. For more information about the meaning and exact position of a sequence modification, move the cursor over the icon.
Validation Track

For more details on the Validation Track (Structure Summary Page only) see the dedicated help page.

Data in red indicates combined ranges of Homology Models from the SWISS-MODEL Repository  
The PDB to UniProt mapping is based on the data provided by the EBI SIFTS project. See also Velankar et al., Nucleic Acids Research 33, D262-265 (2005).
Organism icons generated by under CC BY. The authors are: Freepik, Icons8, OCHA, Scott de Jonge.

For more details on the Protein Feature view see the dedicated help page.