P62960 · YBOX1_MOUSE
- ProteinY-box-binding protein 1
- GeneYbx1
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids322 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
DNA- and RNA-binding protein involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation (PubMed:29712925, PubMed:8505341).
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) (By similarity).
Promotes mRNA stabilization: acts by binding to m5C-containing mRNAs and recruiting the mRNA stability maintainer ELAVL1, thereby preventing mRNA decay (By similarity).
Component of the CRD-mediated complex that promotes MYC mRNA stability (By similarity).
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 (By similarity).
Probably sorts RNAs in exosomes by recognizing and binding C5-methylcytosine (m5C)-containing RNAs (By similarity).
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 (By similarity).
Binds to TSC22D1 transcripts, thereby inhibiting their translation and negatively regulating TGF-beta-mediated transcription of COL1A2 (PubMed:20713358).
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' (By similarity).
Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes (By similarity).
Promotes separation of DNA strands that contain mismatches or are modified by cisplatin (By similarity).
Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA, suggesting a role in DNA repair (By similarity).
The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation (By similarity).
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) (By similarity).
Promotes mRNA stabilization: acts by binding to m5C-containing mRNAs and recruiting the mRNA stability maintainer ELAVL1, thereby preventing mRNA decay (By similarity).
Component of the CRD-mediated complex that promotes MYC mRNA stability (By similarity).
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 (By similarity).
Probably sorts RNAs in exosomes by recognizing and binding C5-methylcytosine (m5C)-containing RNAs (By similarity).
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 (By similarity).
Binds to TSC22D1 transcripts, thereby inhibiting their translation and negatively regulating TGF-beta-mediated transcription of COL1A2 (PubMed:20713358).
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' (By similarity).
Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes (By similarity).
Promotes separation of DNA strands that contain mismatches or are modified by cisplatin (By similarity).
Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA, suggesting a role in DNA repair (By similarity).
The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation (By similarity).
Features
Showing features for site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Site | 63 | Important for C5-methylcytosine-recognition | ||||
Sequence: W | ||||||
Site | 217-218 | Cleavage; by 20S proteasomal protease | ||||
Sequence: EG |
GO annotations
Keywords
- Molecular function
- Biological process
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameY-box-binding protein 1
- Short namesYB-1
- Alternative names
Gene names
Organism names
- Organism
- Strains
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Glires > Rodentia > Myomorpha > Muroidea > Muridae > Murinae > Mus > Mus
Accessions
- Primary accessionP62960
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
UniProt Annotation
GO Annotation
Note: Predominantly cytoplasmic in proliferating cells. Cytotoxic stress and DNA damage enhance translocation to the nucleus. Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Shuttles between nucleus and cytoplasm. Localized with DDX1, MBNL1 and TIAL1 in stress granules upon stress. Secreted by mesangial and monocytic cells after inflammatory challenges.
Keywords
- Cellular component
Phenotypes & Variants
Disruption phenotype
Perinatal lethality (PubMed:15899865).
Embryos develop normally up to embryonic day 13.5 dpc and then show progressive mortality (PubMed:15899865).
Embryos display severe growth retardation caused by hypoplasia in multiple organs (PubMed:15899865).
Fibroblasts show a normal rate of protein synthesis and minimal alterations in the transcriptome and proteome (PubMed:15899865).
Mice show defects in the architecture of the skin characterized by markedly reduced thickness of the epidermis and delayed onset of the placodes to hair follicle transition (PubMed:29712925).
Embryos develop normally up to embryonic day 13.5 dpc and then show progressive mortality (PubMed:15899865).
Embryos display severe growth retardation caused by hypoplasia in multiple organs (PubMed:15899865).
Fibroblasts show a normal rate of protein synthesis and minimal alterations in the transcriptome and proteome (PubMed:15899865).
Mice show defects in the architecture of the skin characterized by markedly reduced thickness of the epidermis and delayed onset of the placodes to hair follicle transition (PubMed:29712925).
Variants
We now provide the "Disease & Variants" viewer in its own tab.
The viewer provides 38 variants from UniProt as well as other sources including ClinVar and dbSNP.
PTM/Processing
Features
Showing features for initiator methionine, modified residue, chain, cross-link.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Initiator methionine | 1 | Removed | ||||
Sequence: M | ||||||
Modified residue | 2 | N-acetylserine | ||||
Sequence: S | ||||||
Chain | PRO_0000100220 | 2-322 | Y-box-binding protein 1 | |||
Sequence: SSEAETQQPPAAPAAALSAADTKPGSTGSGAGSGGPGGLTSAAPAGGDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFPPYYMRRPYARRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENSSAPEAEQGGAE | ||||||
Cross-link | 24 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) | ||||
Sequence: K | ||||||
Modified residue | 100 | Phosphoserine; by PKB/AKT1 | ||||
Sequence: S | ||||||
Cross-link | 135 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) | ||||
Sequence: K | ||||||
Modified residue | 160 | Phosphotyrosine | ||||
Sequence: Y | ||||||
Modified residue | 163 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 165 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 172 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 174 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 299 | N6-acetyllysine | ||||
Sequence: K | ||||||
Modified residue | 302 | N6-acetyllysine | ||||
Sequence: K | ||||||
Modified residue | 312 | Phosphoserine | ||||
Sequence: S |
Post-translational modification
Ubiquitinated by RBBP6; leading to a decrease of YBX1 transactivational ability.
Phosphorylated; increased by TGFB1 treatment (PubMed:20713358).
Phosphorylation by PKB/AKT1 reduces interaction with cytoplasmic mRNA (By similarity).
In the absence of phosphorylation the protein is retained in the cytoplasm (By similarity).
Phosphorylation by PKB/AKT1 reduces interaction with cytoplasmic mRNA (By similarity).
In the absence of phosphorylation the protein is retained in the cytoplasm (By similarity).
Cleaved by a 20S proteasomal protease in response to agents that damage DNA. Cleavage takes place in the absence of ubiquitination and ATP. The resulting N-terminal fragment accumulates in the nucleus (By similarity).
Keywords
- PTM
Proteomic databases
PTM databases
Expression
Tissue specificity
Expressed in kidney glomeruli (at protein level) (PubMed:20713358).
In epidermis, expression is restricted to the cycling keratinocyte progenitors (at protein level) (PubMed:29712925).
Expressed at high levels in the testis (PubMed:8505341).
Present in the mRNP particles that mediate the storage and masking of mRNAs during spermiogenesis (PubMed:8505341).
In epidermis, expression is restricted to the cycling keratinocyte progenitors (at protein level) (PubMed:29712925).
Expressed at high levels in the testis (PubMed:8505341).
Present in the mRNP particles that mediate the storage and masking of mRNAs during spermiogenesis (PubMed:8505341).
Developmental stage
Found at very low levels at day 10 and levels increase at day 15 and persist throughout adulthood.
Gene expression databases
Interaction
Subunit
Homodimer in the presence of ATP (PubMed:10318844, PubMed:8505341).
Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1 (By similarity).
Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs (By similarity).
Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (By similarity).
Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1 (PubMed:11162447).
Interacts with IGF2BP1 and RBBP6 (By similarity).
Component of cytoplasmic messenger ribonucleoprotein particles (mRNPs) (By similarity).
Interacts with AKT1, MBNL1, SFRS9, SFRS12, ALYREF/THOC4, MSH2, XRCC5, WRN and NCL (By similarity).
Interacts (via C-terminus) with APEX1 (via N-terminus); the interaction is increased with APEX1 acetylated at 'Lys-6' and 'Lys-7' (By similarity).
Interacts with AGO1 and AGO2 (By similarity).
Interacts with ANKRD2 (By similarity).
Interacts with DERA (By similarity).
Interacts with FMR1; this interaction occurs in association with polyribosome (PubMed:11162447).
Interacts with ZBTB7B (PubMed:28784777).
Interacts with HDGF. Interacts with ELAVL1; leading to ELAVL1 recruitment on C5-methylcytosine (m5C)-containing mRNAs and subsequent mRNA stability (By similarity).
Interacts with PURB (PubMed:27064749).
Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1 (By similarity).
Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs (By similarity).
Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (By similarity).
Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1 (PubMed:11162447).
Interacts with IGF2BP1 and RBBP6 (By similarity).
Component of cytoplasmic messenger ribonucleoprotein particles (mRNPs) (By similarity).
Interacts with AKT1, MBNL1, SFRS9, SFRS12, ALYREF/THOC4, MSH2, XRCC5, WRN and NCL (By similarity).
Interacts (via C-terminus) with APEX1 (via N-terminus); the interaction is increased with APEX1 acetylated at 'Lys-6' and 'Lys-7' (By similarity).
Interacts with AGO1 and AGO2 (By similarity).
Interacts with ANKRD2 (By similarity).
Interacts with DERA (By similarity).
Interacts with FMR1; this interaction occurs in association with polyribosome (PubMed:11162447).
Interacts with ZBTB7B (PubMed:28784777).
Interacts with HDGF. Interacts with ELAVL1; leading to ELAVL1 recruitment on C5-methylcytosine (m5C)-containing mRNAs and subsequent mRNA stability (By similarity).
Interacts with PURB (PubMed:27064749).
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | P62960 | Elavl1 P70372 | 5 | EBI-529779, EBI-6877056 |
Protein-protein interaction databases
Miscellaneous
Structure
Family & Domains
Features
Showing features for region, domain, compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 1-47 | Disordered | ||||
Sequence: MSSEAETQQPPAAPAAALSAADTKPGSTGSGAGSGGPGGLTSAAPAG | ||||||
Region | 16-69 | Interaction with ss-DNA | ||||
Sequence: AALSAADTKPGSTGSGAGSGGPGGLTSAAPAGGDKKVIATKVLGTVKWFNVRNG | ||||||
Domain | 59-123 | CSD | ||||
Sequence: GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANV | ||||||
Region | 63-68 | C5-methylcytosine binding | ||||
Sequence: WFNVRN | ||||||
Region | 118-322 | Disordered | ||||
Sequence: AEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFPPYYMRRPYARRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENSSAPEAEQGGAE | ||||||
Compositional bias | 154-179 | Polar residues | ||||
Sequence: RNYQQNYQNSESGEKNEGSESAPEGQ | ||||||
Compositional bias | 248-267 | Basic and acidic residues | ||||
Sequence: PRQRQPREDGNEEDKENQGD | ||||||
Compositional bias | 286-304 | Basic and acidic residues | ||||
Sequence: RRRRPENPKPQDGKETKAA |
Domain
In the CSD domain, Trp-63 specifically recognizes C5-methylcytosine (m5C) modification through its indole ring.
Sequence similarities
Belongs to the YBX1 family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length322
- Mass (Da)35,730
- Last updated2007-01-23 v3
- ChecksumC6667CF7CA10D45D
Computationally mapped potential isoform sequences
There is 1 potential isoform mapped to this entry
Entry | Entry name | Gene name | Length | ||
---|---|---|---|---|---|
A2BGG7 | A2BGG7_MOUSE | Ybx1 | 214 |
Features
Showing features for sequence conflict, compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 29 | in Ref. 2; AAA63390 | ||||
Sequence: G → A | ||||||
Sequence conflict | 43-45 | in Ref. 3; CAA40847 | ||||
Sequence: AAP → RR | ||||||
Compositional bias | 154-179 | Polar residues | ||||
Sequence: RNYQQNYQNSESGEKNEGSESAPEGQ | ||||||
Sequence conflict | 238 | in Ref. 3; CAA40847 | ||||
Sequence: G → P | ||||||
Compositional bias | 248-267 | Basic and acidic residues | ||||
Sequence: PRQRQPREDGNEEDKENQGD | ||||||
Compositional bias | 286-304 | Basic and acidic residues | ||||
Sequence: RRRRPENPKPQDGKETKAA |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
M60419 EMBL· GenBank· DDBJ | AAA40577.1 EMBL· GenBank· DDBJ | mRNA | ||
M62867 EMBL· GenBank· DDBJ | AAA63390.1 EMBL· GenBank· DDBJ | mRNA | ||
X57621 EMBL· GenBank· DDBJ | CAA40847.1 EMBL· GenBank· DDBJ | mRNA | ||
BC013450 EMBL· GenBank· DDBJ | AAH13450.1 EMBL· GenBank· DDBJ | mRNA | ||
BC013620 EMBL· GenBank· DDBJ | AAH13620.1 EMBL· GenBank· DDBJ | mRNA | ||
BC029747 EMBL· GenBank· DDBJ | AAH29747.1 EMBL· GenBank· DDBJ | mRNA | ||
BC031472 EMBL· GenBank· DDBJ | AAH31472.1 EMBL· GenBank· DDBJ | mRNA | ||
BC061634 EMBL· GenBank· DDBJ | AAH61634.1 EMBL· GenBank· DDBJ | mRNA |